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comparison roary.xml @ 6:15ac71df11a0 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit b65bd3e275828e8f4729c0f8211bc2bf6da71689"
author iuc
date Mon, 29 Jun 2020 08:40:27 -0400
parents dbe2b2204555
children 78608ec02d62
comparison
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5:dbe2b2204555 6:15ac71df11a0
1 <tool id="roary" name="Roary" version="3.13.0"> 1 <tool id="roary" name="Roary" version="3.13.0+galaxy0">
2 <description>the pangenome pipeline - Quickly generate a core gene alignment from gff3 files</description> 2 <description>the pangenome pipeline - Quickly generate a core gene alignment from gff3 files</description>
3 3
4 <requirements> 4 <requirements>
5 <requirement type="package" version="3.13.0">roary</requirement> 5 <requirement type="package" version="3.13.0">roary</requirement>
6 </requirements> 6 </requirements>
61 <option value="genepa_rtab">Gene Presence Absence file in Rtab format</option> 61 <option value="genepa_rtab">Gene Presence Absence file in Rtab format</option>
62 <option value="numcons_rtab">Number of Conserved Genes in Rtab format</option> 62 <option value="numcons_rtab">Number of Conserved Genes in Rtab format</option>
63 <option value="numpangene_rtab">Number of Genes in Pan Genome in Rtab format</option> 63 <option value="numpangene_rtab">Number of Genes in Pan Genome in Rtab format</option>
64 <option value="numnew_rtab">Number of New Genes in Rtab format</option> 64 <option value="numnew_rtab">Number of New Genes in Rtab format</option>
65 <option value="numuniq_rtab">Number of Unique Genes in Rtab format</option> 65 <option value="numuniq_rtab">Number of Unique Genes in Rtab format</option>
66 <option value="pangenomeref">FASTA file which contains a single representative nucleotide sequence from each of the clusters in the pan genome (core and accessory)</option>
66 </param> 67 </param>
67 68
68 <section name="advanced" title="Advanced options" expanded="false"> 69 <section name="advanced" title="Advanced options" expanded="false">
69 <param name="maxclust" type="integer" value="50000" label="Maximum number of clusters" help="The maximum number of clusters to assign proteins" /> 70 <param name="maxclust" type="integer" value="50000" label="Maximum number of clusters" help="The maximum number of clusters to assign proteins" />
70 <param name="split_para" type="boolean" checked="False" truevalue="-s" falsevalue="" label="Don't split paralogs" help="Click yes so that paralogs aren't split."/> 71 <param name="split_para" type="boolean" checked="False" truevalue="-s" falsevalue="" label="Don't split paralogs" help="Click yes so that paralogs aren't split."/>
121 <filter>outputs and 'numnew_rtab' in outputs</filter> 122 <filter>outputs and 'numnew_rtab' in outputs</filter>
122 </data> 123 </data>
123 <data format="txt" name="num_uniq_rtab" label="${tool.name} on ${on_string} Number of Unique Genes" from_work_dir="out/number_of_unique_genes.Rtab" > 124 <data format="txt" name="num_uniq_rtab" label="${tool.name} on ${on_string} Number of Unique Genes" from_work_dir="out/number_of_unique_genes.Rtab" >
124 <filter>outputs and 'numuniq_rtab' in outputs</filter> 125 <filter>outputs and 'numuniq_rtab' in outputs</filter>
125 </data> 126 </data>
127 <data format="fasta" name="pan_genome_ref" label="${tool.name} on ${on_string} pan-genome reference" from_work_dir="out/pan_genome_reference.fa" >
128 <filter>outputs and 'pangenomeref' in outputs</filter>
129 </data>
126 </outputs> 130 </outputs>
127 131
128 <tests> 132 <tests>
129 <test> 133 <test>
130 <param name="gff_input_selector" value="individual"/> 134 <param name="gff_input_selector" value="individual"/>