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1 <tool id="createControlSubset" name="CreateControlSubset" version="1.0">
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2 <description>Get Subset for ChIP Control</description>
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3 <command interpreter="bash">
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4 #if $input_type.input_type_selector == "bam" #createControlSubSet_wrapper.sh -f $inputfile -c $controlfile -t $input_type.input_type_selector -o $BAMcontrolOutBAM -s $BAMsampleOutBAM -q $if_Process_Sample -p "No" #elif $input_type.input_type_selector == "sam" #createControlSubSet_wrapper.sh -f $inputfile -c $controlfile -t $input_type.input_type_selector -o $SAMcontrolOut -s $SAMsampleOut -q $if_Process_Sample #else #createControlSubSet_wrapper.sh -f $inputfile -c $controlfile -t $input_type.input_type_selector -o $ELANDcontrolOut -s $ELANDsampleOut -q $if_Process_Sample #end if
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5 </command>
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6 <inputs>
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7 <conditional name="input_type">
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8 <param name="input_type_selector" type="select" label="Alignment Format">
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9 <option value="eland" selected="true">Eland</option>
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10 <option value="sam">SAM</option>
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11 <option value="bam">BAM</option>
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12 </param>
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13 <when value="eland">
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14 <param name="inputfile" type="data" label="ChIP-Seq Tag File" value="ChIP-Seq Tag File" format="eland"/>
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15 <param name="controlfile" type="data" label="Control Tag File" value="Control Tag File" format="eland"/>
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16
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17 </when>
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18 <when value="sam">
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19 <param name="inputfile" type="data" label="ChIP-Seq Tag File" value="ChIP-Seq Tag File" format="sam"/>
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20 <param name="controlfile" type="data" label="Control Tag File" value="Control Tag File" format="sam"/>
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21
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22 </when>
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23 <when value="bam">
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24 <param name="inputfile" type="data" label="ChIP-Seq Tag File" value="ChIP-Seq Tag File" format="bam"/>
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25 <param name="controlfile" type="data" label="Control Tag File" value="Control Tag File" format="bam"/>
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26 </when>
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27 </conditional>
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28 <param name="if_Process_Sample" type="boolean" label="Do you want to filter duplicates in the ChIP dataset?" truevalue="Yes" falsevalue="No" checked="False"/>
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29 </inputs>
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30 <outputs>
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31 <data name="ELANDcontrolOut" format="eland" label="Subset for Control">
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32 <filter>(input_type['input_type_selector'] == 'eland')</filter>
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33 </data>
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34 <data name="SAMcontrolOut" format="sam" label="Subset for Control">
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35 <filter>(input_type['input_type_selector'] == 'sam')</filter>
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36 </data>
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37 <data name="BAMcontrolOutBAM" format="bam" label="Subset for Control">
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38 <filter>(input_type['input_type_selector'] == 'bam')</filter>
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39 </data>
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40
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41
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42 <data name="ELANDsampleOut" format="eland" label="Subset for ChIP">
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43 <filter>if_Process_Sample == True</filter>
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44 <filter>(input_type['input_type_selector'] == 'eland')</filter>
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45 </data>
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46 <data name="SAMsampleOut" format="sam" label="Subset for ChIP">
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47 <filter>if_Process_Sample == True</filter>
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48 <filter>(input_type['input_type_selector'] == 'sam')</filter>
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49 </data>
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50 <data name="BAMsampleOutBAM" format="bam" label="Subset for ChIP">
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51 <filter>if_Process_Sample == True</filter>
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52 <filter>(input_type['input_type_selector'] == 'bam')</filter>
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53 </data>
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54
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55 </outputs>
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56 <help>
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57 **What it does**
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58
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59 This tool does preprocessing of ChIP-seq aligned reads before calling FindPeaks:
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60
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61 Filter out dulpicates from the SAMPLE (optional) and create a CONTROL dataset w/o duplicates with the same number of reads as in the SAMPLE
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62
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63 Only eland, sam and bam files are accepted.
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64
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65 </help>
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66 </tool>
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