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comparison macs2_predictd.xml @ 17:35a80f8dda5c draft

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author iuc
date Sat, 15 Feb 2014 15:43:39 -0500
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16:d9a0a017896a 17:35a80f8dda5c
1 <tool id="macs2_predictd" name="MACS2 predictd" version="2.0.10.0">
2 <description>Predict 'd' or fragment size from alignment results</description>
3 <expand macro="requirements">
4 <requirement type="package" version="3.0.1">R_3_0_1</requirement>
5 <requirement type="package" version="4.1.0">awk</requirement>
6 </expand>
7 <expand macro="version_command" />
8 <macros>
9 <import>macs2_macros.xml</import>
10 </macros>
11 <command>
12 macs2 predictd
13 -i #echo ' '.join( map( str, $infiles) )#
14 @tag_size@
15 @effective_genome_size@
16 --bw $band_width
17 --mfold $mfoldlo $mfoldhi
18
19 ## remove the timepoint and strip the output
20 2>&amp;1 | awk -F: '{print $4}' | awk '{$1=$1}1'
21
22 &gt; $outfile;
23
24 Rscript predictd;
25 </command>
26 <expand macro="stdio" />
27 <inputs>
28 <param name="infiles" type="data" format="bam,sam,bed" multiple="True" label="ChIP-seq alignment file" help="If multiple files are given, then they will all be read and combined. Note that pair-end data is not supposed to work with this command. (-i)" />
29 <expand macro="conditional_effective_genome_size" />
30 <expand macro="tag_size" />
31 <expand macro="band_width" />
32
33 <param name="mfoldlo" type="integer" label="Fold-enrichment lower limit" value="5"
34 help="Select the regions with MFOLD high-confidence enrichment ratio against background to build model (--mfold)"/>
35 <param name="mfoldhi" type="integer" label="Fold-enrichment upper-limit" value="50"
36 help="Select the regions with MFOLD high-confidence enrichment ratio against background to build model (--mfold)"/>
37
38 </inputs>
39
40 <outputs>
41 <data name="outfile" format="txt" label="${tool.name} on ${on_string} - d value" />
42 <data name="outfile_image" from_work_dir="predictd_model.pdf" format="pdf" label="${tool.name} on ${on_string} - X-correlation image" />
43 </outputs>
44 <tests>
45 <test>
46 <param name="infiles" value="Control_200K.bed,ChIP_200K.bed" ftype="bed" />
47 <param name="effective_genome_size_options_selector" value="3300000000" />
48 <param name="tsize" value="-1.0"/>
49 <param name="band_width" value="300"/>
50 <param name="mfoldlo" value="5"/>
51 <param name="mfoldhi" value="50"/>
52 <output name="outfile" file="predictd_on_ChIP_200K_and_Control_200K.txt"/>
53 <output name="outfile_image" file="predictd_on_ChIP_200K_and_Control_200K.pdf" lines_diff="5"/>
54 </test>
55 </tests>
56 <help>
57 **What it does**
58
59 predictd from macs2
60
61
62 Note that pair-end data is not supposed to work with this command.
63
64
65 @citation@
66 </help>
67 </tool>