# HG changeset patch
# User galaxyp
# Date 1515005701 18000
# Node ID dc1b0f54f6264e3591566b9296c472f560920a0a
# Parent  149ed6a9680f8f38e6c494cd9a9624b7649064e3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pep_pointer commit e70efe967398bc8d01f4847a5d22ae9f3575f4ef

diff -r 149ed6a9680f -r dc1b0f54f626 pep_pointer.xml
--- a/pep_pointer.xml	Fri Dec 29 12:37:22 2017 -0500
+++ b/pep_pointer.xml	Wed Jan 03 13:55:01 2018 -0500
@@ -1,20 +1,24 @@
-<tool id="pep_pointer" name="PepPointer" version="0.1.1">
+<tool id="pep_pointer" name="PepPointer" version="0.1.2">
     <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_input.gtf' '$bed' '$classified'
+        #if $gtf_input.gtf_source == "cached":
+            python '$__tool_directory__/pep_pointer.py' '$gtf_input.gtf.fields.path' '$bed' '$classified'
+        #else
+            python '$__tool_directory__/pep_pointer.py' '$gtf_input.gtf' '$bed' '$classified'
+        #end if
     ]]></command>
     <inputs>
         <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="cached" selected="true">Locally installed</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"/>
+                    <options from_data_table="gff_gene_annotations"/>
                 </param>
             </when>
             <when value="history">
diff -r 149ed6a9680f -r dc1b0f54f626 tool-data/gene_annotation.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/gene_annotation.loc.sample	Wed Jan 03 13:55:01 2018 -0500
@@ -0,0 +1,3 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of gtf data files.
+#value name path
diff -r 149ed6a9680f -r dc1b0f54f626 tool-data/pep_pointer.loc.sample
--- a/tool-data/pep_pointer.loc.sample	Fri Dec 29 12:37:22 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
-#This is a sample file distributed with Galaxy that enables tools
-#to use a directory of gtf data files.
-#name value
-#mouse	/path/to/directory/with/mouse.gtf
diff -r 149ed6a9680f -r dc1b0f54f626 tool_data_table_conf.xml.sample
--- a/tool_data_table_conf.xml.sample	Fri Dec 29 12:37:22 2017 -0500
+++ b/tool_data_table_conf.xml.sample	Wed Jan 03 13:55:01 2018 -0500
@@ -1,6 +1,8 @@
+<?xml version="1.0"?>
 <tables>
-    <table name="pep_pointer" comment_char="#">
-        <columns>name,value</columns>
-        <file path="tool-data/pep_pointer.loc"/>
+    <!-- Locations of gene annotation data -->
+    <table name="gff_gene_annotations" comment_char="#">
+        <columns>value, name, path</columns>
+        <file path="tool-data/gene_annotation.loc" />
     </table>
 </tables>