| Previous changeset 3:15ca041134a9 (2019-08-21) Next changeset 5:dbe2b2204555 (2020-01-19) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit d2e1ee6304af1062175ca87aab59c4042ace3116" |
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modified:
roary.xml |
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| diff -r 15ca041134a9 -r 809e42326fc2 roary.xml --- a/roary.xml Wed Aug 21 11:11:15 2019 -0400 +++ b/roary.xml Thu Nov 14 03:51:08 2019 -0500 |
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| @@ -1,14 +1,16 @@ <tool id="roary" name="Roary" version="3.12.0+galaxy0"> <description>the pangenome pipeline - Quickly generate a core gene alignment from gff3 files</description> - + <requirements> <requirement type="package" version="3.12.0">roary</requirement> </requirements> - + <command detect_errors="exit_code"><![CDATA[ - + #set $filenames = list() #for $gff in $gff_input.gffs - cp $gff '${gff.element_identifier}'.gff && + cp '$gff' '${gff.element_identifier}.gff' && + #set $filename = str($gff.element_identifier) + '.gff' + $filenames.append(str($filename)) #end for roary @@ -23,10 +25,12 @@ -t '$advanced.trans_tab' -iv '$advanced.mcl' - *.gff - + #for $f in $filenames + '$f' + #end for + ]]></command> - + <inputs> <conditional name="gff_input"> <param name="gff_input_selector" type="select" label="Individual gff files or a dataset collection" help="Select between individual gff files or a collection of gff files"> @@ -42,7 +46,7 @@ </conditional> <param name="percent_ident" type="integer" label="minimum percentage identity for blastp" help="Sets the minimum percentage identity for protein matches" value="95"/> <param name="core_diff" type="float" label="percentage of isolates a gene must be in to be core" help="The total percentage of the isolates that must have the gene for it to be considered a core gene." value="99.0"/> - + <param name="outputs" type="select" multiple="true" display="checkboxes" label="Additional outputs" help="Summary statistics, core gene alignments and Gene Presence/Absence tables are always produced."> <option value="abg_nw">Accessory binary genes in newick format</option> <option value="abg_fa">Accessory binary genes in fasta format</option> @@ -60,16 +64,16 @@ <option value="numnew_rtab">Number of New Genes in Rtab format</option> <option value="numuniq_rtab">Number of Unique Genes in Rtab format</option> </param> - + <section name="advanced" title="Advanced options" expanded="false"> <param name="maxclust" type="integer" value="50000" label="Maximum number of clusters" help="The maximum number of clusters to assign proteins" /> <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."/> <param name="trans_tab" type="integer" value="11" label="Translation table to use [1 or 4 or 11]" help="DNA -> RNA translation table to use. Roary is designed for prokaryotes and so tables 1, 4 or 11 will work, others could be problematic." /> <param name="mcl" type="float" value="1.5" label="MCL inflation value" help="This is an advanced setting, change only if you know what you are doing and then at your own risk!" /> </section> - + </inputs> - + <outputs> <data format="tabular" name="sumstats" label="${tool.name} on ${on_string} Summary statistics" from_work_dir="out/summary_statistics.txt" /> <data format="fasta" name="core_gene_aln" label="${tool.name} on ${on_string} Core Gene Alignment" from_work_dir="out/core_gene_alignment.aln" /> @@ -120,7 +124,7 @@ <filter>outputs and 'numuniq_rtab' in outputs</filter> </data> </outputs> - + <tests> <test> <param name="gff_input_selector" value="individual"/> @@ -135,7 +139,7 @@ <output name="sumstats" file="test2/summary_statistics.txt" ftype="tabular"/> </test> </tests> - + <help><![CDATA[ **Roary** @@ -143,35 +147,35 @@ To use Roary, select two or more gff3 files OR a collection of gff3 files -**Options**: +**Options**: - Minimum percentage identity for blastp - an integer, default is [95] - + - Percentage of isolates a gene must be in to be core - a float, default is [99.0] - - + + **Advanced Options**: - + - Maximum number of clusters - integer, default is [50000] - + - Don't split paralogs - check box - + - Translation table - which translation table to use, an integer, default is [11] - + - Change the MCL inflation value - a float, default is [1.5] - + For further info see: http://sanger-pathogens.github.io/Roary/ - + ]]></help> - + <citations> <citation type="doi">10.1093/bioinformatics/btv421</citation> </citations> - + </tool> |