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1 <tool id="pep_pointer" name="PepPointer" version="0.1.0">
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2 <description>classify genomic location of peptides</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 '$__tool_directory__/pep_pointer.py' '$gtf_input.gtf' '$bed' '$classified'
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8 ]]></command>
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9 <inputs>
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10 <conditional name="gtf_input">
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11 <param type="select" name="gtf_source" label="Choose the source of the GTF file">
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12 <option value="cached" selected="true">Built-in</option>
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13 <option value="history">From history</option>
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14 </param>
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15 <when value="cached">
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16 <param name="gtf" type="select" format="gtf" label="GTF file with the genome of interest">
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17 <options from_data_table="pep_pointer"/>
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18 </param>
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19 </when>
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20 <when value="history">
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21 <param type="data" name="gtf" format="gtf" label="GTF file with the genome of interest"/>
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22 </when>
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23 </conditional>
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24 <param type="data" name="bed" format="bed" label="BED file with chromosomal coordinates of peptide"/>
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25 </inputs>
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26 <outputs>
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27 <data format="tabular" name="classified" label="${tool.name} on ${on_string}">
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28 <actions>
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29 <action name="column_names" type="metadata" default="chrom,chromStart,chromStop,name,score,strand,annotation"/>
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30 </actions>
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31 </data>
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32 </outputs>
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33 <tests>
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34 <test>
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35 <param name="gtf_source" value="history"/>
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36 <param name="gtf" value="mus17.gtf"/>
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37 <param name="bed" value="novel_peptides_17.bed"/>
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38 <output name="classified" file="classified_novel_peptides.txt"/>
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39 </test>
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40 </tests>
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41 <help><![CDATA[
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42 **PepPointer**
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43
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44 Given chromosomal locations of peptides in a BED file, PepPointer classifies them as CDS, UTR, exon, intron, or intergene.
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45 ]]></help>
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46 <citations>
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47 <citation type="bibtex">
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48 @misc{peppointer,
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49 author={Kumar, Praveen},
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50 year={2017},
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51 title={PepPointer}
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52 }
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53 </citation>
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54 </citations>
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55 </tool>
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