Mercurial > repos > pravs > peptidegenomiccoordinate

comparison peptideGenomicCoordinate.xml @ 3:95d606bdfef7 draft

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planemo upload
author pravs
date Sun, 17 Jun 2018 04:55:42 -0400
parents 1b61f7aafb61
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2:1b61f7aafb61 3:95d606bdfef7
4 <requirement type="package" version="2.7.9">python</requirement> 4 <requirement type="package" version="2.7.9">python</requirement>
5 </requirements> 5 </requirements>
6 <command detect_errors="aggressive"><![CDATA[ 6 <command detect_errors="aggressive"><![CDATA[
7 python '$__tool_directory__/peptideGenomicCoordinate.py' '$peptideinput' '$mzsqlite' '$mapping' '$peptide_bed' 7 python '$__tool_directory__/peptideGenomicCoordinate.py' '$peptideinput' '$mzsqlite' '$mapping' '$peptide_bed'
8 ]]></command> 8 ]]></command>
9
9 <inputs> 10 <inputs>
10 <param type="data" name="peptideinput" format="tabular" label="Peptide List (without any header line)"/> 11 <param type="data" name="peptideinput" format="tabular" label="Peptide List (without any header line)"/>
11 <param type="data" name="mzsqlite" format="sqlite" label="mz to sqlite (mzsqlite) file"/> 12 <param type="data" name="mzsqlite" format="sqlite" label="mz to sqlite (mzsqlite) file"/>
12 <param type="data" name="mapping" format="sqlite" label="genomic mapping sqlite file"/> 13 <param type="data" name="mapping" format="sqlite" label="genomic mapping sqlite file"/>
13 </inputs> 14 </inputs>
15
14 <outputs> 16 <outputs>
15 <data format="bed" name="peptide_bed" label="${tool.name} on ${on_string}"> 17 <data format="bed" name="peptide_bed" label="${tool.name} on ${on_string}">
16 <actions> 18 <actions>
17 <action name="column_names" type="metadata" default="chrom,chromStart,chromStop,name,score,strand,thickStart,thickEnd,itemRgb,blockCount,blockSizes,blockStarts"/> 19 <action name="column_names" type="metadata" default="chrom,chromStart,chromStop,name,score,strand,thickStart,thickEnd,itemRgb,blockCount,blockSizes,blockStarts"/>
18 </actions> 20 </actions>
19 </data> 21 </data>
20 </outputs> 22 </outputs>
23
21 <tests> 24 <tests>
22 <test> 25 <test>
23 <param name="peptide_input" value="peptides.tabular"/> 26 <param name="peptide_input" value="peptides.tabular"/>
24 <param name="sqlite" value="test_mz_to_sqlite.sqlite"/> 27 <param name="sqlite" value="test_mz_to_sqlite.sqlite"/>
25 <param name="sqlite" value="test_genomic_mapping_sqlite.sqlite"/> 28 <param name="sqlite" value="test_genomic_mapping_sqlite.sqlite"/>