Mercurial > repos > iuc > macs2

comparison macs2_predict.xml @ 7:da0a1fcf7fe0 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author bgruening
date Tue, 21 Jan 2014 13:14:33 -0500
parents
children 16dc0e3d659b
comparison
equal deleted inserted replaced
6:97449a3c1f27 7:da0a1fcf7fe0
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 &gt; $outfile;
18
19 Rscript predicted_model.R &gt; $outfile_image
20 </command>
21 <expand macro="stdio" />
22 <inputs>
23 <repeat name="infiles" title="ChIP-seq alignment files" min="1"
24 help="If multiple files are given, then they will all be read and combined. Note that pair-end data is not supposed to work with this command.">
25
26 <param name="infile" type="data" format="bam,sam,bed" multiple="True" optional="True" label="ChIP-seq alignment file" help="-i" />
27 </repeat>
28
29 <expand macro="conditional_effective_genome_size" />
30 <expand macro="tag_size" />
31
32 <param name="band_width" type="integer" value="300" label="Band width for picking regions to compute fragment size"
33 help="This value is only used while building the shifting model. (--bw)" />
34
35 <param name="mfoldlo" type="integer" label="Fold-enrichment lower limit" value="5"
36 help="Select the regions with MFOLD high-confidence enrichment ratio against background to build model (--mfold)"/>
37 <param name="mfoldhi" type="integer" label="Fold-enrichment upper-limit" value="50"
38 help="Select the regions with MFOLD high-confidence enrichment ratio against background to build model (--mfold)"/>
39
40 </inputs>
41
42 <outputs>
43 <data name="outfile" format="txt" label="${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>