# HG changeset patch
# User iuc
# Date 1723408186 0
# Node ID 1126e07fb6c61e32b22bc5a439f5a15434b84b28
# Parent  9e962399fe9ee69473bfbdaf723e08c263a6e536
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 2652aac9012d0a19c17e06536bb0e300d048bbf5

diff -r 9e962399fe9e -r 1126e07fb6c6 roary.xml
--- a/roary.xml	Wed Nov 24 21:06:03 2021 +0000
+++ b/roary.xml	Sun Aug 11 20:29:46 2024 +0000
@@ -1,8 +1,8 @@
-<tool id="roary" name="Roary" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
+<tool id="roary" name="Roary" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">
     <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@">2</token>
+        <token name="@VERSION_SUFFIX@">3</token>
     </macros>
     <xrefs>
         <xref type="bio.tools">roary</xref>
@@ -10,7 +10,6 @@
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">roary</requirement>
     </requirements>
-
     <command detect_errors="exit_code"><![CDATA[
         #import re
         #set $filenames = list()
@@ -23,23 +22,23 @@
         #end for
 
         roary
-          -f out
-          -p \${GALAXY_SLOTS:-1}
-          -e
-          -n
-          -i '$percent_ident'
-          -cd '$core_diff'
-          -g '$advanced.maxclust'
-          $advanced.split_para
-          -t '$advanced.trans_tab'
-          -iv '$advanced.mcl'
+            -f out
+            -p \${GALAXY_SLOTS:-1}
+            -e
+            -z
+            -n
+            -i '$percent_ident'
+            -cd '$core_diff'
+            -g '$advanced.maxclust'
+            $advanced.split_para
+            -t '$advanced.trans_tab'
+            -iv '$advanced.mcl'
 
-          #for $f in $filenames
-            '$f'
-          #end for
+            #for $f in $filenames
+                '$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">
@@ -47,16 +46,15 @@
                 <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." />
+                <param name="gffs" type="data" format="gff,gff3" min="2" 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." multiple="true"/>
             </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 value="collection">
+                <param name="gffs" type="data_collection" format="gff,gff3" label="Dataset collection to submit to Roary" help="A dataset list collection of gff3 files to send to Roary for analysis." collection_type="list"/>
             </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.">
+        <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" label="Additional outputs" help="Summary statistics, core gene alignments and Gene Presence/Absence tables are always produced." multiple="true" display="checkboxes">
             <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>
@@ -74,20 +72,17 @@
             <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!" />
+            <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" truevalue="-s" falsevalue="" checked="False" 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 -&gt; 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 ${on_string} Gene Presence Absence" from_work_dir="out/gene_presence_absence.csv" />
+        <data format="tabular" name="sumstats" label="${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>
@@ -137,22 +132,20 @@
             <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 expect_num_outputs="3">
+            <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 expect_num_outputs="3">
+            <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[
 **Roary**
 
@@ -186,9 +179,7 @@
 For further info see: http://sanger-pathogens.github.io/Roary/
 
     ]]>    </help>
-
     <citations>
         <citation type="doi">10.1093/bioinformatics/btv421</citation>
     </citations>
-
 </tool>