diff pep_pointer.xml @ 1:dc1b0f54f626 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pep_pointer commit e70efe967398bc8d01f4847a5d22ae9f3575f4ef

--- 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">