diff tools/protein_analysis/signalp3.xml @ 26:20139cb4c844 draft

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

--- a/tools/protein_analysis/signalp3.xml	Fri Nov 21 08:17:36 2014 -0500
+++ b/tools/protein_analysis/signalp3.xml	Wed May 13 06:14:42 2015 -0400
@@ -1,18 +1,22 @@
-<tool id="signalp3" name="SignalP 3.0" version="0.0.14">
+<tool id="signalp3" name="SignalP 3.0" version="0.0.15">
     <description>Find signal peptides in protein sequences</description>
     <!-- If job splitting is enabled, break up the query file into parts -->
     <!-- Using 2000 chunks meaning 4 threads doing 500 each is ideal -->
     <parallelism method="basic" split_inputs="fasta_file" split_mode="to_size" split_size="2000" merge_outputs="tabular_file"></parallelism>
+    <requirements>
+        <requirement type="binary">signalp</requirement>
+        <requirement type="package">signalp</requirement>
+    </requirements>
+    <stdio>
+        <!-- Anything other than zero is an error -->
+        <exit_code range="1:" />
+        <exit_code range=":-1" />
+    </stdio>
     <command interpreter="python">
       signalp3.py $organism $truncate "\$GALAXY_SLOTS" $fasta_file $tabular_file
       ##If the environment variable isn't set, get "", and the python wrapper
       ##defaults to four threads.
     </command>
-    <stdio>
-        <!-- Anything other than zero is an error -->
-        <exit_code range="1:" />
-        <exit_code range=":-1" />
-    </stdio>
     <inputs>
         <param name="fasta_file" type="data" format="fasta" label="FASTA file of protein sequences"/> 
         <param name="organism" type="select" display="radio" label="Organism">
@@ -27,9 +31,6 @@
     <outputs>
         <data name="tabular_file" format="tabular" label="SignalP $organism results" />
     </outputs>
-    <requirements>
-        <requirement type="binary">signalp</requirement>
-    </requirements>
     <tests>
         <test>
             <param name="fasta_file" value="four_human_proteins.fasta" ftype="fasta"/>