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1 <tool id="callfilter" name="Filter" description="segmented and called data" force_history_refresh="True" version="0.1.0">
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2 <requirement type="package" version="1.1.2">mpagenomics</requirement>
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3 <command interpreter="python">
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4 filter.py '$input' '$length' '$probes' '$__new_file_path__' '$nbcall' '$output' '$outputlog' '$log'
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5 </command>
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6 <inputs>
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7 <param name="input" type="data" format="scr" label="Segmented and called data file" help="Input file with labelled segments"/>
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8 <param name="length" type="integer" min="1" value="1" label="Minimum length for a segment" help="minimal length (in bp) to keep in a segment"/>
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9 <param name="probes" type="integer" min="1" value="1" label="Minimum probes for a segment" help="minimal number of probes to keep in a segment"/>
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10 <param name="nbcall" type="select" multiple="true" label="Label(s) to keep">
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11 <option value="double loss">double loss</option>
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12 <option value="loss">loss</option>
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13 <option value="normal">normal</option>
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14 <option value="gain">gain</option>
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15 <option value="amplification">amplification</option>
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16 </param>
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17 <param name="outputlog" type="select" label="Output log">
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18 <option value="TRUE">Yes</option>
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19 <option value="FALSE">No</option>
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20 </param>
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21 </inputs>
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22
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23 <outputs>
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24 <data format="txt" name="output" label="filter of ${on_string}" />
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25
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26 <data format="log" name="log" label="log of segmentation of ${input.name}">
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27 <filter>outputlog == "TRUE"</filter>
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28 </data>
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29 </outputs>
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30
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31 <stdio>
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32 <exit_code range="1:" level="fatal" description="See logs for more details" />
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33 </stdio>
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34 <help>
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35
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36 **What it does**
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37
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38 This tool filters results obtained by the segmentation and calling tool.
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39
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40 -----
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41
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42 Input/Output file:
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43
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44 *A tabular text file containing 7 columns:*
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45
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46 - sampleNames: Name of the file.
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47 - chrom: Chromosome of the segment.
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48 - chromStart: Starting position (in bp) of the segment. This position is not included in the segment.
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49 - chromEnd: Ending position (in bp) of the segment. This position is included in the segment.
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50 - probes: Number of probes in the segment.
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51 - means: Mean of the segment.
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52 - calls: Calling of the segment (”double loss”, ”loss”, ”normal”, ”gain” or ”amplification”).
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53
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54 -----
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55
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56 **Citation**
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57
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58 If you use this tool please cite :
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59
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60 `Q. Grimonprez, A. Celisse, M. Cheok, M. Figeac, and G. Marot. MPAgenomics : An R package for multi-patients analysis of genomic markers, 2014. Preprint <http://fr.arxiv.org/abs/1401.5035>`_
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61
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62 </help>
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63 </tool>
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