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1 <tool id="span" name="SPAN" version="0.7.1.4272">
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2 <description>ChIP-Seq analysis</description>
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3 <requirements>
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4 <requirement type="package" version="0.7.1.4272">package_span_jar</requirement>
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5 <!--<container type="docker">biolabs/span</container>-->
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6 </requirements>
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7 <stdio>
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8 <!-- Wrapper ensures anything other than zero is an error -->
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9 <exit_code range="1:"/>
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10 <exit_code range=":-1"/>
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11 </stdio>
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12 <command interpreter="python">
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13 #if str($action.action_selector) == "model"
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14 #if $control.control_selector
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15 span_wrapper.py model with_control "${genome}" "${treatment_file}" "${bin}" "${action.model_file}" "${control.control_file}"
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16 #else
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17 span_wrapper.py model without_control "${genome}" "${treatment_file}" "${bin}" "${action.model_file}"
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18 #end if
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19 #else
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20 #if $control.control_selector
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21 span_wrapper.py peaks with_control "${genome}" "${treatment_file}" "${bin}" "${action.model_file}" "${control.control_file}" "${fdr}" "${gap}" "${action.peaks_file}"
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22 #else
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23 span_wrapper.py peaks without_control "${genome}" "${treatment_file}" "${bin}" "${action.model_file}" "${fdr}" "${gap}" "${action.peaks_file}"
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24 #end if
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25 #end if
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26 </command>
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27 <inputs>
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28 <param name="treatment_file" type="data" format="bam" label="Treatment BAM"
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29 description="Treatment BAM reads to process"/>
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30 <param name="genome" type="data" format="chrom.sizes" label="Genome chrom.sizes"
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31 description="Genome build chrom.sizes file"/>
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32
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33 <conditional name="control">
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34 <param name="control_selector" type="boolean" label="Control available" value="false"/>
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35 <when value="true">
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36 <param name="control_file" type="data" format="bam" label="Control BAM"
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37 description="Control BAM reads to process"/>
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38 </when>
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39 </conditional>
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40
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41 <conditional name="action">
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42 <param name="action_selector" type="select" label="Action">
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43 <option value="model">Compute SPAN model</option>
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44 <option value="peaks">Compute SPAN model and produce peaks file</option>
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45 </param>
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46 <when value="model">
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47 <param name="model_file" type="text" value="model.span" label="Model name"/>
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48 </when>
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49 <when value="peaks">
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50 <param name="model_file" type="text" value="model.span" label="Model file name"/>
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51 <param name="fdr" size="5" type="float" value="0.0001" label="FDR"/>
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52 <param name="gap" size="5" type="integer" value="5" label="GAP"/>
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53 <param name="peaks_file" type="text" value="result.peak" label="Peaks file name"/>
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54 </when>
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55 </conditional>
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56
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57 <param name="bin" size="5" type="integer" value="200" label="Bin size"/>
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58 </inputs>
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59 <outputs>
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60 <data name="${action.model_file}" format="span" label="SPAN model file"/>
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61 <data name="${action.peaks_file}" format="bed" label="SPAN peaks file">
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62 <filter>action['action_selector'] == "peaks"</filter>
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63 </data>
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64 </outputs>
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65 <help>
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66 SPAN Semi-supervised Peak Analyzer is a tool for analyzing ChIP-seq data.
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67 Details: http://artyomovlab.wustl.edu/aging/span.html
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68 </help>
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69 </tool>
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