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comparison macs2_predictd.xml @ 2:bfe57d6e0c4c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 63955994af5090ec444c03c221df0012d5ae4e74
author iuc
date Mon, 12 Oct 2015 11:24:39 -0400
parents fe62ba547975
children 6d4babad010f
comparison
equal deleted inserted replaced
1:859c982b1f7f 2:bfe57d6e0c4c
1 <tool id="macs2_predictd" name="MACS2 predictd" version="@VERSION_STRING@.0"> 1 <tool id="macs2_predictd" name="MACS2 predictd" version="@VERSION_STRING@.0">
2 <description>Predict 'd' or fragment size from alignment results</description> 2 <description>Predict 'd' or fragment size from alignment results</description>
3 <macros>
4 <import>macs2_macros.xml</import>
5 </macros>
3 <expand macro="requirements"> 6 <expand macro="requirements">
4 <requirement type="package" version="3.0.1">R_3_0_1</requirement> 7 <requirement type="package" version="3.0.1">R_3_0_1</requirement>
5 <requirement type="package" version="4.1.0">gnu_awk</requirement> 8 <requirement type="package" version="4.1.0">gnu_awk</requirement>
6 </expand> 9 </expand>
10 <expand macro="stdio" />
7 <expand macro="version_command" /> 11 <expand macro="version_command" />
8 <macros>
9 <import>macs2_macros.xml</import>
10 </macros>
11 <command> 12 <command>
12 macs2 predictd 13 macs2 predictd
13 -i ${ ' '.join( map( lambda x:'"%s"' % ( x ), $infiles ) ) } 14 -i ${ ' '.join( map( lambda x:'"%s"' % ( x ), $infiles ) ) }
14 @tag_size@ 15 @tag_size@
15 @effective_genome_size@ 16 @effective_genome_size@
18 19
19 ## remove the timepoint and strip the output 20 ## remove the timepoint and strip the output
20 2>&amp;1 | awk -F: '{print $4}' | awk '{$1=$1}1' 21 2>&amp;1 | awk -F: '{print $4}' | awk '{$1=$1}1'
21 22
22 &gt; "${ outfile }" 23 &gt; "${ outfile }"
23 24
24 &amp;&amp; 25 &amp;&amp;
25 26
26 Rscript predictd 27 Rscript predictd
27 </command> 28 </command>
28 <expand macro="stdio" />
29 <inputs> 29 <inputs>
30 <param name="infiles" type="data" format="bam,sam,bed" multiple="True" label="ChIP-seq alignment file" 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)" /> 30 <param name="infiles" type="data" format="bam,sam,bed" multiple="True" label="ChIP-seq alignment file" 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 <expand macro="conditional_effective_genome_size" /> 31 <expand macro="conditional_effective_genome_size" />
32 <expand macro="tag_size" /> 32 <expand macro="tag_size" />
33 <expand macro="band_width" /> 33 <expand macro="band_width" />