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1 <!--create control subset - developed by Jocelyn Brayet <jocelyn.brayet@curie.fr>
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2 Copyright (C) 2015 Institut Curie
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3
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4 This program is free software: you can redistribute it and/or modify
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5 it under the terms of the GNU General Public License as published by
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6 the Free Software Foundation, either version 3 of the License, or
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7 (at your option) any later version.
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8
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9 This program is distributed in the hope that it will be useful,
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10 but WITHOUT ANY WARRANTY; without even the implied warranty of
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11 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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12 GNU General Public License for more details.
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13
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14 You should have received a copy of the GNU General Public License
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15 along with this program. If not, see <http://www.gnu.org/licenses/>.-->
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16 <tool id="createControlSubset" name="Get Subset for ChIP Control" version="1.0">
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17 <description> </description>
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18 <requirements>
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19 <container type="docker">institutcuriengsintegration/controlsubset:1.0</container>
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20 </requirements>
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21 <command interpreter="bash">
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22 #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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23 </command>
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24
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25 <inputs>
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26 <conditional name="input_type">
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27 <param name="input_type_selector" type="select" label="Alignment Format">
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28 <option value="eland" selected="true">Eland</option>
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29 <option value="sam">SAM</option>
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30 <option value="bam">BAM</option>
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31 </param>
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32 <when value="eland">
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33 <param name="inputfile" type="data" label="ChIP-Seq Tag File" value="ChIP-Seq Tag File" format="eland"/>
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34 <param name="controlfile" type="data" label="Control Tag File" value="Control Tag File" format="eland"/>
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35
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36 </when>
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37 <when value="sam">
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38 <param name="inputfile" type="data" label="ChIP-Seq Tag File" value="ChIP-Seq Tag File" format="sam"/>
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39 <param name="controlfile" type="data" label="Control Tag File" value="Control Tag File" format="sam"/>
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40
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41 </when>
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42 <when value="bam">
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43 <param name="inputfile" type="data" label="ChIP-Seq Tag File" value="ChIP-Seq Tag File" format="bam"/>
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44 <param name="controlfile" type="data" label="Control Tag File" value="Control Tag File" format="bam"/>
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45 <!-- <param name="if_OutPut_In_Sam" type="boolean" label="Do you want to get the output in SAM instead of BAM?" help="recommended if you want to run FindPeaks on it" truevalue="Yes" falsevalue="No" checked="False"/>
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46 -->
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47 </when>
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48 </conditional>
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49
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50
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51 <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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52
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53
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54 </inputs>
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55 <outputs>
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56 <data name="ELANDcontrolOut" format="eland" label="Subset for Control">
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57 <filter>(input_type['input_type_selector'] == 'eland')</filter>
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58 </data>
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59 <data name="SAMcontrolOut" format="sam" label="Subset for Control">
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60 <filter>(input_type['input_type_selector'] == 'sam')</filter>
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61 </data>
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62
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63 <data name="BAMcontrolOutBAM" format="bam" label="Subset for Control">
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64 <filter>(input_type['input_type_selector'] == 'bam')</filter>
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65 </data>
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66
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67
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68 <data name="ELANDsampleOut" format="eland" label="Subset for ChIP">
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69 <filter>if_Process_Sample == True</filter>
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70 <filter>(input_type['input_type_selector'] == 'eland')</filter>
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71 </data>
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72 <data name="SAMsampleOut" format="sam" label="Subset for ChIP">
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73 <filter>if_Process_Sample == True</filter>
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74 <filter>(input_type['input_type_selector'] == 'sam')</filter>
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75 </data>
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76
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77 <data name="BAMsampleOutBAM" format="bam" label="Subset for ChIP">
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78 <filter>if_Process_Sample == True</filter>
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79 <filter>(input_type['input_type_selector'] == 'bam')</filter>
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80 </data>
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81
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82 </outputs>
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83 <help>
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84 **What it does**
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85
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86 This tool does preprocessing of ChIP-seq aligned reads before calling FindPeaks:
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87
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88 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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89
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90 Only eland, sam and bam files are accepted.
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91
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92 </help>
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93 </tool>
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