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comparison macs2_predictd.xml @ 19:05aca18fd8dc draft

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author iuc
date Wed, 23 Apr 2014 18:25:51 -0400
parents ab352bb83cb2
children 59845dc3331f
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18:ab352bb83cb2 19:05aca18fd8dc
8 <macros> 8 <macros>
9 <import>macs2_macros.xml</import> 9 <import>macs2_macros.xml</import>
10 </macros> 10 </macros>
11 <command> 11 <command>
12 macs2 predictd 12 macs2 predictd
13 -i #echo ' '.join( map( str, $infiles) )# 13 -i ${ ' '.join( map( lambda x:'"%s"' % ( x ), $infiles ) ) }
14 @tag_size@ 14 @tag_size@
15 @effective_genome_size@ 15 @effective_genome_size@
16 --bw $band_width 16 --bw "${ band_width }"
17 --mfold $mfoldlo $mfoldhi 17 --mfold "${ mfoldlo }" "${ mfoldhi }"
18 18
19 ## remove the timepoint and strip the output 19 ## remove the timepoint and strip the output
20 2>&amp;1 | awk -F: '{print $4}' | awk '{$1=$1}1' 20 2>&amp;1 | awk -F: '{print $4}' | awk '{$1=$1}1'
21 21
22 &gt; $outfile; 22 &gt; "${ outfile }"
23
24 &amp;&amp;
23 25
24 Rscript predictd; 26 Rscript predictd
25 </command> 27 </command>
26 <expand macro="stdio" /> 28 <expand macro="stdio" />
27 <inputs> 29 <inputs>
28 <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)" />
29 <expand macro="conditional_effective_genome_size" /> 31 <expand macro="conditional_effective_genome_size" />