Mercurial > repos > galaxyp > map_peptides_to_bed
changeset 2:78b8213e122d draft
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(-) [+] |
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--- 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>