|
12
|
1 <tool id="macs2_predictd" name="MACS2 predictd" version="2.0.10.0">
|
|
|
2 <description>Predict 'd' or fragment size from alignment results</description>
|
|
6
|
3 <expand macro="requirements">
|
|
|
4 <requirement type="package" version="3.0.1">R_3_0_1</requirement>
|
|
|
5 </expand>
|
|
|
6 <expand macro="version_command" />
|
|
|
7 <macros>
|
|
|
8 <import>macs2_macros.xml</import>
|
|
|
9 </macros>
|
|
|
10 <command>
|
|
12
|
11 macs2 predictd
|
|
|
12 -i #echo ','.join( map( str, $infiles) )#
|
|
6
|
13 --tsize $tsize
|
|
|
14 @effective_genome_size@
|
|
|
15 --bw $band_width
|
|
12
|
16 --mfold $mfoldlo $mfoldhi
|
|
6
|
17 > $outfile;
|
|
|
18
|
|
|
19 Rscript predicted_model.R > $outfile_image
|
|
|
20 </command>
|
|
12
|
21 <expand macro="stdio" />
|
|
6
|
22 <inputs>
|
|
12
|
23 <param name="infiles" type="data" format="bam,sam,bed" multiple="True" label="ChIP-seq alignment file" help="If multiple files are given, then they will all be read and combined. Note that pair-end data is not supposed to work with this command. (-i)" />
|
|
6
|
24 <expand macro="conditional_effective_genome_size" />
|
|
|
25 <expand macro="tag_size" />
|
|
|
26
|
|
|
27 <param name="band_width" type="integer" value="300" label="Band width for picking regions to compute fragment size"
|
|
|
28 help="This value is only used while building the shifting model. (--bw)" />
|
|
|
29
|
|
|
30 <param name="mfoldlo" type="integer" label="Fold-enrichment lower limit" value="5"
|
|
|
31 help="Select the regions with MFOLD high-confidence enrichment ratio against background to build model (--mfold)"/>
|
|
|
32 <param name="mfoldhi" type="integer" label="Fold-enrichment upper-limit" value="50"
|
|
|
33 help="Select the regions with MFOLD high-confidence enrichment ratio against background to build model (--mfold)"/>
|
|
|
34
|
|
|
35 </inputs>
|
|
|
36
|
|
|
37 <outputs>
|
|
|
38 <data name="outfile" format="txt" label="${tool.name} on ${on_string} - d value" />
|
|
|
39 <data name="outfile_image" format="png" label="${tool.name} on ${on_string} - X-correlation image" />
|
|
|
40 </outputs>
|
|
|
41 <tests>
|
|
|
42 <!--none yet for macs2-->
|
|
|
43 </tests>
|
|
|
44 <help>
|
|
|
45 **What it does**
|
|
|
46
|
|
|
47 bdgdiff from macs2
|
|
|
48
|
|
|
49
|
|
|
50 Note that pair-end data is not supposed to work with this command.
|
|
|
51
|
|
|
52
|
|
12
|
53 @citation@
|
|
6
|
54 </help>
|
|
|
55 </tool>
|
