| Previous changeset 6:15ac71df11a0 (2020-06-29) Next changeset 8:e88a7de55d6e (2021-09-23) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 442b1247ee31ec9872633be18784f346e4762486" |
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modified:
roary.xml |
| b |
| diff -r 15ac71df11a0 -r 78608ec02d62 roary.xml --- a/roary.xml Mon Jun 29 08:40:27 2020 -0400 +++ b/roary.xml Sat Feb 13 11:59:15 2021 +0000 |
| [ |
| b'@@ -1,16 +1,19 @@\n-<tool id="roary" name="Roary" version="3.13.0+galaxy0">\n+<tool id="roary" name="Roary" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">\n <description>the pangenome pipeline - Quickly generate a core gene alignment from gff3 files</description>\n-\n+ <macros>\n+ <token name="@TOOL_VERSION@">3.13.0</token>\n+ <token name="@VERSION_SUFFIX@">1</token>\n+ </macros>\n <requirements>\n- <requirement type="package" version="3.13.0">roary</requirement>\n+ <requirement type="package" version="@TOOL_VERSION@">roary</requirement>\n </requirements>\n \n <command detect_errors="exit_code"><![CDATA[\n #set $filenames = list()\n #for $gff in $gff_input.gffs\n- cp \'$gff\' \'${gff.element_identifier}.gff\' &&\n- #set $filename = str($gff.element_identifier) + \'.gff\'\n- $filenames.append(str($filename))\n+ cp \'$gff\' \'${gff.element_identifier}.gff\' &&\n+ #set $filename = str($gff.element_identifier) + \'.gff\'\n+ $filenames.append(str($filename))\n #end for\n \n roary\n@@ -29,119 +32,119 @@\n \'$f\'\n #end for\n \n- ]]></command>\n+ ]]> </command>\n \n <inputs>\n- <conditional name="gff_input">\n- <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">\n- <option value="individual">Individual</option>\n- <option value="collection">Collection</option>\n- </param>\n- <when value="individual">\n- <param name="gffs" type="data" multiple="true" format="gff,gff3" label="select gff inputs to Roary" help="Select the files you wish to send to Roary, must be in gff3 format with the sequence data at the end of the file." />\n- </when>\n- <when value=\'collection\'>\n- <param name="gffs" type="data_collection" collection_type="list" format="gff,gff3" label="Dataset collection to submit to Roary" help="A dataset list collection of gff3 files to send to Roary for analysis." />\n- </when>\n- </conditional>\n- <param name="percent_ident" type="integer" label="minimum percentage identity for blastp" help="Sets the minimum percentage identity for protein matches" value="95"/>\n- <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"/>\n+ <conditional name="gff_input">\n+ <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">\n+ <option value="individual">Individual</option>\n+ <option value="collection">Collection</option>\n+ </param>\n+ <when value="individual">\n+ <param name="gffs" type="data" multiple="true" min="2" format="gff,gff3" label="select gff inputs to Roary" help="Select the files you wish to send to Roary, must be in gff3 format with the sequence data at the end of the file." />\n+ </when>\n+ <when value=\'collection\'>\n+ <param name="gffs" type="data_collection" collection_type="list" format="gff,gff3" label="Dataset collection to submit to Roary" help="A dataset list collection of gff3 files to send to Roary for analysis." />\n+ </when>\n+ </conditional>\n+ <param name="percent_ident" type="integer" value="95" label="minimum percentage identity for blastp" help="Sets the minimum percentage identity for protein matches" />\n+ <param name="core_diff" type="float" value="99.0" 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." />\n \n- <param name="outputs" type="select" multi'..b'b">\n+ <filter>outputs and \'blastfreq\' in outputs</filter>\n+ </data>\n+ <data format="txt" name="clust_file" label="${tool.name} on ${on_string} Clustered Proteins" from_work_dir="out/clustered_proteins">\n+ <filter>outputs and \'clust\' in outputs</filter>\n+ </data>\n+ <data format="dot" name="core_acc_graph" label="${tool.name} on ${on_string} Core Accessory Graph" from_work_dir="out/core_accessory_graph.dot">\n+ <filter>outputs and \'coreaccgraph\' in outputs</filter>\n+ </data>\n+ <data format="embl" name="core_acc_embl" label="${tool.name} on ${on_string} Core Accessory EMBL" from_work_dir="out/core_accessory.header.embl">\n+ <filter>outputs and \'coreaccembl\' in outputs</filter>\n+ </data>\n+ <data format="tabular" name="core_acc_tab" label="${tool.name} on ${on_string} Core Accessory Table" from_work_dir="out/core_accessory.tab">\n+ <filter>outputs and \'coreacctab\' in outputs</filter>\n+ </data>\n+ <data format="txt" name="gene_p_a_rtab" label="${tool.name} on ${on_string} Gene Presence Absence Rtab" from_work_dir="out/gene_presence_absence.Rtab">\n+ <filter>outputs and \'genepa_rtab\' in outputs</filter>\n+ </data>\n+ <data format="txt" name="num_cons_rtab" label="${tool.name} on ${on_string} Number of Conserved Genes" from_work_dir="out/number_of_conserved_genes.Rtab">\n+ <filter>outputs and \'numcons_rtab\' in outputs</filter>\n+ </data>\n+ <data format="txt" name="num_pangene_rtab" label="${tool.name} on ${on_string} Number of Genes in Pan Geneome" from_work_dir="out/number_of_genes_in_pan_genome.Rtab">\n+ <filter>outputs and \'numpangene_rtab\' in outputs</filter>\n+ </data>\n+ <data format="txt" name="num_new_rtab" label="${tool.name} on ${on_string} Number of New Genes" from_work_dir="out/number_of_new_genes.Rtab">\n+ <filter>outputs and \'numnew_rtab\' in outputs</filter>\n+ </data>\n+ <data format="txt" name="num_uniq_rtab" label="${tool.name} on ${on_string} Number of Unique Genes" from_work_dir="out/number_of_unique_genes.Rtab">\n+ <filter>outputs and \'numuniq_rtab\' in outputs</filter>\n+ </data>\n+ <data format="fasta" name="pan_genome_ref" label="${tool.name} on ${on_string} pan-genome reference" from_work_dir="out/pan_genome_reference.fa">\n+ <filter>outputs and \'pangenomeref\' in outputs</filter>\n+ </data>\n </outputs>\n \n <tests>\n- <test>\n- <param name="gff_input_selector" value="individual"/>\n- <param name="gffs" value="ex1.gff,ex2.gff" ftype="gff3"/>\n- <output name="sumstats" file="out/summary_statistics.txt" ftype="tabular"/>\n- </test>\n- <test>\n- <param name="gff_input_selector" value="individual"/>\n- <param name="gffs" value="ex1.gff,ex2.gff" ftype="gff3"/>\n- <param name="percent_ident" value="50"/>\n- <param name="core_diff" value="50.0"/>\n- <output name="sumstats" file="test2/summary_statistics.txt" ftype="tabular"/>\n- </test>\n+ <test>\n+ <param name="gff_input_selector" value="individual" />\n+ <param name="gffs" value="ex1.gff,ex2.gff" ftype="gff3" />\n+ <output name="sumstats" file="out/summary_statistics.txt" ftype="tabular" />\n+ </test>\n+ <test>\n+ <param name="gff_input_selector" value="individual" />\n+ <param name="gffs" value="ex1.gff,ex2.gff" ftype="gff3" />\n+ <param name="percent_ident" value="50" />\n+ <param name="core_diff" value="50.0" />\n+ <output name="sumstats" file="test2/summary_statistics.txt" ftype="tabular" />\n+ </test>\n </tests>\n \n <help><![CDATA[\n@@ -176,7 +179,7 @@\n \n For further info see: http://sanger-pathogens.github.io/Roary/\n \n- ]]></help>\n+ ]]> </help>\n \n <citations>\n <citation type="doi">10.1093/bioinformatics/btv421</citation>\n' |