|
6
|
1 <tool id="macs2_predict" name="Predict" version="2.0.10.0">
|
|
|
2 <description>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 </expand>
|
|
|
6 <expand macro="version_command" />
|
|
|
7 <macros>
|
|
|
8 <import>macs2_macros.xml</import>
|
|
|
9 </macros>
|
|
|
10 <command>
|
|
|
11 macs2 predict
|
|
|
12 -i #echo ','.join($infiles)#
|
|
|
13 --tsize $tsize
|
|
|
14 @effective_genome_size@
|
|
|
15 --bw $band_width
|
|
|
16 --mfold $advanced_options.mfoldlo $advanced_options.mfoldhi
|
|
|
17 > $outfile;
|
|
|
18
|
|
|
19 Rscript predicted_model.R > $outfile_image
|
|
|
20 </command>
|
|
|
21 <expand macro="stdio" />
|
|
|
22 <inputs>
|
|
|
23 <repeat name="infiles" title="ChIP-seq alignment files" min="1"
|
|
|
24 help="If multiple files are given, then they will all be read and combined. Note that pair-end data is not supposed to work with this command.">
|
|
|
25
|
|
|
26 <param name="infile" type="data" format="bam,sam,bed" multiple="True" optional="True" label="ChIP-seq alignment file" help="-i" />
|
|
|
27 </repeat>
|
|
|
28
|
|
|
29 <expand macro="conditional_effective_genome_size" />
|
|
|
30 <expand macro="tag_size" />
|
|
|
31
|
|
|
32 <param name="band_width" type="integer" value="300" label="Band width for picking regions to compute fragment size"
|
|
|
33 help="This value is only used while building the shifting model. (--bw)" />
|
|
|
34
|
|
|
35 <param name="mfoldlo" type="integer" label="Fold-enrichment lower limit" value="5"
|
|
|
36 help="Select the regions with MFOLD high-confidence enrichment ratio against background to build model (--mfold)"/>
|
|
|
37 <param name="mfoldhi" type="integer" label="Fold-enrichment upper-limit" value="50"
|
|
|
38 help="Select the regions with MFOLD high-confidence enrichment ratio against background to build model (--mfold)"/>
|
|
|
39
|
|
|
40 </inputs>
|
|
|
41
|
|
|
42 <outputs>
|
|
|
43 <data name="outfile" format="txt" label="${tool.name} on ${on_string} - d value" />
|
|
|
44 <data name="outfile_image" format="png" label="${tool.name} on ${on_string} - X-correlation image" />
|
|
|
45 </outputs>
|
|
|
46 <tests>
|
|
|
47 <!--none yet for macs2-->
|
|
|
48 </tests>
|
|
|
49 <help>
|
|
|
50 **What it does**
|
|
|
51
|
|
|
52 bdgdiff from macs2
|
|
|
53
|
|
|
54
|
|
|
55 Note that pair-end data is not supposed to work with this command.
|
|
|
56
|
|
|
57
|
|
|
58 ------
|
|
|
59
|
|
|
60 **Citation**
|
|
|
61
|
|
|
62 For the underlying tool, please cite Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, Liu XS. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008;9(9):R137.
|
|
|
63
|
|
|
64 Integration of MACS2 with Galaxy performed by Ziru Zhou ( ziruzhou@gmail.com ). Please send your comments/questions to modENCODE DCC at help@modencode.org.
|
|
|
65 </help>
|
|
|
66 </tool>
|
