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comparison macs2_predictd.xml @ 33:c82a1f154c60 draft

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author iuc
date Tue, 28 Apr 2015 22:56:08 -0400
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32:a2b093982c38 33:c82a1f154c60
1 <tool id="macs2_predictd" name="MACS2 predictd" version="@VERSION_STRING@.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">gnu_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 ${ ' '.join( map( lambda x:'"%s"' % ( x ), $infiles ) ) }
14 @tag_size@
15 @effective_genome_size@
16 --bw "${ 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 &amp;&amp;
25
26 Rscript predictd
27 </command>
28 <expand macro="stdio" />
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)" />
31 <expand macro="conditional_effective_genome_size" />
32 <expand macro="tag_size" />
33 <expand macro="band_width" />
34
35 <param name="mfoldlo" type="integer" label="Fold-enrichment lower limit" value="5"
36 help="Select the regions with MFOLD high-confidence enrichment ratio against background to build model (--mfold)"/>
37 <param name="mfoldhi" type="integer" label="Fold-enrichment upper-limit" value="50"
38 help="Select the regions with MFOLD high-confidence enrichment ratio against background to build model (--mfold)"/>
39
40 </inputs>
41
42 <outputs>
43 <data name="outfile" format="txt" label="${tool.name} on ${on_string} - d value" />
44 <data name="outfile_image" from_work_dir="predictd_model.pdf" format="pdf" label="${tool.name} on ${on_string} - X-correlation image" />
45 </outputs>
46 <tests>
47 <test>
48 <param name="infiles" value="Control_200K.bed,ChIP_200K.bed" ftype="bed" />
49 <param name="effective_genome_size_options_selector" value="user_defined" />
50 <param name="gsize" value="3300000000" />
51 <param name="tsize" value="-1.0"/>
52 <param name="band_width" value="300"/>
53 <param name="mfoldlo" value="5"/>
54 <param name="mfoldhi" value="50"/>
55 <output name="outfile" file="predictd_on_ChIP_200K_and_Control_200K.txt"/>
56 <output name="outfile_image" file="predictd_on_ChIP_200K_and_Control_200K.pdf" compare="sim_size"/>
57 </test>
58 </tests>
59 <help>
60 **What it does**
61
62 predictd from macs2
63
64
65 Note that pair-end data is not supposed to work with this command.
66
67
68 @citation@
69 </help>
70 <expand macro="citations" />
71 </tool>