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comparison macs21_wrapper.xml @ 19:51303ba3fbbe draft

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Uploaded version 2.1.1.0 (update Macs2 version and switch to conda dependency resolution).
author pjbriggs
date Fri, 09 Mar 2018 09:21:56 -0500
parents 4e85d68a2347
children 4d41e5cda4e6
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18:4e85d68a2347 19:51303ba3fbbe
1 <tool id="macs2_1_peakcalling" name="MACS2.1.0" version="2.1.0-6"> 1 <tool id="macs2_1_peakcalling" name="MACS2.1.1" version="2.1.1.0">
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="2.1.1">macs2</requirement>
6 <requirement type="package" version="2.1.0.20140616">macs2</requirement> 6 <requirement type="package" version="3.4">R</requirement>
7 <requirement type="package" version="3.1.2">R</requirement> 7 <requirement type="package" version="357">ucsc-fetchchromsizes</requirement>
8 <requirement type="package" version="2.0">ucsc_tools_for_macs21</requirement> 8 <requirement type="package" version="357">ucsc-bedclip</requirement>
9 <requirement type="package" version="357">ucsc-bedsort</requirement>
10 <requirement type="package" version="357">ucsc-bedgraphtobigwig</requirement>
9 </requirements> 11 </requirements>
10 <version_command>macs2 --version</version_command> 12 <version_command>macs2 --version</version_command>
11 <command interpreter="python"> 13 <command><![CDATA[
12 macs21_wrapper.py callpeak 14 python $__tool_directory__/macs21_wrapper.py callpeak
13 ## 15 ##
14 ## ChIP-seq input 16 ## ChIP-seq input
15 $input_chipseq_file1 17 $input_chipseq_file1
16 ## 18 ##
17 ## ChIP-seq control 19 ## ChIP-seq control
94 #if str($xls_to_interval) == 'True' 96 #if str($xls_to_interval) == 'True'
95 --output-xls-to-interval=$output_xls_to_interval_peaks_file 97 --output-xls-to-interval=$output_xls_to_interval_peaks_file
96 #else 98 #else
97 --output-peaks=$output_peaks_file 99 --output-peaks=$output_peaks_file
98 #end if 100 #end if
99 </command> 101 ]]></command>
100 <inputs> 102 <inputs>
101 <!--experiment name used as base for output file names --> 103 <!--experiment name used as base for output file names -->
102 <param name="experiment_name" type="text" value="MACS2.1.0 in Galaxy" size="50" 104 <param name="experiment_name" type="text" value="MACS2.1.0 in Galaxy" size="50"
103 label="Experiment Name"/> 105 label="Experiment Name"/>
104 <!--choose 'broad' or 'narrow' regions--> 106 <!--choose 'broad' or 'narrow' regions-->