Mercurial > repos > jbrayet > controlsubset_1_0_docker
comparison createControlSubSet_wrapper.xml @ 1:d9fb544723cb draft
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author | jbrayet |
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date | Tue, 02 Feb 2016 09:02:25 -0500 |
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0:3b1e9f048405 | 1:d9fb544723cb |
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1 <!--create control subset - developed by Jocelyn Brayet <jocelyn.brayet@curie.fr> | |
2 Copyright (C) 2015 Institut Curie | |
3 | |
4 This program is free software: you can redistribute it and/or modify | |
5 it under the terms of the GNU General Public License as published by | |
6 the Free Software Foundation, either version 3 of the License, or | |
7 (at your option) any later version. | |
8 | |
9 This program is distributed in the hope that it will be useful, | |
10 but WITHOUT ANY WARRANTY; without even the implied warranty of | |
11 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | |
12 GNU General Public License for more details. | |
13 | |
14 You should have received a copy of the GNU General Public License | |
15 along with this program. If not, see <http://www.gnu.org/licenses/>.--> | |
16 <tool id="createControlSubset" name="Get Subset for ChIP Control" version="1.0"> | |
17 <description> </description> | |
18 <requirements> | |
19 <container type="docker">institutcuriengsintegration/controlsubset:1.0</container> | |
20 </requirements> | |
21 <command interpreter="bash"> | |
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 | |
23 </command> | |
24 | |
25 <inputs> | |
26 <conditional name="input_type"> | |
27 <param name="input_type_selector" type="select" label="Alignment Format"> | |
28 <option value="eland" selected="true">Eland</option> | |
29 <option value="sam">SAM</option> | |
30 <option value="bam">BAM</option> | |
31 </param> | |
32 <when value="eland"> | |
33 <param name="inputfile" type="data" label="ChIP-Seq Tag File" value="ChIP-Seq Tag File" format="eland"/> | |
34 <param name="controlfile" type="data" label="Control Tag File" value="Control Tag File" format="eland"/> | |
35 | |
36 </when> | |
37 <when value="sam"> | |
38 <param name="inputfile" type="data" label="ChIP-Seq Tag File" value="ChIP-Seq Tag File" format="sam"/> | |
39 <param name="controlfile" type="data" label="Control Tag File" value="Control Tag File" format="sam"/> | |
40 | |
41 </when> | |
42 <when value="bam"> | |
43 <param name="inputfile" type="data" label="ChIP-Seq Tag File" value="ChIP-Seq Tag File" format="bam"/> | |
44 <param name="controlfile" type="data" label="Control Tag File" value="Control Tag File" format="bam"/> | |
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"/> | |
46 --> | |
47 </when> | |
48 </conditional> | |
49 | |
50 | |
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"/> | |
52 | |
53 | |
54 </inputs> | |
55 <outputs> | |
56 <data name="ELANDcontrolOut" format="eland" label="Subset for Control"> | |
57 <filter>(input_type['input_type_selector'] == 'eland')</filter> | |
58 </data> | |
59 <data name="SAMcontrolOut" format="sam" label="Subset for Control"> | |
60 <filter>(input_type['input_type_selector'] == 'sam')</filter> | |
61 </data> | |
62 | |
63 <data name="BAMcontrolOutBAM" format="bam" label="Subset for Control"> | |
64 <filter>(input_type['input_type_selector'] == 'bam')</filter> | |
65 </data> | |
66 | |
67 | |
68 <data name="ELANDsampleOut" format="eland" label="Subset for ChIP"> | |
69 <filter>if_Process_Sample == True</filter> | |
70 <filter>(input_type['input_type_selector'] == 'eland')</filter> | |
71 </data> | |
72 <data name="SAMsampleOut" format="sam" label="Subset for ChIP"> | |
73 <filter>if_Process_Sample == True</filter> | |
74 <filter>(input_type['input_type_selector'] == 'sam')</filter> | |
75 </data> | |
76 | |
77 <data name="BAMsampleOutBAM" format="bam" label="Subset for ChIP"> | |
78 <filter>if_Process_Sample == True</filter> | |
79 <filter>(input_type['input_type_selector'] == 'bam')</filter> | |
80 </data> | |
81 | |
82 </outputs> | |
83 <help> | |
84 **What it does** | |
85 | |
86 This tool does preprocessing of ChIP-seq aligned reads before calling FindPeaks: | |
87 | |
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 | |
89 | |
90 Only eland, sam and bam files are accepted. | |
91 | |
92 </help> | |
93 </tool> |