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comparison macs2_predictd.xml @ 53:8f6b37d29df5 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 586ecaebf9e6020fac2674fbda368e293d1c9bc2
author iuc
date Thu, 25 Jan 2018 02:11:22 -0500
parents 1b3f899ef044
children ea526bc73f8a
comparison
equal deleted inserted replaced
52:6c9ea5f92ddb 53:8f6b37d29df5
4 <import>macs2_macros.xml</import> 4 <import>macs2_macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <expand macro="stdio" /> 7 <expand macro="stdio" />
8 <expand macro="version_command" /> 8 <expand macro="version_command" />
9 <command> 9 <command><![CDATA[
10 <![CDATA[ 10 @home_dir@
11 macs2 predictd 11 macs2 predictd
12 12
13 -i ${ ' '.join(["'%s'" % $x for $x in $infiles ]) } 13 -i ${ ' '.join(["'%s'" % $x for $x in $infiles ]) }
14 @tag_size@ 14 @tag_size@
15 @effective_genome_size@ 15 @effective_genome_size@
22 > '${ outfile }' 22 > '${ outfile }'
23 23
24 && 24 &&
25 25
26 Rscript predictd 26 Rscript predictd
27 ]]> 27 ]]></command>
28 </command>
29 <inputs> 28 <inputs>
30 <param name="infiles" type="data" format="bam,sam,bed" multiple="True" 29 <param name="infiles" type="data" format="bam,sam,bed" multiple="True"
31 label="ChIP-seq alignment file" 30 label="ChIP-seq alignment file"
32 help="If multiple files are given, then they will all be read and combined. Note that pair-end data is not supposed to work with this command. (-i)" /> 31 help="If multiple files are given, then they will all be read and combined. Note that pair-end data is not supposed to work with this command. (-i)" />
33 <expand macro="conditional_effective_genome_size" /> 32 <expand macro="conditional_effective_genome_size" />
47 <param name="gsize" value="3300000000" /> 46 <param name="gsize" value="3300000000" />
48 <param name="tsize" value=""/> 47 <param name="tsize" value=""/>
49 <param name="band_width" value="300"/> 48 <param name="band_width" value="300"/>
50 <param name="lower" value="5"/> 49 <param name="lower" value="5"/>
51 <param name="upper" value="50"/> 50 <param name="upper" value="50"/>
52 <output name="outfile" file="predictd_on_ChIP_200K_and_Control_200K.txt"/> 51 <output name="outfile" file="predictd_on_ChIP_200K_and_Control_200K.txt" lines_diff="2"/>
53 <output name="outfile_image" file="predictd_on_ChIP_200K_and_Control_200K.pdf" compare="sim_size"/> 52 <output name="outfile_image" file="predictd_on_ChIP_200K_and_Control_200K.pdf" compare="sim_size"/>
54 </test> 53 </test>
55 </tests> 54 </tests>
56 <help> 55 <help>
57 <![CDATA[ 56 <![CDATA[