diff tools/protein_analysis/rxlr_motifs.xml @ 20:a19b3ded8f33 draft

v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes

--- a/tools/protein_analysis/rxlr_motifs.xml	Wed Feb 01 09:46:42 2017 -0500
+++ b/tools/protein_analysis/rxlr_motifs.xml	Thu Sep 21 11:35:20 2017 -0400
@@ -1,28 +1,23 @@
-<tool id="rxlr_motifs" name="RXLR Motifs" version="0.0.11">
+<tool id="rxlr_motifs" name="RXLR Motifs" version="0.0.14">
     <description>Find RXLR Effectors of Plant Pathogenic Oomycetes</description>
     <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>
+        <requirement type="package">hmmer2</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"
+    <version_command>
+python $__tool_directory__/rxlr_motifs.py -v
+    </version_command>
+    <command detect_errors="aggressive">
+python $__tool_directory__/rxlr_motifs.py '$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="fasta_file" type="data" format="fasta" label="FASTA file of protein sequences" />
         <param name="model" type="select" label="Which RXLR model?">
             <option value="Bhattacharjee2006">Bhattacharjee et al. (2006) RXLR</option>
             <option value="Win2007">Win et al. (2007) RXLR</option>
-            <option value="Whisson2007" selected="True">Whisson et al. (2007) RXLR-EER with HMM</option>
+            <option value="Whisson2007" selected="true">Whisson et al. (2007) RXLR-EER with HMM</option>
         </param>
     </inputs>
     <outputs>
@@ -51,7 +46,7 @@
         </test>
     </tests>
     <help>
-    
+
 **Background**
 
 Many effector proteins from oomycete plant pathogens for manipulating the host