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comparison macs21_wrapper.xml @ 1:02a01ea54722 draft

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Uploaded latest version 2.1.0-5.
author pjbriggs
date Tue, 26 Jul 2016 10:34:49 -0400
parents 06cb587a5e87
children 00d73c812399
comparison
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0:06cb587a5e87 1:02a01ea54722
1 <tool id="macs2_1_peakcalling" name="MACS2.1.0" version="2.1.0-4"> 1 <tool id="macs2_1_peakcalling" name="MACS2.1.0" version="2.1.0-5">
2 <description>Model-based Analysis of ChIP-Seq: peak calling</description> 2 <description>Model-based Analysis of ChIP-Seq: peak calling</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="2.7">python</requirement> 4 <requirement type="package" version="2.7">python</requirement>
5 <requirement type="package" version="1.9">numpy</requirement> 5 <requirement type="package" version="1.9">numpy</requirement>
6 <requirement type="package" version="2.1.0.20140616">macs2</requirement> 6 <requirement type="package" version="2.1.0.20140616">macs2</requirement>
17 ## ChIP-seq control 17 ## ChIP-seq control
18 #if str($input_control_file1) != 'None' 18 #if str($input_control_file1) != 'None'
19 -c $input_control_file1 19 -c $input_control_file1
20 #end if 20 #end if
21 ## 21 ##
22 --format=$input_chipseq_file1.extension 22 --format=$format
23 --name="$experiment_name" 23 --name="$experiment_name"
24 --bw=$bw 24 --bw=$bw
25 ## 25 ##
26 ## Genome size 26 ## Genome size
27 #if str($genome_size.gsize) == '' 27 #if str($genome_size.gsize) == ''
112 <param name="broad_cutoff" type="float" 112 <param name="broad_cutoff" type="float"
113 label="Cutoff for broad regions" 113 label="Cutoff for broad regions"
114 value="0.1" help="default: 0.1 (--broad-cutoff)"/> 114 value="0.1" help="default: 0.1 (--broad-cutoff)"/>
115 </when> 115 </when>
116 </conditional> 116 </conditional>
117 <param name="format" type="select" label="Format of input read data"
118 help="Specify the format of the input data and whether or not it is paired end (--format)">
119 <option value="BAMPE" selected="true">BAM (paired-end)</option>
120 <option value="BAM">BAM (single-end)</option>
121 <option value="BEDPE">BED (paired-end)</option>
122 <option value="BED">BED (single-end)</option>
123 <option value="SAMPE">SAM (paired-end)</option>
124 <option value="SAM">SAM (single-end)</option>
125 </param>
117 <param name="input_chipseq_file1" type="data" format="bed,sam,bam" 126 <param name="input_chipseq_file1" type="data" format="bed,sam,bam"
118 label="ChIP-seq read file" /> 127 label="ChIP-seq read file" />
119 <param name="input_control_file1" type="data" format="bed,sam,bam" optional="True" 128 <param name="input_control_file1" type="data" format="bed,sam,bam" optional="True"
120 label="ChIP-seq control read file" /> 129 label="ChIP-seq control read file" />
121 <conditional name="genome_size"> 130 <conditional name="genome_size">
268 <!-- Peak calling without bigwig output --> 277 <!-- Peak calling without bigwig output -->
269 <test> 278 <test>
270 <!-- Inputs --> 279 <!-- Inputs -->
271 <param name="experiment_name" value="test_MACS2.1.0" /> 280 <param name="experiment_name" value="test_MACS2.1.0" />
272 <param name="broad_regions" value="" /> 281 <param name="broad_regions" value="" />
282 <param name="format" value="BED" />
273 <param name="input_chipseq_file1" value="test_region_IP.bed" dbkey="galGal3" 283 <param name="input_chipseq_file1" value="test_region_IP.bed" dbkey="galGal3"
274 ftype="bed" /> 284 ftype="bed" />
275 <param name="input_control_file1" value="test_region_Input.bed" 285 <param name="input_control_file1" value="test_region_Input.bed"
276 ftype="bed" /> 286 ftype="bed" />
277 <param name="gsize" value="" /> 287 <param name="gsize" value="" />
306 <!-- Peak calling with bigwig output --> 316 <!-- Peak calling with bigwig output -->
307 <test> 317 <test>
308 <!-- Inputs --> 318 <!-- Inputs -->
309 <param name="experiment_name" value="test_MACS2.1.0" /> 319 <param name="experiment_name" value="test_MACS2.1.0" />
310 <param name="broad_regions" value="" /> 320 <param name="broad_regions" value="" />
321 <param name="format" value="BED" />
311 <param name="input_chipseq_file1" value="test_region_IP.bed" dbkey="galGal3" 322 <param name="input_chipseq_file1" value="test_region_IP.bed" dbkey="galGal3"
312 ftype="bed" /> 323 ftype="bed" />
313 <param name="input_control_file1" value="test_region_Input.bed" 324 <param name="input_control_file1" value="test_region_Input.bed"
314 ftype="bed" /> 325 ftype="bed" />
315 <param name="gsize" value="" /> 326 <param name="gsize" value="" />