# HG changeset patch
# User pravs
# Date 1514499937 18000
# Node ID 2b9fa951a6b5fc43b7ccc764f0b80609e62ed212
# Parent  032f1ee171edcf5403a624c8490d09aa544df788
planemo upload

diff -r 032f1ee171ed -r 2b9fa951a6b5 pep_pointer.xml
--- a/pep_pointer.xml	Fri Dec 22 04:33:12 2017 -0500
+++ b/pep_pointer.xml	Thu Dec 28 17:25:37 2017 -0500
@@ -1,19 +1,38 @@
-<tool id="pep_pointer" name="PepPointer: classify genomic location of peptides" version="0.1.0">
+<tool id="pep_pointer" name="PepPointer" version="0.1.0">
+    <description>classify genomic location of peptides</description>
     <requirements>
         <requirement type="package" version="2.7.9">python</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
-        python '$__tool_directory__/pep_pointer.py' '$gtf' '$bed' '$classified'
+        python '$__tool_directory__/pep_pointer.py' '$gtf_input.gtf' '$bed' '$classified'
     ]]></command>
     <inputs>
-        <param type="data" name="gtf" format="gtf" label="GTF file with the genome of interest"/>
+        <conditional name="gtf_input">
+            <param type="select" name="gtf_source" label="Choose the source of the GTF file">
+                <option value="cached" selected="true">Built-in</option>
+                <option value="history">From history</option>
+            </param>
+            <when value="cached">
+                <param name="gtf" type="select" format="gtf" label="GTF file with the genome of interest">
+                    <options from_data_table="pep_pointer"/>
+                </param>
+            </when>
+            <when value="history">
+                <param type="data" name="gtf" format="gtf" label="GTF file with the genome of interest"/>
+            </when>
+        </conditional>
         <param type="data" name="bed" format="bed" label="BED file with chromosomal coordinates of peptide"/>
     </inputs>
     <outputs>
-        <data format="tabular" name="classified"/>
+        <data format="tabular" name="classified" label="${tool.name} on ${on_string}">
+            <actions>
+                <action name="column_names" type="metadata" default="chrom,chromStart,chromStop,name,score,strand,annotation"/>
+            </actions>
+        </data>
     </outputs>
     <tests>
         <test>
+            <param name="gtf_source" value="history"/>
             <param name="gtf" value="mus17.gtf"/>
             <param name="bed" value="novel_peptides_17.bed"/>
             <output name="classified" file="classified_novel_peptides.txt"/>