diff peptideGenomicCoordinate.xml @ 4:b56922070a1b draft default tip

planemo upload

--- a/peptideGenomicCoordinate.xml	Sun Jun 17 04:55:42 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,57 +0,0 @@
-<tool id="peptidegenomiccoordinate" name="Peptide Genomic Coordinate" version="0.1.2">
-    <description>Get genomic location/coordinate of peptides using mzsqlite DB and genomic mapping sqlite DB</description>
-    <requirements>
-        <requirement type="package" version="2.7.9">python</requirement>
-    </requirements>
-    <command detect_errors="aggressive"><![CDATA[
-        python '$__tool_directory__/peptideGenomicCoordinate.py' '$peptideinput' '$mzsqlite' '$mapping' '$peptide_bed'
-    ]]></command>
-    
-    <inputs>
-        <param type="data" name="peptideinput" format="tabular" label="Peptide List (without any header line)"/>
-        <param type="data" name="mzsqlite" format="sqlite" label="mz to sqlite (mzsqlite) file"/>
-        <param type="data" name="mapping" format="sqlite" label="genomic mapping sqlite file"/>
-    </inputs>
-    
-    <outputs>
-        <data format="bed" name="peptide_bed" label="${tool.name} on ${on_string}">
-            <actions>
-                <action name="column_names" type="metadata" default="chrom,chromStart,chromStop,name,score,strand,thickStart,thickEnd,itemRgb,blockCount,blockSizes,blockStarts"/>
-            </actions>
-        </data>
-    </outputs>
-    
-    <tests>
-        <test>
-            <param name="peptide_input" value="peptides.tabular"/>
-            <param name="sqlite" value="test_mz_to_sqlite.sqlite"/>
-            <param name="sqlite" value="test_genomic_mapping_sqlite.sqlite"/>
-            <output name="peptide_bed" file="peptides_BED.bed"/>
-        </test>
-    </tests>
-    <help><![CDATA[
-        **PeptideGenomicCoordinate**
-
-        Gets genomic coordinate of peptides based on the information in mzsqlite and genomic mapping sqlite files. 
-        This program loads two sqlite databases (mzsqlite and genomic mapping sqlite files) and calculates the genomic coordinates of the peptides provided as input. This outputs bed file for peptides.
-    
-        Input: Peptide list file, mzsqlite sqlite DB file, and genomic mapping sqlite DB file 
-        Output: Tabular BED file with all the columns
-    
-        mzsqlite file from: https://toolshed.g2.bx.psu.edu/repos/galaxyp/mz_to_sqlite/mz_to_sqlite/2.0.0
-        genome mapping sqlite file from: https://toolshed.g2.bx.psu.edu/view/galaxyp/translate_bed/038ecf54cbec
-    
-    
-    P.S. : Requires sqlite
-        
-    ]]></help>
-    <citations>
-      <citation type="bibtex">
-@misc{peptidegenomiccoodinate,
-    author={Kumar, Praveen},
-    year={2018},
-    title={PeptideGenomicCoordinate}
-}
-      </citation>
-    </citations>
-</tool>