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1 <tool id="generate_pyclone_input" name="Generate PyClone input" version="14.2">
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2 <description>
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3 Generate PyClone input files from SNV and copy number data
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4 </description>
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5
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6 <requirements>
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7 <requirement type="package" version="1.0">generate_pyclone_input</requirement>
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8 <requirement type="package" version="14.2">morinlab_scripts</requirement>
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9 <requirement type="set_environment">MORINLAB_SCRIPTS</requirement>
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10 </requirements>
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11
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12 <stdio>
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13 <exit_code range="1:" level="warning" />
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14 <exit_code range=":-1" level="warning" />
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15 <regex match="Error:" />
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16 <regex match="Exception:" />
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17 </stdio>
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18
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19 <command>
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20 Rscript \$MORINLAB_SCRIPTS/generate_pyclone_input/generate_pyclone_input.R
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21 $segments $segments_mode $maf $sample_id .;
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22
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23 mv ./${sample_id}_pyclone_in.tsv $pyclone_input;
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24 </command>
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25
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26 <inputs>
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27 <!-- Required inputs -->
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28 <param type="data" name="segments" format="tabular" label="Sequenza, Titan, OncoSNP, or IGV-friendly segments file"/>
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29 <param name="segments_mode" label="Specify the source of the segments file" type="select">
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30 <option value="S">Sequenza</option>
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31 <option value="T">Titan</option>
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32 <option value="I">IGV-friendly</option>
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33 </param>
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34 <param type="data" name="maf" format="tabular" label="Patient MAF file"/>
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35 <param type="text" name="sample_id" size="20" label="Sample ID"/>
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36 </inputs>
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37
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38 <outputs>
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39 <data format="tabular" name="pyclone_input"/>
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40 </outputs>
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41
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42 <tests>
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43 </tests>
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44
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45 <help>
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46 </help>
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47
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48 </tool>
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49
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