Mercurial > repos > edward-kirton > prodigal

changeset 4:cffbad01eb55 draft

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Added the possibility to save results in genbank format (default still gff)
author lionelguy
date Tue, 13 Aug 2013 08:12:41 -0400
parents 1241efb254e9
children 96d94a7ea6fc
files prodigal/prodigal.xml
diffstat 1 files changed, 17 insertions(+), 6 deletions(-) [+]
line wrap: on
line diff
--- a/prodigal/prodigal.xml	Tue Aug 13 08:11:27 2013 -0400
+++ b/prodigal/prodigal.xml	Tue Aug 13 08:12:41 2013 -0400
@@ -1,10 +1,17 @@
-<tool id="prodigal" name="prodigal" version="1.0.0">
+<tool id="prodigal" name="prodigal" version="1.0.1">
 <description>Find genes</description>
-<command>prodigal -a $trans_file $closed_ends -d $nuc_file -f gff -g $tr_table -i $input_file $m $n
+<requirements>
+  <requirement type="package" version="1.6.0">prodigal</requirement>
+</requirements>
+<command>prodigal -a $trans_file $closed_ends -d $nuc_file -f $output_format -g $tr_table -i $input_file $m $n
 -o $output_file -p $mode -q -s $start_file</command>
 <!-- NYI -t training_file -->
 <inputs>
     <param name="input_file" type="data" format="fasta" label="[-i] Contig sequences"/> 
+    <param name="output_format" type="select" display="radio" lable="[-f] Output format">
+      <option value="gbk">gbk (genbank)</option>
+      <option value="gff" selected="true">gff (general feature format)</option>
+    </param>
     <param name="closed_ends" type="boolean" truevalue="-c" falsevalue="" checked="false" label="[-c] Closed ends" help="Do not allow genes to run off edges" />
     <param name="tr_table" type="select" display="radio" label="[-g] Translation table">
         <option value="1">The Standard Code</option>
@@ -33,10 +40,14 @@
     <param name="n" type="boolean" truevalue="-n" falsevalue="" selected="false" label="[-n] Bypass the Shine-Dalgarno trainer and force the program to scan for motifs" />
 </inputs>
 <outputs>
-    <data name="output_file" format="gff" />
-    <data name="start_file" format="tabular" label="Potential genes (with scores)" />
-    <data name="nuc_file" format="fasta" label="Nucleotide sequences of genes" />
-    <data name="trans_file" format="fasta" label="Protein translations" />
+  <data name="output_file" format="gff">
+    <change_format>
+      <when input="output_format" value="gbk" format="genbank"/>
+    </change_format>
+  </data>
+  <data name="start_file" format="tabular" label="Potential genes (with scores)" />
+  <data name="nuc_file" format="fasta" label="Nucleotide sequences of genes" />
+  <data name="trans_file" format="fasta" label="Protein translations" />
 </outputs>
 <help>
 **What it does**