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author morinlab
date Sun, 29 Jan 2017 11:42:51 -0500
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1 <tool id="sequenza_pipeline" name="Analyze Seqz File" version="2.1.2">
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2 <description>
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3 using general R sequenza pipeline
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4 </description>
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5 <requirements>
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6 <requirement type="package" version="2.1.2">sequenza</requirement>
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7 <requirement type="set_environment" version="2.1.2">SEQUENZA_INSTALL_DIR</requirement>
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8 </requirements>
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9 <command>
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11 Rscript $__tool_directory__/sequenza_pipeline.R $input
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13 #if $sampleid_source.sampleid_selector == "bamfile":
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14 \$(basename $sampleid_source.id | sed 's/.bam$//g' )
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15 #else:
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16 $sampleid_source.id
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17 #end if
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19 output
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21 #if $choose_fit_option.fit_option == "manual":
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23 $ploidy $cellularity
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25 #end if
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27 2>&amp;1 ;
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29 cat ./output/*segments.txt > $output;
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30
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31 </command>
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32 <inputs>
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33 <conditional name="sampleid_source">
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34 <param label="Choose the source to open the Sample Id" name="sampleid_selector" type="select">
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35 <option value="bamfile">BAM File Name</option>
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36 <option value="manual">Manual</option>
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37 </param>
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38 <when value="manual">
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39 <param name="id" type="text" label="Tumour ID (Name)"/>
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40 </when>
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41 <when value="bamfile">
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42 <param type="data" format="bam" name="id" label="Sequence Alignment File"/>
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43 </when>
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44 </conditional>
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45 <conditional name="choose_fit_option">
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46 <param label="Use the best fit or manually set the ploidy and cellularity" name="fit_option" type="select">
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47 <option value="bestfit">Best fit</option>
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48 <option value="manual">Manually specify</option>
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49 </param>
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50 <when value="manual">
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51 <param name="ploidy" type="float" label="ploidy" value="2" />
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52 <param name="cellularity" type="float" label="cellularity" value="1" />
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53 </when>
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54 </conditional>
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55 <param name="input" format="txt,tabular" type="data" label="Input Sequenza Seqz File"/>
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56 </inputs>
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57 <outputs>
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58 <data name="output" format="seg,txt"/>
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59 <collection name="list_output" type="list" description="Sequenza outputs">
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60 <discover_datasets pattern="__name_and_ext__" directory="output" visible="true"/>
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61 </collection>
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62 </outputs>
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63 </tool>