Mercurial > repos > iuc > roary

diff roary.xml @ 7:78608ec02d62 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 442b1247ee31ec9872633be18784f346e4762486"
author iuc
date Sat, 13 Feb 2021 11:59:15 +0000
parents 15ac71df11a0
children e88a7de55d6e
line wrap: on
line diff
--- a/roary.xml	Mon Jun 29 08:40:27 2020 -0400
+++ b/roary.xml	Sat Feb 13 11:59:15 2021 +0000
@@ -1,16 +1,19 @@
-<tool id="roary" name="Roary" version="3.13.0+galaxy0">
+<tool id="roary" name="Roary" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
     <description>the pangenome pipeline - Quickly generate a core gene alignment from gff3 files</description>
-
+    <macros>
+        <token name="@TOOL_VERSION@">3.13.0</token>
+        <token name="@VERSION_SUFFIX@">1</token>
+    </macros>
     <requirements>
-      <requirement type="package" version="3.13.0">roary</requirement>
+        <requirement type="package" version="@TOOL_VERSION@">roary</requirement>
     </requirements>
 
     <command detect_errors="exit_code"><![CDATA[
         #set $filenames = list()
         #for $gff in $gff_input.gffs
-          cp '$gff' '${gff.element_identifier}.gff' &&
-          #set $filename = str($gff.element_identifier) + '.gff'
-          $filenames.append(str($filename))
+            cp '$gff' '${gff.element_identifier}.gff' &&
+            #set $filename = str($gff.element_identifier) + '.gff'
+            $filenames.append(str($filename))
         #end for
 
         roary
@@ -29,119 +32,119 @@
             '$f'
           #end for
 
-    ]]></command>
+    ]]>    </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">
-          <option value="individual">Individual</option>
-          <option value="collection">Collection</option>
-        </param>
-        <when value="individual">
-          <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." />
-        </when>
-        <when value='collection'>
-          <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." />
-        </when>
-      </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"/>
+        <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">
+                <option value="individual">Individual</option>
+                <option value="collection">Collection</option>
+            </param>
+            <when value="individual">
+                <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." />
+            </when>
+            <when value='collection'>
+                <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." />
+            </when>
+        </conditional>
+        <param name="percent_ident" type="integer" value="95" label="minimum percentage identity for blastp" help="Sets the minimum percentage identity for protein matches" />
+        <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." />
 
-      <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>
-        <option value="accgraph">Accessory graph in dot format</option>
-        <option value="acchead_embl">Accessory header file in embl format</option>
-        <option value="acctab">Accessory gene table in tabular format</option>
-        <option value="blastfreq">Blast Identity Frequency Rtab file</option>
-        <option value="clust">Clustered proteins file</option>
-        <option value="coreaccgraph">Core Accessory Graph in dot format</option>
-        <option value="coreaccembl">Core Accessory table in embl format</option>
-        <option value="coreacctab">Core Accessory table in tabular format</option>
-        <option value="genepa_rtab">Gene Presence Absence file in Rtab format</option>
-        <option value="numcons_rtab">Number of Conserved Genes in Rtab format</option>
-        <option value="numpangene_rtab">Number of Genes in Pan Genome in Rtab format</option>
-        <option value="numnew_rtab">Number of New Genes in Rtab format</option>
-        <option value="numuniq_rtab">Number of Unique Genes in Rtab format</option>
-        <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>
-      </param>
+        <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>
+            <option value="accgraph">Accessory graph in dot format</option>
+            <option value="acchead_embl">Accessory header file in embl format</option>
+            <option value="acctab">Accessory gene table in tabular format</option>
+            <option value="blastfreq">Blast Identity Frequency Rtab file</option>
+            <option value="clust">Clustered proteins file</option>
+            <option value="coreaccgraph">Core Accessory Graph in dot format</option>
+            <option value="coreaccembl">Core Accessory table in embl format</option>
+            <option value="coreacctab">Core Accessory table in tabular format</option>
+            <option value="genepa_rtab">Gene Presence Absence file in Rtab format</option>
+            <option value="numcons_rtab">Number of Conserved Genes in Rtab format</option>
+            <option value="numpangene_rtab">Number of Genes in Pan Genome in Rtab format</option>
+            <option value="numnew_rtab">Number of New Genes in Rtab format</option>
+            <option value="numuniq_rtab">Number of Unique Genes in Rtab format</option>
+            <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>
+        </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>
+        <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 ${on_string} Core Gene Alignment" from_work_dir="out/core_gene_alignment.aln" />
-      <data format="csv" name="gene_p_a" label="${tool.name} on ${on_string} Gene Presence Absence" from_work_dir="out/gene_presence_absence.csv" />
-      <data format="fasta" name="acc_bin" label="${tool.name} on ${on_string} Accessory Binary Genes" from_work_dir="out/accessory_binary_genes.fa" >
-        <filter>outputs and 'abg_fa' in outputs</filter>
-      </data>
-      <data format="nhx" name="acc_bin_new" label="${tool.name} on ${on_string} Accessory Binary Genes (Newick)" from_work_dir="out/accessory_binary_genes.fa.newick" >
-        <filter>outputs and 'abg_nw' in outputs</filter>
-      </data>
-      <data format="dot" name="acc_graph" label="${tool.name} on ${on_string} Acsessory Graph" from_work_dir="out/accessory_graph.dot">
-        <filter>outputs and 'accgraph' in outputs</filter>
-      </data>
-      <data format="embl" name="acc_head_embl" label="${tool.name} on ${on_string} Accessory Header" from_work_dir="out/accessory.header.embl" >
-        <filter>outputs and 'acchead_embl' in outputs</filter>
-      </data>
-      <data format="tabular" name="acc_tab" label="${tool.name} on ${on_string} Accessory Gene Table" from_work_dir="out/accessory.tab" >
-        <filter>outputs and 'acctab' in outputs</filter>
-      </data>
-      <data format="txt" name="blast_freq" label="${tool.name} on ${on_string} Blast Identity Frequencies" from_work_dir="out/blast_identity_frequency.Rtab" >
-        <filter>outputs and 'blastfreq' in outputs</filter>
-      </data>
-      <data format="txt" name="clust_file" label="${tool.name} on ${on_string} Clustered Proteins" from_work_dir="out/clustered_proteins" >
-        <filter>outputs and 'clust' in outputs</filter>
-      </data>
-      <data format="dot" name="core_acc_graph" label="${tool.name} on ${on_string} Core Accessory Graph" from_work_dir="out/core_accessory_graph.dot" >
-        <filter>outputs and 'coreaccgraph' in outputs</filter>
-      </data>
-      <data format="embl" name="core_acc_embl" label="${tool.name} on ${on_string} Core Accessory EMBL" from_work_dir="out/core_accessory.header.embl" >
-        <filter>outputs and 'coreaccembl' in outputs</filter>
-      </data>
-      <data format="tabular" name="core_acc_tab" label="${tool.name} on ${on_string} Core Accessory Table" from_work_dir="out/core_accessory.tab" >
-        <filter>outputs and 'coreacctab' in outputs</filter>
-      </data>
-      <data format="txt" name="gene_p_a_rtab" label="${tool.name} on ${on_string} Gene Presence Absence Rtab" from_work_dir="out/gene_presence_absence.Rtab" >
-        <filter>outputs and 'genepa_rtab' in outputs</filter>
-      </data>
-      <data format="txt" name="num_cons_rtab" label="${tool.name} on ${on_string} Number of Conserved Genes" from_work_dir="out/number_of_conserved_genes.Rtab" >
-        <filter>outputs and 'numcons_rtab' in outputs</filter>
-      </data>
-      <data format="txt" name="num_pangene_rtab" label="${tool.name} on ${on_string} Number of Genes in Pan Geneome" from_work_dir="out/number_of_genes_in_pan_genome.Rtab" >
-        <filter>outputs and 'numpangene_rtab' in outputs</filter>
-      </data>
-      <data format="txt" name="num_new_rtab" label="${tool.name} on ${on_string} Number of New Genes" from_work_dir="out/number_of_new_genes.Rtab" >
-        <filter>outputs and 'numnew_rtab' in outputs</filter>
-      </data>
-      <data format="txt" name="num_uniq_rtab" label="${tool.name} on ${on_string} Number of Unique Genes" from_work_dir="out/number_of_unique_genes.Rtab" >
-        <filter>outputs and 'numuniq_rtab' in outputs</filter>
-      </data>
-      <data format="fasta" name="pan_genome_ref" label="${tool.name} on ${on_string} pan-genome reference" from_work_dir="out/pan_genome_reference.fa" >
-        <filter>outputs and 'pangenomeref' in outputs</filter>
-      </data>
+        <data format="tabular" name="sumstats" label="${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 ${on_string} Core Gene Alignment" from_work_dir="out/core_gene_alignment.aln" />
+        <data format="csv" name="gene_p_a" label="${tool.name} on ${on_string} Gene Presence Absence" from_work_dir="out/gene_presence_absence.csv" />
+        <data format="fasta" name="acc_bin" label="${tool.name} on ${on_string} Accessory Binary Genes" from_work_dir="out/accessory_binary_genes.fa">
+            <filter>outputs and 'abg_fa' in outputs</filter>
+        </data>
+        <data format="nhx" name="acc_bin_new" label="${tool.name} on ${on_string} Accessory Binary Genes (Newick)" from_work_dir="out/accessory_binary_genes.fa.newick">
+            <filter>outputs and 'abg_nw' in outputs</filter>
+        </data>
+        <data format="dot" name="acc_graph" label="${tool.name} on ${on_string} Acsessory Graph" from_work_dir="out/accessory_graph.dot">
+            <filter>outputs and 'accgraph' in outputs</filter>
+        </data>
+        <data format="embl" name="acc_head_embl" label="${tool.name} on ${on_string} Accessory Header" from_work_dir="out/accessory.header.embl">
+            <filter>outputs and 'acchead_embl' in outputs</filter>
+        </data>
+        <data format="tabular" name="acc_tab" label="${tool.name} on ${on_string} Accessory Gene Table" from_work_dir="out/accessory.tab">
+            <filter>outputs and 'acctab' in outputs</filter>
+        </data>
+        <data format="txt" name="blast_freq" label="${tool.name} on ${on_string} Blast Identity Frequencies" from_work_dir="out/blast_identity_frequency.Rtab">
+            <filter>outputs and 'blastfreq' in outputs</filter>
+        </data>
+        <data format="txt" name="clust_file" label="${tool.name} on ${on_string} Clustered Proteins" from_work_dir="out/clustered_proteins">
+            <filter>outputs and 'clust' in outputs</filter>
+        </data>
+        <data format="dot" name="core_acc_graph" label="${tool.name} on ${on_string} Core Accessory Graph" from_work_dir="out/core_accessory_graph.dot">
+            <filter>outputs and 'coreaccgraph' in outputs</filter>
+        </data>
+        <data format="embl" name="core_acc_embl" label="${tool.name} on ${on_string} Core Accessory EMBL" from_work_dir="out/core_accessory.header.embl">
+            <filter>outputs and 'coreaccembl' in outputs</filter>
+        </data>
+        <data format="tabular" name="core_acc_tab" label="${tool.name} on ${on_string} Core Accessory Table" from_work_dir="out/core_accessory.tab">
+            <filter>outputs and 'coreacctab' in outputs</filter>
+        </data>
+        <data format="txt" name="gene_p_a_rtab" label="${tool.name} on ${on_string} Gene Presence Absence Rtab" from_work_dir="out/gene_presence_absence.Rtab">
+            <filter>outputs and 'genepa_rtab' in outputs</filter>
+        </data>
+        <data format="txt" name="num_cons_rtab" label="${tool.name} on ${on_string} Number of Conserved Genes" from_work_dir="out/number_of_conserved_genes.Rtab">
+            <filter>outputs and 'numcons_rtab' in outputs</filter>
+        </data>
+        <data format="txt" name="num_pangene_rtab" label="${tool.name} on ${on_string} Number of Genes in Pan Geneome" from_work_dir="out/number_of_genes_in_pan_genome.Rtab">
+            <filter>outputs and 'numpangene_rtab' in outputs</filter>
+        </data>
+        <data format="txt" name="num_new_rtab" label="${tool.name} on ${on_string} Number of New Genes" from_work_dir="out/number_of_new_genes.Rtab">
+            <filter>outputs and 'numnew_rtab' in outputs</filter>
+        </data>
+        <data format="txt" name="num_uniq_rtab" label="${tool.name} on ${on_string} Number of Unique Genes" from_work_dir="out/number_of_unique_genes.Rtab">
+            <filter>outputs and 'numuniq_rtab' in outputs</filter>
+        </data>
+        <data format="fasta" name="pan_genome_ref" label="${tool.name} on ${on_string} pan-genome reference" from_work_dir="out/pan_genome_reference.fa">
+            <filter>outputs and 'pangenomeref' in outputs</filter>
+        </data>
     </outputs>
 
     <tests>
-      <test>
-        <param name="gff_input_selector" value="individual"/>
-        <param name="gffs" value="ex1.gff,ex2.gff" ftype="gff3"/>
-        <output name="sumstats" file="out/summary_statistics.txt" ftype="tabular"/>
-      </test>
-      <test>
-        <param name="gff_input_selector" value="individual"/>
-        <param name="gffs" value="ex1.gff,ex2.gff" ftype="gff3"/>
-        <param name="percent_ident" value="50"/>
-        <param name="core_diff" value="50.0"/>
-        <output name="sumstats" file="test2/summary_statistics.txt" ftype="tabular"/>
-      </test>
+        <test>
+            <param name="gff_input_selector" value="individual" />
+            <param name="gffs" value="ex1.gff,ex2.gff" ftype="gff3" />
+            <output name="sumstats" file="out/summary_statistics.txt" ftype="tabular" />
+        </test>
+        <test>
+            <param name="gff_input_selector" value="individual" />
+            <param name="gffs" value="ex1.gff,ex2.gff" ftype="gff3" />
+            <param name="percent_ident" value="50" />
+            <param name="core_diff" value="50.0" />
+            <output name="sumstats" file="test2/summary_statistics.txt" ftype="tabular" />
+        </test>
     </tests>
 
     <help><![CDATA[
@@ -176,7 +179,7 @@
 
 For further info see: http://sanger-pathogens.github.io/Roary/
 
-    ]]></help>
+    ]]>    </help>
 
     <citations>
         <citation type="doi">10.1093/bioinformatics/btv421</citation>