spades_cpu7mem28: macros.xml annotate

annotate macros.xml @ 1:45b5f747c900 draft default tip

planemo upload commit 611f051119d03ed04af67a33e403496bc3e7cc1e

author	galaxytrakr
date	Thu, 19 Mar 2026 15:43:04 +0000
parents	f69397b32f52
children

rev	line source
0 f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	1 <macros>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	2 <token name="@TOOL_VERSION@">4.2.0</token>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	3 <token name="@VERSION_SUFFIX@">0</token>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	4
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	5 <xml name="requirements">
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	6 <requirements>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	7 <requirement type="package" version="@TOOL_VERSION@">spades</requirement>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	8 </requirements>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	9 </xml>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	10 <xml name="stdio">
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	11 <stdio>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	12 <exit_code range="1:"/>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	13 <regex match="Cannot allocate memory"
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	14 source="stdout"
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	15 level="fatal_oom"
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	16 description="Out of memory error occurred"/>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	17 <regex match="The reads contain too many k-mers to fit into available memory"
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	18 source="stdout"
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	19 level="fatal_oom"
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	20 description="Out of memory error occurred"/>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	21 </stdio>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	22 </xml>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	23 <xml name="version_command">
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	24 <version_command><![CDATA[spades.py --version 2>&1 \| awk -F 'v' '{print $2}']]></version_command>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	25 </xml>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	26 <token name="@FASTA_INTYPES@">fasta,fasta.gz</token>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	27 <token name="@FASTQ_INTYPES@">fastqillumina,fastqillumina.gz,fastqsanger,fastqsanger.gz</token>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	28 <token name="@INTYPES@">@FASTQ_INTYPES@,@FASTA_INTYPES@</token>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	29
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	30 <xml name="citations">
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	31 <citations>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	32 <citation type="doi">10.1093/bioinformatics/btv688</citation>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	33 <citation type="doi">10.1093/bioinformatics/btu266</citation>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	34 <citation type="doi">10.1093/bioinformatics/btv337</citation>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	35 <yield/>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	36 </citations>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	37 </xml>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	38 <xml name="operation_mode" token_help="">
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	39 <param name="operation_mode" type="select" label="Operation mode" help="@HELP@">
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	40 <option value="">Assembly and error correction</option>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	41 <option value="--only-assembler">Only assembler (--only-assembler)</option>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	42 <option value="--only-error-correction">Only error correction (--only-error-correction)</option>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	43 </param>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	44 </xml>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	45
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	46 <token name="@OMP_THREADS@"><![CDATA[
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	47 export OMP_THREAD_LIMIT=\${GALAXY_SLOTS:-4} &&
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	48 ]]></token>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	49
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	50 <!-- PREPARE INPUT FILES-->
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	51
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	52 <token name="@PREPROCESS_INPUT_FILES_MAIN@"><![CDATA[
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	53 #import re
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	54 #def fix_ext($ext):
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	55 #set ext = $ext.replace('fastqsanger', 'fastq')
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	56 #set ext = $ext.replace('fastqillumina', 'fastq')
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	57 #return $ext
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	58 #end def
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	59
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	60 #if $singlePaired.sPaired == "single" or $singlePaired.sPaired == "paired_interlaced"
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	61 mkdir -p reads1 &&
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	62 #set file_paths1 = []
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	63 #for $input_file in $singlePaired.input1
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	64 #set ext = $fix_ext($input_file.ext)
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	65 #set fname = re.sub('[^\w\-_.]', '_', $input_file.element_identifier) + '.' + $ext
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	66 #set file_path = 'reads1/' + $fname
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	67 ln -s '$input_file' '$file_path' &&
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	68 $file_paths1.append($file_path)
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	69 #end for
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	70 #else
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	71 ## one mapped-in paired dataset (Galaxy maps list:paired -> 1 job per pair)
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	72 mkdir -p paired_reads1 &&
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	73 #set fw_reads1 = []
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	74 #set rv_reads1 = []
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	75 #set ext = $fix_ext($singlePaired.input.forward.ext)
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	76 #set base = re.sub('[^\w\-_.]', '_', $singlePaired.input.element_identifier)
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	77 #set f1 = 'paired_reads1/' + $base + '1.' + $ext
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	78 #set f2 = 'paired_reads1/' + $base + '2.' + $ext
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	79 ln -s '$singlePaired.input.forward' '$f1' &&
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	80 ln -s '$singlePaired.input.reverse' '$f2' &&
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	81 $fw_reads1.append($f1)
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	82 $rv_reads1.append($f2)
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	83 #end if
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	84 ]]></token>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	85
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	86 <token name="@PREPROCESS_INPUT_FILES_ADDITIONAL@"><![CDATA[
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	87 #if $additional_reads.singlePaired.sPaired == "single" or $additional_reads.singlePaired.sPaired == "paired_interlaced"
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	88 mkdir -p reads2 &&
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	89 #set file_paths2 = []
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	90 #for $input_file in $additional_reads.singlePaired.input1
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	91 #set ext = $fix_ext($input_file.ext)
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	92 #set fname = re.sub('[^\w\-_.]', '_', $input_file.element_identifier) + '.' + $ext
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	93 #set file_path = 'reads2/' + $fname
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	94 ln -s '$input_file' '$file_path' &&
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	95 $file_paths2.append($file_path)
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	96 #end for
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	97 #else
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	98 ## one mapped-in paired dataset for the additional library
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	99 mkdir -p paired_reads2 &&
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	100 #set fw_reads2 = []
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	101 #set rv_reads2 = []
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	102 #set ext = $fix_ext($additional_reads.singlePaired.input.forward.ext)
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	103 #set base = re.sub('[^\w\-_.]', '_', $additional_reads.singlePaired.input.element_identifier)
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	104 #set f1 = 'paired_reads2/' + $base + '1.' + $ext
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	105 #set f2 = 'paired_reads2/' + $base + '2.' + $ext
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	106 ln -s '$additional_reads.singlePaired.input.forward' '$f1' &&
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	107 ln -s '$additional_reads.singlePaired.input.reverse' '$f2' &&
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	108 $fw_reads2.append($f1)
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	109 $rv_reads2.append($f2)
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	110 #end if
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	111 ]]></token>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	112
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	113 <!-- COMMANDS -->
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	114
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	115 <token name="@RESOURCES@"><![CDATA[
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	116 -t \${GALAXY_SLOTS:-4}
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	117 -m \$((\${GALAXY_MEMORY_MB:-8192}/1024))
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	118 --tmp-dir \${TMPDIR}
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	119 ]]></token>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	120
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	121 <token name="@INPUT_READS_MAIN@"><![CDATA[
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	122 #if $singlePaired.sPaired == "single"
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	123 #for $read in $file_paths1
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	124 --s $library '${read}'
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	125 #end for
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	126 #else if $singlePaired.sPaired == "paired_interlaced"
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	127 #for $read in $file_paths1
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	128 --${singlePaired.type_paired}-12 $library '${read}'
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	129 --${singlePaired.type_paired}-or $library $singlePaired.orientation
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	130 #end for
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	131 #else
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	132 #for $read in $fw_reads1
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	133 --${singlePaired.type_paired}-1 $library '${read}'
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	134 #end for
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	135 #for $read in $rv_reads1
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	136 --${singlePaired.type_paired}-2 $library '${read}'
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	137 --${singlePaired.type_paired}-or $library $singlePaired.orientation
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	138 #end for
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	139 #end if
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	140 ]]></token>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	141
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	142
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	143 <token name="@INPUT_READS_ADDITIONAL@"><![CDATA[
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	144 @LIBRARY_NUMBER@
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	145 #if $additional_reads.singlePaired.sPaired == "single"
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	146 #for $read in $file_paths2
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	147 --s $library '${read}'
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	148 #end for
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	149 #else if $additional_reads.singlePaired.sPaired == "paired_interlaced"
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	150 #for $read in $file_paths2
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	151 --${additional_reads.singlePaired.type_paired}-12 $library '${read}'
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	152 --${additional_reads.singlePaired.type_paired}-or $library $additional_reads.singlePaired.orientation
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	153 #end for
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	154 #else
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	155 #for $read in $fw_reads2
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	156 --${additional_reads.singlePaired.type_paired}-1 $library '${read}'
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	157 #end for
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	158 #for $read in $rv_reads2
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	159 --${additional_reads.singlePaired.type_paired}-2 $library '${read}'
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	160 --${additional_reads.singlePaired.type_paired}-or $library $additional_reads.singlePaired.orientation
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	161 #end for
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	162 #end if
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	163 ]]></token>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	164
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	165 <token name="@PIPELINE_OPTIONS@"><![CDATA[
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	166 #for $i in $mode_sel
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	167 $i
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	168 #end for
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	169 ]]></token>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	170
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	171 <token name="@KMER@"><![CDATA[
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	172 #if $kmer_cond.kmer_sel != 'auto'
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	173 -k '$kmer_cond.manual'
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	174 #end if
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	175 ]]></token>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	176
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	177 <token name="@PHREDOFFSET@"><![CDATA[
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	178 #if $phred_offset != 'auto'
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	179 --phred-offset $phred_offset
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	180 #end if
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	181 ]]></token>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	182
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	183 <!-- ADDITIONAL INPUTS-->
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	184
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	185 <token name="@PREPROCESS_CONTIGS_FILES@"><![CDATA[
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	186 #if $arf.trusted_contigs
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	187 mkdir -p trusted_contigs &&
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	188 #set trusted_contigs = []
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	189 #for $i, $input_file in enumerate($arf.trusted_contigs,1)
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	190 #set $ext = $input_file.ext.replace('fastqsanger', 'fastq')
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	191 #set $fname = 'file' + str($i) + '.' + $ext
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	192 #set $file_path = 'trusted_contigs/' + $fname
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	193 ln -s '$input_file' '$file_path' &&
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	194 $trusted_contigs.append($file_path)
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	195 #end for
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	196 #end if
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	197 #if $arf.untrusted_contigs
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	198 mkdir -p untrusted_contigs &&
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	199 #set untrusted_contigs = []
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	200 #for $i, $input_file in enumerate($arf.untrusted_contigs,1)
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	201 #set $ext = $input_file.ext.replace('fastqsanger', 'fastq')
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	202 #set $fname = 'file' + str($i) + '.' + $ext
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	203 #set $file_path = 'untrusted_contigs/' + $fname
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	204 ln -s '$input_file' '$file_path' &&
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	205 $untrusted_contigs.append($file_path)
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	206 #end for
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	207 #end if
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	208 ]]></token>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	209
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	210 <token name="@PREPROCESS_NANOPORE_PACBIO_FILES@"><![CDATA[
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	211 #if $arf.nanopore
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	212 mkdir -p nanopore_reads &&
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	213 #set nanopore_reads = []
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	214 #for $i, $input_file in enumerate($arf.nanopore,1)
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	215 #set $ext = $input_file.ext.replace('fastqsanger', 'fastq')
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	216 #set $fname = 'file' + str($i) + '.' + $ext
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	217 #set $file_path = 'nanopore_reads/' + $fname
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	218 ln -s '$input_file' '$file_path' &&
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	219 $nanopore_reads.append($file_path)
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	220 #end for
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	221 #end if
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	222 #if $arf.pacbio
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	223 mkdir -p pacbio_reads &&
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	224 #set pacbio_reads = []
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	225 #for $i, $input_file in enumerate($arf.pacbio,1)
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	226 #set $ext = $input_file.ext.replace('fastqsanger', 'fastq')
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	227 #set $fname = 'file' + str($i) + '.' + $ext
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	228 #set $file_path = 'pacbio_reads/' + $fname
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	229 ln -s '$input_file' '$file_path' &&
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	230 $pacbio_reads.append($file_path)
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	231 #end for
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	232 #end if
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	233 ]]></token>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	234
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	235 <token name="@PREPROCESS_SANGER_FILES@"><![CDATA[
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	236 #if $arf.sanger
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	237 mkdir -p sanger_reads &&
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	238 #set sanger_reads = []
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	239 #for $i, $input_file in enumerate($arf.sanger,1)
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	240 #set $ext = $input_file.ext.replace('fastqsanger', 'fastq')
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	241 #set $fname = 'file' + str($i) + '.' + $ext
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	242 #set $file_path = 'sanger_reads/' + $fname
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	243 ln -s '$input_file' '$file_path' &&
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	244 $sanger_reads.append($file_path)
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	245 #end for
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	246 #end if
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	247 ]]></token>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	248
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	249 <token name="@PREPROCESS_FL_RNA_FILES@"><![CDATA[
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	250 #if $arf.flrna
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	251 mkdir -p flrna_reads &&
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	252 #set flrna_reads = []
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	253 #for $i, $input_file in enumerate($arf.flrna,1)
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	254 #set $ext = $input_file.ext.replace('fastqsanger', 'fastq')
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	255 #set $fname = 'file' + str($i) + '.' + $ext
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	256 #set $file_path = 'flrna_reads/' + $fname
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	257 ln -s '$input_file' '$file_path' &&
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	258 $flrna_reads.append($file_path)
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	259 #end for
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	260 #end if
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	261 ]]></token>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	262
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	263 <token name="@PREPROCESS_ASSEMBLY_GRAPH_FILES@"><![CDATA[
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	264 #if $arf.assembly_graph
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	265 mkdir -p assembly_graphs &&
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	266 #set assembly_graphs = []
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	267 #for $i, $input_file in enumerate($arf.assembly_graph,1)
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	268 #set $ext = $input_file.ext.replace('gfa1', 'gfa')
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	269 #set $fname = 'file' + str($i) + '.' + $ext
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	270 #set $file_path = 'assembly_graphs/' + $fname
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	271 ln -s '$input_file' '$file_path' &&
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	272 $assembly_graphs.append($file_path)
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	273 #end for
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	274 #end if
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	275 ]]></token>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	276
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	277
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	278 <token name="@NANOPORE_PACBIO@"><![CDATA[
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	279 #if $arf.nanopore
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	280 #for $read in $nanopore_reads
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	281 --nanopore $read
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	282 #end for
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	283 #end if
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	284 #if $arf.pacbio
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	285 #for $read in $pacbio_reads
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	286 --pacbio $read
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	287 #end for
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	288 #end if
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	289 ]]></token>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	290
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	291
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	292 <token name="@SANGER@"><![CDATA[
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	293 #if $arf.sanger
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	294 #for $read in $sanger_reads
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	295 --sanger $read
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	296 #end for
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	297 #end if
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	298 ]]></token>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	299
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	300 <token name="@FL_RNA@"><![CDATA[
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	301 #if $arf.flrna
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	302 #for $read in $flrna_reads
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	303 --fl-rna $read
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	304 #end for
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	305 #end if
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	306 ]]></token>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	307
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	308 <token name="@ASSEMBLY_GRAPH@"><![CDATA[
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	309 #if $arf.assembly_graph
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	310 #for $graph in $assembly_graphs
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	311 --assembly-graph $graph
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	312 #end for
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	313 #end if
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	314 ]]></token>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	315
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	316 <token name="@CONTIGS@"><![CDATA[
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	317 #if $arf.trusted_contigs
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	318 #for $read in $trusted_contigs
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	319 --trusted-contigs $read
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	320 #end for
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	321 #end if
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	322 #if $arf.untrusted_contigs
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	323 #for $read in $untrusted_contigs
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	324 --untrusted-contigs $read
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	325 #end for
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	326 #end if
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	327 ]]></token>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	328
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	329 <token name="@LIBRARY_NUMBER@"><![CDATA[
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	330 #if $additional_reads.selector == 'true' and $additional_reads.library_number == 'false'
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	331 #set $library += 1
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	332 #end if
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	333 ]]></token>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	334
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	335 <!-- POSTPROCESSING -->
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	336
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	337 <token name="@STATS@"><![CDATA[
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	338 #if 'cs' in $optional_output
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	339 && (test -f 'output/contigs.fasta' && python '$__tool_directory__/write_tsv_script.py' < 'output/contigs.fasta' > '$out_cs' \|\| echo 'No contigs.fasta.')
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	340 #end if
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	341 #if 'ss' in $optional_output
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	342 && (test -f 'output/scaffolds.fasta' && python '$__tool_directory__/write_tsv_script.py' < 'output/scaffolds.fasta' > '$out_ss' \|\| echo 'No scaffolds.fasta.')
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	343 #end if
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	344 ]]></token>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	345
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	346 <!--
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	347 input
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	348 -->
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	349
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	350 <xml name="input_files_all" token_format="" token_label="" token_help="It assumes that all samples belong to the same library. If you want to use samples from two different libraries, include the second library as additional set of short-reads.">
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	351 <conditional name="singlePaired">
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	352 <param name="sPaired" type="select" label="Single-end or paired-end short-reads" help="@HELP@">
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	353 <option value="single">Single-end</option>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	354 <option value="paired_interlaced">Paired-end: interlaced reads</option>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	355 <option value="paired_collection" selected="true">Paired-end: list of dataset pairs</option>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	356 </param>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	357 <when value="single">
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	358 <param format="@FORMAT@" name="input1" type="data" multiple="true" label="@LABEL@"/>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	359 </when>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	360 <when value="paired_interlaced">
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	361 <param format="@FORMAT@" name="input1" type="data" multiple="true" label="@LABEL@: interlaced"/>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	362 <expand macro="type_paired"/>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	363 <expand macro="orientation"/>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	364 </when>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	365 <when value="paired_collection">
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	366 <!-- CHANGED: list:paired -> paired (Galaxy maps lists) -->
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	367 <param format="@FORMAT@" name="input" type="data_collection" collection_type="paired" label="@LABEL@: collection (a single pair; lists will map)"/>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	368 <expand macro="type_paired"/>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	369 <expand macro="orientation"/>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	370 </when>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	371 </conditional>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	372 </xml>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	373
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	374 <xml name="input_files_paired" tokens="format,label" token_help="It assumes that all samples belong to the same library. If you want to use samples from two different libraries, include the second library as additional set of short-reads.">
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	375 <conditional name="singlePaired">
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	376 <param name="sPaired" type="select" label="Pair-end reads input format" help="@HELP@">
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	377 <option value="paired_interlaced">Paired-end: interlaced reads</option>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	378 <option value="paired_collection" selected="true">Paired-end: list of dataset pairs</option>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	379 </param>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	380 <when value="paired_interlaced">
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	381 <param format="@FORMAT@" name="input1" type="data" multiple="true" label="@LABEL@: interlaced"/>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	382 <expand macro="type_paired"/>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	383 <expand macro="orientation"/>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	384 </when>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	385 <when value="paired_collection">
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	386 <!-- CHANGED: list:paired -> paired -->
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	387 <param format="@FORMAT@" name="input" type="data_collection" collection_type="paired" label="@LABEL@: collection (a single pair; lists will map)"/>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	388 <expand macro="type_paired"/>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	389 <expand macro="orientation"/>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	390 </when>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	391 </conditional>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	392 <param name="library_number" type="select" label="The samples belong to the same library" help="If the reads have been generated from the same sample, it means that they belong to the same library.">
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	393 <option value="true" selected="true">True</option>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	394 <option value="false">False</option>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	395 </param>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	396 </xml>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	397
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	398 <xml name="orientation">
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	399 <param name="orientation" type="select" label="Select orientation of reads" help="Note: mate-pair fragments are generally in a RF conformation. In general, paired-end reads tend to be in a FR orientation.">
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	400 <option value="fr" selected="true"><![CDATA[FR (-> <-)]]></option>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	401 <option value="rf"><![CDATA[RF (<- ->)]]></option>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	402 <option value="ff"><![CDATA[FF (-> ->)]]></option>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	403 </param>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	404 </xml>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	405
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	406 <xml name="type_paired">
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	407 <param name="type_paired" type="select" label="Type of paired-reads"
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	408 help="In paired-end sequencing, the library preparation yields a set of fragments, and the machine sequences each fragment from both ends. In mate-pair sequencing,
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	409 the library preparation yields two fragments that are distal to each other in the genome and in the opposite in orientation to that of a mate-paired fragment.">
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	410 <option value="pe" selected="true">Default (--pe)</option>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	411 <option value="mp">Mate-pair reads (--mp)</option>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	412 <option value="hqmp">High-quality Nextera mate-pair reads (--hqmp)</option>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	413 </param>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	414 </xml>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	415
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	416 <xml name="input_additional_files_all" tokens="format" token_help="">
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	417 <conditional name="additional_reads">
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	418 <param name="selector" type="select" label="Use an additional set of short-reads" help="Enable this option if you want to combine to data sources (e.g. single and paired reads).">
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	419 <option value="false" selected="true">Disabled</option>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	420 <option value="true">Enabled</option>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	421 </param>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	422 <when value="true">
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	423 <expand macro="input_files_all" format="@FORMAT@" label="FASTA/FASTQ file(s)" help="@HELP@"/>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	424 <param name="library_number" type="select" label="The samples belong to the same library" help="If the reads have been generated from the sample sample, it means that they belong to the same library.">
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	425 <option value="true" selected="true">True</option>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	426 <option value="false">False</option>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	427 </param>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	428 </when>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	429 <when value="false"/>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	430 </conditional>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	431 </xml>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	432
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	433 <xml name="input_additional_files_paired" tokens="format" token_help="" >
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	434 <conditional name="additional_reads">
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	435 <param name="selector" type="select" label="Use an additional set of short-reads" help="Enable this option if you want to combine to data sources (e.g. single and paired reads).">
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	436 <option value="false" selected="true">Disabled</option>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	437 <option value="true">Enabled</option>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	438 </param>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	439 <when value="true">
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	440 <expand macro="input_files_paired" format="@FORMAT@" label="FASTA/FASTQ file(s)" help="@HELP@"/>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	441 </when>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	442 <when value="false"/>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	443 </conditional>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	444 </xml>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	445
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	446 <xml name="covcutoff">
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	447 <conditional name="cov_cond">
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	448 <param argument="--cov-cutoff" type="select" label="Set coverage cutoff option" help="When set to 'auto' SPAdes automatically computes coverage threshold using conservative strategy">
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	449 <option value="off">Off</option>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	450 <option value="auto">Auto</option>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	451 <option value="value">User specific</option>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	452 </param>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	453 <when value="off"/>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	454 <when value="auto"/>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	455 <when value="value">
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	456 <param name="manual" type="float" min="0" value="" label="Set value"/>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	457 </when>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	458 </conditional>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	459 </xml>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	460 <xml name="pipeline_options" token_additional_help="">
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	461 <param name="mode_sel" type="select" label="Pipeline options" multiple="true" optional="true" display="checkboxes" help="Error correction requires FASTQ input files. @ADDITIONAL_HELP@">
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	462 <option value="--disable-rr">Disable repeat resolution (--disable-rr)</option>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	463 <yield/>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	464 </param>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	465 </xml>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	466 <xml name="kmer" token_help="" token_default="21,33,55,77">
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	467 <conditional name="kmer_cond">
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	468 <param name="kmer_sel" argument="-k" type="select" label="Select k-mer detection option" help="@HELP@ Comma-separated list, all values must be odd, less than 128 and listed in ascending order.">
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	469 <option value="auto">Auto</option>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	470 <option value="manual">User specific</option>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	471 </param>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	472 <when value="auto"/>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	473 <when value="manual">
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	474 <param name="manual" type="text" value="@DEFAULT@" label="K-mer size values" help="List of k-mer sizes (must be odd and less than 128)">
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	475 <sanitizer invalid_char="">
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	476 <valid initial="string.digits">
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	477 <add value="," />
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	478 </valid>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	479 </sanitizer>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	480 <validator type="regex">[0-9,]+</validator>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	481 </param>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	482 </when>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	483 </conditional>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	484 </xml>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	485 <xml name="nanopore_pacbio">
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	486 <param argument="--nanopore" type="data" format="@FASTQ_INTYPES@" multiple="true" optional="true" label="Nanopore reads" help="SPAdes will use Oxford Nanopore reads for gap closure and repeat resolution"/>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	487 <param argument="--pacbio" type="data" format="@FASTQ_INTYPES@" multiple="true" optional="true" label="PacBio CLR reads" help="It is not recommended to run SPAdes on PacBio reads with low coverage (less than 5). In addition, SPAdes develpers suggest not to run SPAdes on PacBio reads for large genomes. SPAdes will use PacBio CLR reads for gap closure and repeat resolution"/>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	488 </xml>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	489 <xml name="flrna">
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	490 <param argument="--fl-rna" name="flrna" type="data" format="@INTYPES@" multiple="true" optional="true" label="PacBio/Nanopore/contigs that capture full-length transcripts" help="In addition to long reads, you may also provide a separate file with reads capturing the entire transcript sequences using this option. Full-length transcripts in such reads can be typically detected using the adapters. Note, that FL reads should be trimmed so that the adapters are excluded."/>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	491 </xml>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	492
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	493 <xml name="phred">
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	494 <param argument="--phred-offset" type="select" label="Set Phred quality offset" help="Phred quality offset in the input reads. Default: auto-detect">
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	495 <option value="auto" selected="true">Auto</option>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	496 <option value="33">33 (Sanger)</option>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	497 <option value="64">64 (Illumina)</option>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	498 </param>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	499 </xml>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	500 <xml name="reads" token_paramname="reads" token_help="" token_label="">
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	501 <param name="@PARAMNAME@" type="data" format="@FASTQ_INTYPES@" label="@LABEL@ reads" help="@HELP@"/>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	502 </xml>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	503 <xml name="sanger">
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	504 <param argument="--sanger" type="data" format="@FASTQ_INTYPES@" multiple="true" optional="true" label="Sanger reads"/>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	505 </xml>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	506 <xml name="contigs">
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	507 <param argument="--trusted-contigs" type="data" format="@FASTA_INTYPES@" multiple="true" optional="true" label="Trusted contigs" help="Reliable contigs of the same genome, which are likely to have no misassemblies and small rate of other errors (e.g. mismatches and indels). This option is not intended for contigs of the related species."/>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	508 <param argument="--untrusted-contigs" type="data" format="@FASTA_INTYPES@" multiple="true" optional="true" label="Untrusted contigs" help="Contigs of the same genome, quality of which is average or unknown. Contigs of poor quality can be used but may introduce errors in the assembly. This option is also not intended for contigs of the related species."/>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	509 </xml>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	510 <xml name="assembly_graph">
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	511 <param argument="--assembly-graph" type="data" format="gfa1" multiple="true" optional="true" label="Assembly graphs" help=" The primary purpose of this option to run these pipelines on already constructed and simplified assembly graph this way skipping a large part of SPAdes pipeline."/>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	512 </xml>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	513 <xml name="optional_output">
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	514 <param name="optional_output" type="select" multiple="true" optional="false" label="Select optional output file(s)" help="Only shown in history if selected here and generated by the specific run.">
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	515 <option value="ag" selected="true">Assembly graph</option>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	516 <option value="ags" selected="true">Assembly graph with scaffolds</option>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	517 <option value="cn" selected="true">Contigs</option>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	518 <option value="cp">Contigs paths</option>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	519 <option value="cr">Corrected reads</option>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	520 <option value="cs">Contigs stats</option>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	521 <option value="l">Log</option>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	522 <option value="sc" selected="true">Scaffolds</option>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	523 <option value="sp">Scaffolds paths</option>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	524 <option value="ss">Scaffolds stats</option>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	525 </param>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	526 </xml>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	527 <!--
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	528 output macros (unchanged; Galaxy will collect into a list when mapped)
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	529 -->
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	530
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	531 <xml name="out_ag">
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	532 <data name="out_ag" format="fastg" from_work_dir="output/assembly_graph.fastg" label="${tool.name} on ${on_string}: Assembly graph">
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	533 <filter>'ag' in optional_output</filter>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	534 <filter>'operation_mode' not in vars() or operation_mode != '--only-error-correction'</filter>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	535 </data>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	536 </xml>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	537 <xml name="out_ags">
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	538 <data name="out_ags" format="txt" from_work_dir="output/assembly_graph_with_scaffolds.gfa" label="${tool.name} on ${on_string}: Assembly graph with scaffolds">
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	539 <filter>'ags' in optional_output</filter>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	540 <filter>'operation_mode' not in vars() or operation_mode != '--only-error-correction'</filter>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	541 </data>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	542 </xml>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	543 <xml name="out_cn">
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	544 <data name="out_cn" format="fasta" from_work_dir="output/contigs.fasta" label="${tool.name} on ${on_string}: Contigs">
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	545 <filter>'cn' in optional_output</filter>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	546 <filter>'operation_mode' not in vars() or operation_mode != '--only-error-correction'</filter>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	547 </data>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	548 </xml>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	549 <xml name="out_cp">
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	550 <data name="out_cp" format="txt" from_work_dir="output/contigs.paths" label="${tool.name} on ${on_string}: Contigs paths">
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	551 <filter>'cp' in optional_output</filter>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	552 <filter>'operation_mode' not in vars() or operation_mode != '--only-error-correction'</filter>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	553 </data>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	554 </xml>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	555 <xml name="out_cr">
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	556 <collection name="out_cr" type="list" label="${tool.name} on ${on_string}: Corrected reads">
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	557 <filter>'cr' in optional_output</filter>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	558 <filter>'operation_mode' not in vars() or operation_mode != '--only-assembler'</filter>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	559 <discover_datasets pattern="(?P<designation>.+)\.cor\.fastq\.gz" format="fastq" directory="output/corrected"/>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	560 <discover_datasets pattern="(?P<designation>.+)\.cor\.fasta\.gz" format="fasta" directory="output/corrected"/>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	561 </collection>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	562 </xml>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	563 <xml name="out_cs">
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	564 <data name="out_cs" format="tabular" label="${tool.name} on ${on_string}: Contigs stats">
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	565 <actions>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	566 <action name="column_names" type="metadata" default="name,length,coverage"/>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	567 </actions>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	568 <filter>'cs' in optional_output</filter>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	569 <filter>'operation_mode' not in vars() or operation_mode != '--only-error-correction'</filter>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	570 </data>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	571 </xml>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	572 <xml name="out_l">
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	573 <data name="out_l" format="txt" from_work_dir="output/spades.log" label="${tool.name} on ${on_string}: Log">
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	574 <filter>'l' in optional_output</filter>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	575 </data>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	576 </xml>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	577 <xml name="out_sc">
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	578 <data name="out_sc" format="fasta" from_work_dir="output/scaffolds.fasta" label="${tool.name} on ${on_string}: Scaffolds">
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	579 <filter>'sc' in optional_output</filter>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	580 <filter>'operation_mode' not in vars() or operation_mode != '--only-error-correction'</filter>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	581 </data>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	582 </xml>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	583 <xml name="out_sp">
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	584 <data name="out_sp" format="txt" from_work_dir="output/scaffolds.paths" label="${tool.name} on ${on_string}: Scaffolds paths">
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	585 <filter>'sp' in optional_output</filter>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	586 <filter>'operation_mode' not in vars() or operation_mode != '--only-error-correction'</filter>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	587 </data>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	588 </xml>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	589 <xml name="out_ss">
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	590 <data name="out_ss" format="tabular" label="${tool.name} on ${on_string}: Scaffolds stats">
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	591 <actions>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	592 <action name="column_names" type="metadata" default="name,length,coverage"/>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	593 </actions>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	594 <filter>'ss' in optional_output</filter>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	595 <filter>'operation_mode' not in vars() or operation_mode != '--only-error-correction'</filter>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	596 </data>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	597 </xml>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	598 <xml name="out_rs">
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	599 <data name="out_rs" format="fasta" from_work_dir="output/raw_scaffolds.fasta" label="${tool.name} on ${on_string}: Raw scaffolds">
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	600 <filter>'rs' in optional_output</filter>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	601 </data>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	602 </xml>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	603 <xml name="out_b">
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	604 <data name="out_b" format="txt" from_work_dir="output/hmm_statistics.txt" label="${tool.name} on ${on_string}: HMM statistics">
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	605 <filter>'b' in optional_output</filter>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	606 </data>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	607 </xml>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	608 <xml name="out_dg">
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	609 <data name="out_dg" format="fasta" from_work_dir="output/domain_graph.dot" label="${tool.name} on ${on_string}: Domain graph">
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	610 <filter>'dg' in optional_output</filter>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	611 </data>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	612 </xml>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	613
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	614 <!-- help tokens unchanged -->
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	615 <token name="@HELP_IN@"><![CDATA[
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	616 ... (unchanged help text) ...
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	617 ]]></token>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	618 <token name="@HELP_OUT_AG@">- Assembly graph</token>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	619 <token name="@HELP_OUT_AGS@">- Assembly graph with scaffolds</token>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	620 <token name="@HELP_OUT_C@">- Contigs</token>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	621 <token name="@HELP_OUT_CP@">- Contigs paths in the assembly graph</token>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	622 <token name="@HELP_OUT_CS@">- Contigs stats</token>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	623 <token name="@HELP_OUT_CR@">- Corrected reads by BayesHammer</token>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	624 <token name="@HELP_OUT_L@">- Log file</token>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	625 <token name="@HELP_OUT_S@">- Scaffolds (recommended for use as resulting sequences)</token>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	626 <token name="@HELP_OUT_SP@">- Scaffolds paths in the assembly graph</token>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	627 <token name="@HELP_OUT_SS@">- Scaffolds stats</token>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	628 <token name="@HELP_WID@">SPAdes - St. Petersburg genome assembler - is an assembly toolkit containing various assembly pipelines.</token>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	629 <token name="@IONTORRENT@"><![CDATA[
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	630 ... (unchanged IonTorrent help) ...
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	631 ]]></token>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	632
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	633 </macros>
f69397b32f52 planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b estrain parents: diff changeset	634

Mercurial > repos > estrain > spades_cpu7mem28

annotate macros.xml @ 1:45b5f747c900 draft default tip