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annotate peptide_genomic_coordinate.xml @ 0:5f49ffce52cb draft

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author galaxyp
date Wed, 03 Apr 2019 04:04:18 -0400
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1 <tool id="peptide_genomic_coordinate" name="Peptide Genomic Coodinate" version="0.1.1">
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2 <description>Get Peptide's genomic coordinate using mzsqlite DB and genomic mapping sqlite DB</description>
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3 <requirements>
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4 <requirement type="package" version="3.7.1">python</requirement>
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5 </requirements>
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6 <command detect_errors="aggressive"><![CDATA[
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7 python '$__tool_directory__/peptide_genomic_coordinate.py'
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8 '$peptideinput'
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9 '$mzsqlite'
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10 '$mapping'
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11 '$peptide_bed'
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12 ]]></command>
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13 <inputs>
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14 <param type="data" name="peptideinput" format="tabular" label="Peptide List (without any header line)"/>
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15 <param type="data" name="mzsqlite" format="sqlite" label="mz to sqlite (mzsqlite) file"/>
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16 <param type="data" name="mapping" format="sqlite" label="genomic mapping sqlite file"/>
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17 </inputs>
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18 <outputs>
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19 <data format="bed" name="peptide_bed" label="${tool.name} on ${on_string}">
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20 <actions>
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21 <action name="column_names" type="metadata" default="chrom,chromStart,chromStop,name,score,strand,thickStart,thickEnd,itemRgb,blockCount,blockSizes,blockStarts"/>
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22 </actions>
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23 </data>
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24 </outputs>
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25 <tests>
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26 <test>
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27 <param name="peptideinput" value="peptides.tabular"/>
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28 <param name="mzsqlite" value="test_mz_to_sqlite.sqlite"/>
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29 <param name="mapping" value="test_genomic_mapping_sqlite.sqlite"/>
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30 <output name="peptide_bed">
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31 <assert_contents>
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32 <has_text text="115176449" />
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33 </assert_contents>
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34 </output>
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35 </test>
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36 </tests>
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37 <help><![CDATA[
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38 **Peptide Genomic Coodinate**
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39
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40 Gets genomic coordinate of peptides based on the information in mzsqlite and genomic mapping sqlite files. This tool is useful in a proteogenomics workflow.
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41 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.
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42
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43 Input: Peptide list file, mzsqlite sqlite DB file, and genomic mapping sqlite DB file
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44 Output: Tabular BED file with all the columns
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45
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46
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47
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48 ]]></help>
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49 <citations>
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50 <citation type="bibtex">
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51 @misc{peptidegenomiccoodinate,
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52 author={Kumar, Praveen},
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53 year={2018},
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54 title={Peptide Genomic Coordinate}
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55 }
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56 </citation>
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57 </citations>
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58 </tool>