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1 <tool id="peptidegenomiccoordinate" name="Peptide Genomic Coordinate" version="0.1.1">
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2 <description>Get genomic location/coordinate of peptides using mzsqlite DB and genomic mapping sqlite DB</description>
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3 <requirements>
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4 <requirement type="package" version="2.7.9">python</requirement>
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5 </requirements>
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6 <command detect_errors="aggressive"><![CDATA[
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7 python '$__tool_directory__/peptideGenomicCoordinate.py' '$peptideinput' '$mzsqlite' '$mapping' '$peptide_bed'
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8 ]]></command>
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9 <inputs>
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10 <param type="data" name="peptideinput" format="tabular" label="Peptide List (without any header line)"/>
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11 <param type="data" name="mzsqlite" format="sqlite" label="mz to sqlite (mzsqlite) file"/>
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12 <param type="data" name="mapping" format="sqlite" label="genomic mapping sqlite file"/>
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13 </inputs>
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14 <outputs>
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15 <data format="bed" name="peptide_bed" label="${tool.name} on ${on_string}">
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16 <actions>
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17 <action name="column_names" type="metadata" default="chrom,chromStart,chromStop,name,score,strand,thickStart,thickEnd,itemRgb,blockCount,blockSizes,blockStarts"/>
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18 </actions>
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19 </data>
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20 </outputs>
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21 <tests>
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22 <test>
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23 <param name="peptide_input" value="peptides.tabular"/>
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24 <param name="sqlite" value="test_mz_to_sqlite.sqlite"/>
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25 <param name="sqlite" value="test_genomic_mapping_sqlite.sqlite"/>
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26 <output name="peptide_bed" file="peptides_BED.bed"/>
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27 </test>
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28 </tests>
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29 <help><![CDATA[
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30 **PeptideGenomicCoordinate**
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31
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32 Gets genomic coordinate of peptides based on the information in mzsqlite and genomic mapping sqlite files.
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33 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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34
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35 Input: Peptide list file, mzsqlite sqlite DB file, and genomic mapping sqlite DB file
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36 Output: Tabular BED file with all the columns
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37
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38 mzsqlite file from: https://toolshed.g2.bx.psu.edu/repos/galaxyp/mz_to_sqlite/mz_to_sqlite/2.0.0
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39 genome mapping sqlite file from: https://toolshed.g2.bx.psu.edu/view/galaxyp/translate_bed/038ecf54cbec
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40
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41
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42 P.S. : Requires sqlite
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43
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44 ]]></help>
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45 <citations>
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46 <citation type="bibtex">
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47 @misc{peptidegenomiccoodinate,
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48 author={Kumar, Praveen},
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49 year={2018},
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50 title={PeptideGenomicCoordinate}
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51 }
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52 </citation>
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53 </citations>
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54 </tool>
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