Mercurial > repos > galaxyp > map_peptides_to_bed

changeset 2:78b8213e122d draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit bd3b68ee27bc3b50b9970d4fe801cb1a13900f4c
author galaxyp
date Thu, 15 Dec 2016 18:36:55 -0500
parents db90662d26f9
children 704ea6303c4c
files map_peptides_to_bed.xml tool_dependencies.xml
diffstat 2 files changed, 8 insertions(+), 14 deletions(-) [+]
line wrap: on
line diff
--- a/map_peptides_to_bed.xml	Mon Feb 22 17:30:45 2016 -0500
+++ b/map_peptides_to_bed.xml	Thu Dec 15 18:36:55 2016 -0500
@@ -1,4 +1,4 @@
-<tool id="map_peptides_to_bed" name="Map peptides to a bed file" version="0.1.0">
+<tool id="map_peptides_to_bed" name="Map peptides to a bed file" version="0.1.1">
     <description>for viewing in a genome browser</description>
     <requirements>
         <requirement type="package" version="1.62">biopython</requirement>
@@ -6,10 +6,10 @@
     <stdio>
         <exit_code range="1:" />
     </stdio>
-    <command interpreter="python"><![CDATA[
-        map_peptides_to_bed.py 
-          --translated_bed="$translated_bed" 
-          --input="$input" 
+    <command><![CDATA[
+        python '$__tool_directory__/map_peptides_to_bed.py'
+          --translated_bed='$translated_bed'
+          --input='$input'
           #if $peptide_column:
             --peptide_column=$peptide_column 
           #end if
@@ -20,7 +20,7 @@
             --start_column=$start_column
           #end if
           $gffTags
-          --bed="$mapped_peptides"
+          --bed='$mapped_peptides'
     ]]></command>
     <inputs>
         <param name="translated_bed" type="data" format="bed" label="Translated BED" 
@@ -45,8 +45,8 @@
     </outputs>
     <tests>
         <test>
-            <param name="translated_bed" type="data" ftype="bed" value="translated_bed_sequences.bed"/>
-            <param name="input" type="data" ftype="tabular" value="peptides.tsv"/>
+            <param name="translated_bed" ftype="bed" value="translated_bed_sequences.bed"/>
+            <param name="input" ftype="tabular" value="peptides.tsv"/>
             <param name="peptide_column" value="2"/>
             <param name="name_column" value="1"/>
             <output name="mapped_peptides" file="mapped_peptides.bed"/>
--- a/tool_dependencies.xml	Mon Feb 22 17:30:45 2016 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="biopython" version="1.62">
-        <repository changeset_revision="f06c96348778" name="package_biopython_1_62" owner="biopython" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-</tool_dependency>