Mercurial > repos > estrain > metaspades

annotate metaspades.xml @ 0:292d633441ad draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
author estrain
date Fri, 13 Mar 2026 12:07:47 +0000
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
1 <tool id="metaspades" name="metaSPAdes" version="3.15.5+galaxy1.01" profile="20.01">
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
2 <description>metagenome assembler (minimal; interlaced / R1+R2 / paired collection; maps list:paired)</description>
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
3
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
4 <requirements>
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
5 <requirement type="package" version="4.2.0">spades</requirement>
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
6
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
7 </requirements>
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
8
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
9 <stdio>
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
10 <exit_code range="1:" level="fatal"/>
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
11 </stdio>
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
12
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
13 <version_command><![CDATA[
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
14 metaspades.py --version
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
15 ]]></version_command>
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
16
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
17 <command detect_errors="exit_code"><![CDATA[
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
18 ## ---------------------------------
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
19 ## Prep short-read inputs / symlinks
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
20 ## ---------------------------------
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
21 #set $library = 1
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
22
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
23 #if str($singlePaired.sPaired) == "paired_interlaced"
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
24 mkdir -p reads1 &&
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
25 #set $ext = $singlePaired.input1.ext.replace('fastqsanger','fastq').replace('fastqillumina','fastq')
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
26 ln -s '$singlePaired.input1' 'reads1/interlaced_1.${ext}' &&
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
27 #end if
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
28
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
29 #if str($singlePaired.sPaired) == "paired_two_files"
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
30 mkdir -p paired_reads1 &&
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
31 #set $ext1 = $singlePaired.input1.ext.replace('fastqsanger','fastq').replace('fastqillumina','fastq')
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
32 #set $ext2 = $singlePaired.input2.ext.replace('fastqsanger','fastq').replace('fastqillumina','fastq')
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
33 ln -s '$singlePaired.input1' 'paired_reads1/reads_1.${ext1}' &&
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
34 ln -s '$singlePaired.input2' 'paired_reads1/reads_2.${ext2}' &&
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
35 #end if
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
36
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
37 #if str($singlePaired.sPaired) == "paired_collection"
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
38 mkdir -p paired_reads1 &&
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
39 #set $extc = $singlePaired.input.forward.ext.replace('fastqsanger','fastq').replace('fastqillumina','fastq')
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
40 ln -s '$singlePaired.input.forward' 'paired_reads1/reads_1.${extc}' &&
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
41 ln -s '$singlePaired.input.reverse' 'paired_reads1/reads_2.${extc}' &&
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
42 #end if
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
43
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
44 ## ---------------------------------
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
45 ## Optional long-read inputs / links
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
46 ## ---------------------------------
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
47 #set $nano_paths = []
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
48 #if $longreads.nanopore and len($longreads.nanopore) > 0
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
49 mkdir -p lr_nanopore &&
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
50 #for $lri, $lr in enumerate($longreads.nanopore)
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
51 #set $link = 'lr_nanopore/nano_%s.%s' % ($lri, $lr.ext)
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
52 ln -s '$lr' '$link' &&
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
53 $nano_paths.append($link)
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
54 #end for
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
55 #end if
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
56
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
57 #set $pbhifi_paths = []
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
58 #if $longreads.pacbio_hifi and len($longreads.pacbio_hifi) > 0
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
59 mkdir -p lr_pbhifi &&
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
60 #for $lri, $lr in enumerate($longreads.pacbio_hifi)
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
61 #set $link2 = 'lr_pbhifi/pbhifi_%s.%s' % ($lri, $lr.ext)
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
62 ln -s '$lr' '$link2' &&
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
63 $pbhifi_paths.append($link2)
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
64 #end for
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
65 #end if
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
66
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
67 #set $nano_joined = ' '.join(["'%s'" % p for p in $nano_paths]) if $nano_paths else ''
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
68 #set $pbhifi_joined = ' '.join(["'%s'" % p for p in $pbhifi_paths]) if $pbhifi_paths else ''
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
69
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
70 ## ----------
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
71 ## Run SPAdes
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
72 ## ----------
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
73 metaspades.py
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
74 -o 'output'
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
75 -t \${GALAXY_SLOTS:-4}
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
76 #if $resources.ram_gb
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
77 -m ${resources.ram_gb}
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
78 #end if
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
79 ## short-read layout
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
80 #if str($singlePaired.sPaired) == "paired_interlaced"
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
81 --${singlePaired.type_paired}-12 ${library} 'reads1/interlaced_1.${ext}'
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
82 --${singlePaired.type_paired}-or ${library} ${singlePaired.orientation}
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
83 #elif str($singlePaired.sPaired) == "paired_two_files"
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
84 --${singlePaired.type_paired}-1 ${library} 'paired_reads1/reads_1.${ext1}'
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
85 --${singlePaired.type_paired}-2 ${library} 'paired_reads1/reads_2.${ext2}'
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
86 --${singlePaired.type_paired}-or ${library} ${singlePaired.orientation}
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
87 #else
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
88 ## paired_collection (and list:paired maps to this one pair per job)
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
89 --${singlePaired.type_paired}-1 ${library} 'paired_reads1/reads_1.${extc}'
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
90 --${singlePaired.type_paired}-2 ${library} 'paired_reads1/reads_2.${extc}'
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
91 --${singlePaired.type_paired}-or ${library} ${singlePaired.orientation}
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
92 #end if
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
93 ## long-reads
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
94 #if $nano_paths
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
95 --nanopore ${nano_joined}
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
96 #end if
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
97 #if $pbhifi_paths
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
98 --pacbio-hifi ${pbhifi_joined}
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
99 #end if
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
100 ## chemistry / pipeline flags
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
101 #if $pipeline.iontorrent
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
102 --iontorrent
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
103 #end if
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
104 #if $pipeline.phred and str($pipeline.phred) != ''
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
105 --phred-offset ${pipeline.phred}
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
106 #end if
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
107 #if $pipeline.kmers and str($pipeline.kmers) != ''
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
108 -k '${pipeline.kmers}'
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
109 #end if
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
110 ]]></command>
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
111
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
112 <inputs>
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
113 <!-- Short-read entry points -->
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
114 <conditional name="singlePaired" label="Short-read layout">
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
115 <param name="sPaired" type="select" label="Reads are">
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
116 <option value="paired_interlaced">Interlaced paired reads (single FASTQ)</option>
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
117 <option value="paired_two_files">Paired-end reads in two files (R1/R2, not a collection)</option>
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
118 <option value="paired_collection">Paired-end reads as a paired collection</option>
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
119 </param>
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
120
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
121 <!-- (1) Interlaced -->
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
122 <when value="paired_interlaced">
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
123 <param name="input1" type="data" format="fastqsanger,fastqsanger.gz,fastq,fastq.gz"
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
124 label="Interlaced FASTQ"/>
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
125 <param name="type_paired" type="select" label="Library type">
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
126 <option value="pe" selected="true">Paired-end (--pe-*)</option>
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
127 <option value="hqmp">High-quality mate-pairs (--hqmp-*)</option>
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
128 <option value="mp">Mate-pairs (--mp-*)</option>
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
129 </param>
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
130 <param name="orientation" type="select" label="Orientation (--*-or)">
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
131 <option value="fr" selected="true">fr (forward-reverse)</option>
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
132 <option value="rf">rf (reverse-forward)</option>
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
133 <option value="ff">ff (forward-forward)</option>
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
134 </param>
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
135 </when>
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
136
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
137 <!-- (2) Two files (R1/R2) -->
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
138 <when value="paired_two_files">
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
139 <param name="input1" type="data" format="fastqsanger,fastqsanger.gz,fastq,fastq.gz"
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
140 label="Forward (R1) FASTQ"/>
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
141 <param name="input2" type="data" format="fastqsanger,fastqsanger.gz,fastq,fastq.gz"
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
142 label="Reverse (R2) FASTQ"/>
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
143 <param name="type_paired" type="select" label="Library type">
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
144 <option value="pe" selected="true">Paired-end (--pe-*)</option>
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
145 <option value="hqmp">High-quality mate-pairs (--hqmp-*)</option>
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
146 <option value="mp">Mate-pairs (--mp-*)</option>
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
147 </param>
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
148 <param name="orientation" type="select" label="Orientation (--*-or)">
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
149 <option value="fr" selected="true">fr (forward-reverse)</option>
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
150 <option value="rf">rf (reverse-forward)</option>
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
151 <option value="ff">ff (forward-forward)</option>
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
152 </param>
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
153 </when>
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
154
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
155 <!-- (3) Paired collection (maps list:paired automatically) -->
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
156 <when value="paired_collection">
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
157 <param name="input" type="data_collection" collection_type="paired"
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
158 label="Paired collection (forward/reverse). To run one job per pair from a list:paired, map the list to this input."/>
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
159 <param name="type_paired" type="select" label="Library type">
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
160 <option value="pe" selected="true">Paired-end (--pe-*)</option>
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
161 <option value="hqmp">High-quality mate-pairs (--hqmp-*)</option>
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
162 <option value="mp">Mate-pairs (--mp-*)</option>
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
163 </param>
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
164 <param name="orientation" type="select" label="Orientation (--*-or)">
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
165 <option value="fr" selected="true">fr (forward-reverse)</option>
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
166 <option value="rf">rf (reverse-forward)</option>
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
167 <option value="ff" >ff (forward-forward)</option>
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
168 </param>
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
169 </when>
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
170 </conditional>
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
171
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
172 <!-- Optional long-reads -->
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
173 <section name="longreads" title="Optional long-read data">
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
174 <param name="nanopore" type="data" multiple="true"
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
175 format="fastq,fastq.gz,fastqsanger,fastqsanger.gz,fasta,fasta.gz"
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
176 optional="true" label="Nanopore reads (--nanopore)"/>
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
177 <param name="pacbio_hifi" type="data" multiple="true"
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
178 format="fastq,fastq.gz,fastqsanger,fastqsanger.gz,fasta,fasta.gz"
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
179 optional="true" label="PacBio HiFi reads (--pacbio-hifi)"/>
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
180 </section>
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
181
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
182 <!-- Simple knobs -->
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
183 <section name="resources" title="Resources">
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
184 <param name="ram_gb" type="integer" value="16" min="1"
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
185 label="Max RAM for SPAdes (-m, in GB)"/>
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
186 </section>
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
187
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
188 <section name="pipeline" title="Chemistry and pipeline options">
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
189 <param name="iontorrent" type="boolean" truevalue="true" falsevalue=""
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
190 checked="false" label="IonTorrent data (--iontorrent)"/>
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
191 <param name="phred" type="select" optional="true" label="Phred offset (--phred-offset)">
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
192 <option value="" selected="true">auto (default)</option>
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
193 <option value="33">33</option>
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
194 <option value="64">64</option>
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
195 </param>
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
196 <param name="kmers" type="text" optional="true"
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
197 label="K-mer sizes (-k)" help="Comma-separated odd integers between 21 and 127, e.g. 21,33,55"/>
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
198 </section>
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
199 </inputs>
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
200
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
201 <outputs>
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
202 <data name="out_cn" format="fasta" from_work_dir="output/contigs.fasta"
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
203 label="metaSPAdes on ${on_string}: contigs"/>
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
204 <data name="out_sc" format="fasta" from_work_dir="output/scaffolds.fasta"
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
205 label="metaSPAdes on ${on_string}: scaffolds"/>
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
206 <data name="out_ag" format="fasta" from_work_dir="output/assembly_graph.fastg"
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
207 label="metaSPAdes on ${on_string}: assembly graph (FASTG)"/>
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
208 <data name="out_ags" format="gfa1" from_work_dir="output/assembly_graph_with_scaffolds.gfa"
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
209 label="metaSPAdes on ${on_string}: assembly graph with scaffolds (GFA)"/>
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
210 <data name="out_l" format="txt" from_work_dir="output/spades.log"
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
211 label="metaSPAdes on ${on_string}: log"/>
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
212 </outputs>
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
213
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
214 <help><![CDATA[
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
215 ]]></help>
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
216
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
217 <citations>
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
218 <citation type="doi">10.1101/gr.213959.116</citation>
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
219 </citations>
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
220 </tool>
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
221