diff tools/protein_analysis/rxlr_motifs.xml @ 26:20139cb4c844 draft

planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty

--- a/tools/protein_analysis/rxlr_motifs.xml	Fri Nov 21 08:17:36 2014 -0500
+++ b/tools/protein_analysis/rxlr_motifs.xml	Wed May 13 06:14:42 2015 -0400
@@ -1,13 +1,22 @@
-<tool id="rxlr_motifs" name="RXLR Motifs" version="0.0.9">
+<tool id="rxlr_motifs" name="RXLR Motifs" version="0.0.11">
     <description>Find RXLR Effectors of Plant Pathogenic Oomycetes</description>
-    <command interpreter="python">
-      rxlr_motifs.py "$fasta_file" "\$GALAXY_SLOTS" $model "$tabular_file"
-    </command>
+    <requirements>
+        <!-- Need SignalP for all the models -->
+        <requirement type="binary">signalp</requirement>
+        <requirement type="package">signalp</requirement>
+        <!-- Need HMMER for Whisson et al. (2007) -->
+        <requirement type="binary">hmmsearch</requirement>
+        <requirement type="package">hmmsearch</requirement>
+    </requirements>
     <stdio>
         <!-- Anything other than zero is an error -->
         <exit_code range="1:" />
         <exit_code range=":-1" />
     </stdio>
+    <version_command interpreter="python">rxlr_motifs.py -v</version_command>
+    <command interpreter="python">
+      rxlr_motifs.py "$fasta_file" "\$GALAXY_SLOTS" $model "$tabular_file"
+    </command>
     <inputs>
         <param name="fasta_file" type="data" format="fasta" label="FASTA file of protein sequences" /> 
         <param name="model" type="select" label="Which RXLR model?">
@@ -19,12 +28,6 @@
     <outputs>
         <data name="tabular_file" format="tabular" label="$model.value_label" />
     </outputs>
-    <requirements>
-        <!-- Need SignalP for all the models -->
-        <requirement type="binary">signalp</requirement>
-        <!-- Need HMMER for Whisson et al. (2007) -->
-        <requirement type="binary">hmmsearch</requirement>
-    </requirements>
     <tests>
         <test>
             <param name="fasta_file" value="rxlr_win_et_al_2007.fasta" ftype="fasta" />