Mercurial > repos > iuc > spades_metaviralspades

comparison metaviralspades.xml @ 8:5b26685e5d3b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 066e075c1599b29e92708194db2b2ccc30b7677c
author iuc
date Mon, 12 Feb 2024 21:46:08 +0000
parents 328aa71f0f3c
children
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7:328aa71f0f3c 8:5b26685e5d3b
1 <tool id="spades_metaviralspades" name="metaviralSPAdes" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01"> 1 <tool id="spades_metaviralspades" name="metaviralSPAdes" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
2 <description>extract and assembly viral genomes from metagenomic data</description> 2 <description>extract and assembly viral genomes from metagenomic data</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <xrefs>
7 <xref type="bio.tools">metaviralspades</xref>
8 </xrefs>
6 <expand macro="requirements"/> 9 <expand macro="requirements"/>
7 <expand macro="stdio"/> 10 <expand macro="stdio"/>
8 <expand macro="version_command"/> 11 <expand macro="version_command"/>
9 <command detect_errors="exit_code"><![CDATA[ 12 <command detect_errors="exit_code"><![CDATA[
10 13
20 @PREPROCESS_ASSEMBLY_GRAPH_FILES@ 23 @PREPROCESS_ASSEMBLY_GRAPH_FILES@
21 24
22 @OMP_THREADS@ 25 @OMP_THREADS@
23 ## run 26 ## run
24 spades.py --metaviral 27 spades.py --metaviral
28 $operation_mode
25 -o 'output' 29 -o 'output'
26 @RESOURCES@ 30 @RESOURCES@
27 @INPUT_READS_MAIN@ 31 @INPUT_READS_MAIN@
28 #if $additional_reads.selector == 'true' 32 #if $additional_reads.selector == 'true'
29 @INPUT_READS_ADDITIONAL@ 33 @INPUT_READS_ADDITIONAL@
50 <expand macro="contigs"/> 54 <expand macro="contigs"/>
51 <expand macro="assembly_graph"/> 55 <expand macro="assembly_graph"/>
52 </section> 56 </section>
53 <expand macro="kmer"/> 57 <expand macro="kmer"/>
54 <expand macro="phred"/> 58 <expand macro="phred"/>
59 <expand macro="operation_mode"/>
55 <expand macro="pipeline_options"> 60 <expand macro="pipeline_options">
56 <option value="--careful">Careful: ties to reduce the number of mismatches and short indels. Only recommended for small genomes (--careful)</option> 61 <option value="--careful">Careful: ties to reduce the number of mismatches and short indels. Only recommended for small genomes (--careful)</option>
57 <option value="--iontorrent">Iontorrent: required when assembling IonTorrent data (--iontorrent)</option> 62 <option value="--iontorrent">Iontorrent: required when assembling IonTorrent data (--iontorrent)</option>
58 </expand> 63 </expand>
59 <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."> 64 <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.">