Mercurial > repos > estrain > spades_cpu7mem28

comparison spades_cpu7mem28.xml @ 0:f69397b32f52 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b
author estrain
date Fri, 13 Mar 2026 12:21:18 +0000
parents
children 45b5f747c900
comparison
equal deleted inserted replaced
-1:000000000000 0:f69397b32f52
1 <tool id="spades_cpu7mem28" name="SPAdes" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
2 <description>genome assembler for genomes of regular and single-cell projects</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <xrefs>
7 <xref type="bio.tools">spades</xref>
8 </xrefs>
9 <expand macro="requirements"/>
10 <expand macro="stdio"/>
11 <expand macro="version_command"/>
12 <command detect_errors="exit_code"><![CDATA[
13
14 #set $library = 1
15
16 @PREPROCESS_INPUT_FILES_MAIN@
17 #if $additional_reads.selector == 'true'
18 @PREPROCESS_INPUT_FILES_ADDITIONAL@
19 #end if
20 @PREPROCESS_NANOPORE_PACBIO_FILES@
21 @PREPROCESS_CONTIGS_FILES@
22 @PREPROCESS_SANGER_FILES@
23
24 @OMP_THREADS@
25 ## run
26 spades.py
27 $operation_mode
28 -o 'output'
29 @RESOURCES@
30 @INPUT_READS_MAIN@
31 #if $additional_reads.selector == 'true'
32 @INPUT_READS_ADDITIONAL@
33 #end if
34 ## additional reads
35 @NANOPORE_PACBIO@
36 @SANGER@
37 @CONTIGS@
38 ## parameter
39 #if $cov_cond.cov_cutoff == 'value':
40 --cov-cutoff $cov_cond.manual
41 #else:
42 --cov-cutoff $cov_cond.cov_cutoff
43 #end if
44 @KMER@
45 @PIPELINE_OPTIONS@
46 @PHREDOFFSET@
47
48 ## postprocessing
49 @STATS@
50 ]]></command>
51 <inputs>
52 <expand macro="operation_mode" help="To run read error correction, reads should be in FASTQ format."/>
53 <expand macro="input_files_all" format="@INTYPES@" label="FASTA/FASTQ file(s)"/>
54 <expand macro="input_additional_files_all" format="@INTYPES@" label="FASTA/FASTQ file(s)"/>
55 <section name="arf" title="Additional read files">
56 <expand macro="nanopore_pacbio"/>
57 <expand macro="sanger"/>
58 <expand macro="contigs"/>
59 </section>
60 <expand macro="pipeline_options" additional_help="&quot;Isolate&quot; is not compatible with &quot;Careful&quot; and Operation mode &quot;Only error correction&quot;">
61 <option value="--sc">Single cell mode: required for MDA (single-cell) data (--sc)</option>
62 <option value="--isolate">Isolate: highly recommended for high-coverage isolate and multi-cell data (--isolate)</option>
63 <option value="--careful">Careful: ties to reduce the number of mismatches and short indels. Only recommended for small genomes (--careful)</option>
64 <option value="--iontorrent">Iontorrent: required when assembling IonTorrent data (--iontorrent)</option>
65 </expand>
66 <expand macro="covcutoff"/>
67 <expand macro="kmer" help="If --sc is set the default values are 21,33,55. For multicell datasets K values are automatically selected using maximum read length."/>
68 <expand macro="phred"/>
69 <expand macro="optional_output"/>
70 </inputs>
71 <outputs>
72 <expand macro="out_ag"/>
73 <expand macro="out_ags"/>
74 <expand macro="out_cn"/>
75 <expand macro="out_cp"/>
76 <expand macro="out_cr"/>
77 <expand macro="out_cs"/>
78 <expand macro="out_l"/>
79 <expand macro="out_sc"/>
80 <expand macro="out_sp"/>
81 <expand macro="out_ss"/>
82 </outputs>
83 <!-- tests/help/citations unchanged -->
84 </tool>
85