diff tools/protein_analysis/promoter2.xml @ 26:20139cb4c844 draft

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

--- a/tools/protein_analysis/promoter2.xml	Fri Nov 21 08:17:36 2014 -0500
+++ b/tools/protein_analysis/promoter2.xml	Wed May 13 06:14:42 2015 -0400
@@ -1,27 +1,28 @@
-<tool id="promoter2" name="Promoter 2.0" version="0.0.8">
+<tool id="promoter2" name="Promoter 2.0" version="0.0.9">
     <description>Find eukaryotic PolII promoters in DNA sequences</description>
     <!-- If job splitting is enabled, break up the query file into parts -->
     <!-- Using 2000 per chunk so 4 threads each doing 500 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">promoter</requirement>
+        <requirement type="package">promoter</requirement>
+    </requirements>
+    <stdio>
+        <!-- Anything other than zero is an error -->
+        <exit_code range="1:" />
+        <exit_code range=":-1" />
+    </stdio>
     <command interpreter="python">
         promoter2.py "\$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 DNA sequences"/> 
     </inputs>
     <outputs>
         <data name="tabular_file" format="tabular" label="Promoter2 on ${fasta_file.name}" />
     </outputs>
-    <requirements>
-        <requirement type="binary">promoter</requirement>
-    </requirements>
     <tests>
         <test>
             <param name="fasta_file" value="Adenovirus.fasta" ftype="fasta"/>