annotate macs2_bdgcmp.xml @ 2:bfe57d6e0c4c draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 63955994af5090ec444c03c221df0012d5ae4e74
author iuc
date Mon, 12 Oct 2015 11:24:39 -0400
parents fe62ba547975
children beb902da6e5f
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
fe62ba547975 Uploaded
iuc
parents:
diff changeset
1 <tool id="macs2_bdgcmp" name="MACS2 bdgcmp" version="@VERSION_STRING@.0">
fe62ba547975 Uploaded
iuc
parents:
diff changeset
2 <description>Deduct noise by comparing two signal tracks in bedGraph</description>
fe62ba547975 Uploaded
iuc
parents:
diff changeset
3 <macros>
fe62ba547975 Uploaded
iuc
parents:
diff changeset
4 <import>macs2_macros.xml</import>
fe62ba547975 Uploaded
iuc
parents:
diff changeset
5 </macros>
2
bfe57d6e0c4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 63955994af5090ec444c03c221df0012d5ae4e74
iuc
parents: 0
diff changeset
6 <expand macro="requirements" />
bfe57d6e0c4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 63955994af5090ec444c03c221df0012d5ae4e74
iuc
parents: 0
diff changeset
7 <expand macro="stdio" />
bfe57d6e0c4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 63955994af5090ec444c03c221df0012d5ae4e74
iuc
parents: 0
diff changeset
8 <expand macro="version_command" />
0
fe62ba547975 Uploaded
iuc
parents:
diff changeset
9 <command>
fe62ba547975 Uploaded
iuc
parents:
diff changeset
10 macs2 bdgcmp
fe62ba547975 Uploaded
iuc
parents:
diff changeset
11 -t "${ infile_treatment }"
fe62ba547975 Uploaded
iuc
parents:
diff changeset
12 -c "${ infile_control }"
fe62ba547975 Uploaded
iuc
parents:
diff changeset
13
fe62ba547975 Uploaded
iuc
parents:
diff changeset
14 -m "${ bdgcmp_options.bdgcmp_options_selector }"
fe62ba547975 Uploaded
iuc
parents:
diff changeset
15 #if str($bdgcmp_options.bdgcmp_options_selector) in ['FE', 'logFE', 'logLR']:
fe62ba547975 Uploaded
iuc
parents:
diff changeset
16 -p "${ bdgcmp_options.pseudocount }"
fe62ba547975 Uploaded
iuc
parents:
diff changeset
17 #end if
fe62ba547975 Uploaded
iuc
parents:
diff changeset
18 -o "${ outfile }"
fe62ba547975 Uploaded
iuc
parents:
diff changeset
19
fe62ba547975 Uploaded
iuc
parents:
diff changeset
20 </command>
fe62ba547975 Uploaded
iuc
parents:
diff changeset
21 <inputs>
fe62ba547975 Uploaded
iuc
parents:
diff changeset
22 <param name="infile_treatment" type="data" format="bedgraph" label="Treatment bedGraph file" />
fe62ba547975 Uploaded
iuc
parents:
diff changeset
23 <param name="infile_control" type="data" format="bedgraph" label="Control bedGraph file" />
fe62ba547975 Uploaded
iuc
parents:
diff changeset
24
fe62ba547975 Uploaded
iuc
parents:
diff changeset
25 <conditional name="bdgcmp_options">
fe62ba547975 Uploaded
iuc
parents:
diff changeset
26 <param name="bdgcmp_options_selector" type="select" label="Method to use while calculating a score in any bin by comparing treatment value and control value">
fe62ba547975 Uploaded
iuc
parents:
diff changeset
27 <option value="ppois" selected="true">Poisson pvalue (-log10) using control as lambda and treatment as observation (ppois)</option>
fe62ba547975 Uploaded
iuc
parents:
diff changeset
28 <option value="qpois">q-value through a BH process for poisson pvalues (qpois)</option>
fe62ba547975 Uploaded
iuc
parents:
diff changeset
29 <option value="subtract">subtraction from treatment (subtract)</option>
fe62ba547975 Uploaded
iuc
parents:
diff changeset
30 <option value="logFE">log10 fold enrichment (logFE)</option>
fe62ba547975 Uploaded
iuc
parents:
diff changeset
31 <option value="FE">linear scale fold enrichment (FE)</option>
fe62ba547975 Uploaded
iuc
parents:
diff changeset
32 <option value="logLR">log10 likelihood between ChIP-enriched model and open chromatin model (logLR)</option>
fe62ba547975 Uploaded
iuc
parents:
diff changeset
33 <option value="slogLR">symmetric log10 likelihood between two ChIP-enrichment models (slogLR)</option>
fe62ba547975 Uploaded
iuc
parents:
diff changeset
34 </param>
fe62ba547975 Uploaded
iuc
parents:
diff changeset
35 <when value="FE">
fe62ba547975 Uploaded
iuc
parents:
diff changeset
36 <param name="pseudocount" type="float" label="Set pseudocount" value="0.0" help="The count will be applied after normalization of sequencing depth. default: 0.0, no pseudocount is applied."/>
fe62ba547975 Uploaded
iuc
parents:
diff changeset
37 </when>
fe62ba547975 Uploaded
iuc
parents:
diff changeset
38 <when value="logLR">
fe62ba547975 Uploaded
iuc
parents:
diff changeset
39 <param name="pseudocount" type="float" label="Set pseudocount" value="0.0" help="The count will be applied after normalization of sequencing depth. default: 0.0, no pseudocount is applied."/>
fe62ba547975 Uploaded
iuc
parents:
diff changeset
40 </when>
fe62ba547975 Uploaded
iuc
parents:
diff changeset
41 <when value="logFE">
fe62ba547975 Uploaded
iuc
parents:
diff changeset
42 <param name="pseudocount" type="float" label="Set pseudocount" value="0.0" help="The count will be applied after normalization of sequencing depth. default: 0.0, no pseudocount is applied."/>
fe62ba547975 Uploaded
iuc
parents:
diff changeset
43 </when>
fe62ba547975 Uploaded
iuc
parents:
diff changeset
44 <when value="ppois"/>
fe62ba547975 Uploaded
iuc
parents:
diff changeset
45 <when value="qpois"/>
fe62ba547975 Uploaded
iuc
parents:
diff changeset
46 <when value="subtract"/>
fe62ba547975 Uploaded
iuc
parents:
diff changeset
47 <when value="slogLR"/>
fe62ba547975 Uploaded
iuc
parents:
diff changeset
48 </conditional>
fe62ba547975 Uploaded
iuc
parents:
diff changeset
49 </inputs>
fe62ba547975 Uploaded
iuc
parents:
diff changeset
50 <outputs>
fe62ba547975 Uploaded
iuc
parents:
diff changeset
51 <data name="outfile" format="bedgraph" label="${tool.name} on ${on_string}" />
fe62ba547975 Uploaded
iuc
parents:
diff changeset
52 </outputs>
fe62ba547975 Uploaded
iuc
parents:
diff changeset
53 <tests>
fe62ba547975 Uploaded
iuc
parents:
diff changeset
54 <test>
fe62ba547975 Uploaded
iuc
parents:
diff changeset
55 <param name="infile_control" value="callpeak_control_part.bdg" ftype="bedgraph"/>
fe62ba547975 Uploaded
iuc
parents:
diff changeset
56 <param name="infile_treatment" value="callpeak_treatment_part.bdg" ftype="bedgraph"/>
fe62ba547975 Uploaded
iuc
parents:
diff changeset
57 <param name="bdgcmp_options_selector" value="slogLR"/>
fe62ba547975 Uploaded
iuc
parents:
diff changeset
58 <output name="outfile" file="bdgcmp_on_Control_and_ChIP_slogLR.bdg"/>
fe62ba547975 Uploaded
iuc
parents:
diff changeset
59 </test>
fe62ba547975 Uploaded
iuc
parents:
diff changeset
60 </tests>
fe62ba547975 Uploaded
iuc
parents:
diff changeset
61 <help>
fe62ba547975 Uploaded
iuc
parents:
diff changeset
62 **What it does**
fe62ba547975 Uploaded
iuc
parents:
diff changeset
63
fe62ba547975 Uploaded
iuc
parents:
diff changeset
64 With the improvement of sequencing techniques, chromatin immunoprecipitation followed by high throughput sequencing (ChIP-Seq)
fe62ba547975 Uploaded
iuc
parents:
diff changeset
65 is getting popular to study genome-wide protein-DNA interactions. To address the lack of powerful ChIP-Seq analysis method, we present a novel algorithm, named Model-based Analysis of ChIP-Seq (MACS), for
fe62ba547975 Uploaded
iuc
parents:
diff changeset
66 identifying transcript factor binding sites. MACS captures the influence of genome complexity to evaluate the significance of enriched ChIP regions, and MACS improves the spatial resolution of
fe62ba547975 Uploaded
iuc
parents:
diff changeset
67 binding sites through combining the information of both sequencing tag position and orientation. MACS can be easily used for ChIP-Seq data alone, or with control sample with the increase of specificity.
fe62ba547975 Uploaded
iuc
parents:
diff changeset
68
fe62ba547975 Uploaded
iuc
parents:
diff changeset
69 View the original MACS2 documentation: https://github.com/taoliu/MACS/blob/master/README
fe62ba547975 Uploaded
iuc
parents:
diff changeset
70
fe62ba547975 Uploaded
iuc
parents:
diff changeset
71 ------
fe62ba547975 Uploaded
iuc
parents:
diff changeset
72
fe62ba547975 Uploaded
iuc
parents:
diff changeset
73 **Usage**
fe62ba547975 Uploaded
iuc
parents:
diff changeset
74
fe62ba547975 Uploaded
iuc
parents:
diff changeset
75 **Compare .bdg files**: Deduct noise by comparing two signal tracks in bedGraph.
fe62ba547975 Uploaded
iuc
parents:
diff changeset
76
fe62ba547975 Uploaded
iuc
parents:
diff changeset
77
fe62ba547975 Uploaded
iuc
parents:
diff changeset
78 @citation@
fe62ba547975 Uploaded
iuc
parents:
diff changeset
79 </help>
fe62ba547975 Uploaded
iuc
parents:
diff changeset
80 <expand macro="citations" />
fe62ba547975 Uploaded
iuc
parents:
diff changeset
81 </tool>