|
27
|
1 <tool id="macs2_predictd" name="MACS2 predictd" version="@VERSION_STRING@.0">
|
|
17
|
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>
|
|
18
|
5 <requirement type="package" version="4.1.0">gnu_awk</requirement>
|
|
17
|
6 </expand>
|
|
|
7 <expand macro="version_command" />
|
|
|
8 <macros>
|
|
|
9 <import>macs2_macros.xml</import>
|
|
|
10 </macros>
|
|
|
11 <command>
|
|
|
12 macs2 predictd
|
|
19
|
13 -i ${ ' '.join( map( lambda x:'"%s"' % ( x ), $infiles ) ) }
|
|
17
|
14 @tag_size@
|
|
|
15 @effective_genome_size@
|
|
19
|
16 --bw "${ band_width }"
|
|
|
17 --mfold "${ mfoldlo }" "${ mfoldhi }"
|
|
17
|
18
|
|
|
19 ## remove the timepoint and strip the output
|
|
|
20 2>&1 | awk -F: '{print $4}' | awk '{$1=$1}1'
|
|
|
21
|
|
19
|
22 > "${ outfile }"
|
|
|
23
|
|
|
24 &&
|
|
17
|
25
|
|
19
|
26 Rscript predictd
|
|
17
|
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" />
|
|
27
|
49 <param name="effective_genome_size_options_selector" value="user_defined" />
|
|
|
50 <param name="gsize" value="3300000000" />
|
|
17
|
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"/>
|
|
27
|
56 <output name="outfile_image" file="predictd_on_ChIP_200K_and_Control_200K.pdf" compare="sim_size"/>
|
|
17
|
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>
|
|
26
|
70 <expand macro="citations" />
|
|
17
|
71 </tool>
|
