annotate macs2_bdgpeakcall.xml @ 6:2119d851a53b draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit df97bfd630719a2e1d4e11d67960753184afa238
author iuc
date Tue, 11 Apr 2017 17:46:41 -0400
parents beb902da6e5f
children acbd3fb47f90
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
fe62ba547975 Uploaded
iuc
parents:
diff changeset
1 <tool id="macs2_bdgpeakcall" name="MACS2 bdgpeakcall" version="@VERSION_STRING@.0">
fe62ba547975 Uploaded
iuc
parents:
diff changeset
2 <description>Call peaks from bedGraph output</description>
2
bfe57d6e0c4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 63955994af5090ec444c03c221df0012d5ae4e74
iuc
parents: 0
diff changeset
3 <macros>
bfe57d6e0c4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 63955994af5090ec444c03c221df0012d5ae4e74
iuc
parents: 0
diff changeset
4 <import>macs2_macros.xml</import>
bfe57d6e0c4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 63955994af5090ec444c03c221df0012d5ae4e74
iuc
parents: 0
diff changeset
5 </macros>
5
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 2
diff changeset
6 <expand macro="requirements"/>
2
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" />
0
fe62ba547975 Uploaded
iuc
parents:
diff changeset
8 <expand macro="version_command" />
fe62ba547975 Uploaded
iuc
parents:
diff changeset
9 <command>
5
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 2
diff changeset
10 <![CDATA[
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 2
diff changeset
11
0
fe62ba547975 Uploaded
iuc
parents:
diff changeset
12 macs2 bdgpeakcall
5
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 2
diff changeset
13 --ifile '${ infile }'
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 2
diff changeset
14 --cutoff '${ cutoff }'
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 2
diff changeset
15 --min-length '${ minlen }'
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 2
diff changeset
16 --max-gap '${ maxgap }'
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 2
diff changeset
17 ${ cutoff_analysis }
0
fe62ba547975 Uploaded
iuc
parents:
diff changeset
18 ${ notrackline }
5
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 2
diff changeset
19 --ofile '${ outfile }'
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 2
diff changeset
20
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 2
diff changeset
21 ]]>
0
fe62ba547975 Uploaded
iuc
parents:
diff changeset
22 </command>
fe62ba547975 Uploaded
iuc
parents:
diff changeset
23 <inputs>
fe62ba547975 Uploaded
iuc
parents:
diff changeset
24 <param name="infile" type="data" format="bedgraph" label="MACS score in bedGraph" />
2
bfe57d6e0c4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 63955994af5090ec444c03c221df0012d5ae4e74
iuc
parents: 0
diff changeset
25 <param name="cutoff" type="float" label="Cutoff for peaks" value="5.0"
5
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 2
diff changeset
26 help="Cutoff depends on which method you used for score track. If the file contains pvalue scores from MACS2, score 5 means pvalue 1e-5. Default=5.0 (--cutoff)"/>
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 2
diff changeset
27 <param name="minlen" type="integer" value="200" label="Minimum length of peak" help="better to set it as d value. Default=200 (--min-length)"/>
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 2
diff changeset
28 <param name="maxgap" type="integer" value="30" label="Maximum gap between significant points in a peak" help="better to set it as tag size Default=30 (--max-gap)"/>
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 2
diff changeset
29 <param name="cutoff_analysis" type="boolean" truevalue="--cutoff-analysis" falsevalue="" checked="False" label="Perform cutoff analysis" help="While set, bdgpeakcall will analyze number or total length of peaks that can be called by different cutoff then output a summary table to help user decide a better cutoff. Note, --min-len and --max-gap may affect the results. Default=False (--cutoff-analysis)"/>
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 2
diff changeset
30 <param name="notrackline" type="boolean" truevalue="" falsevalue="--no-trackline" checked="False" label="Include trackline into bedGraph output" help="required by UCSC Genome Browser (--no-trackline)"/>
0
fe62ba547975 Uploaded
iuc
parents:
diff changeset
31 </inputs>
fe62ba547975 Uploaded
iuc
parents:
diff changeset
32 <outputs>
5
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 2
diff changeset
33 <data name="outfile" format="bedgraph" label="${tool.name} on ${on_string}" />
0
fe62ba547975 Uploaded
iuc
parents:
diff changeset
34 </outputs>
fe62ba547975 Uploaded
iuc
parents:
diff changeset
35 <tests>
fe62ba547975 Uploaded
iuc
parents:
diff changeset
36 <test>
5
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 2
diff changeset
37 <param name="infile" value="bdgpeakcall_input.bdg" ftype="bedgraph" />
0
fe62ba547975 Uploaded
iuc
parents:
diff changeset
38 <param name="cutoff" value="5.0"/>
fe62ba547975 Uploaded
iuc
parents:
diff changeset
39 <param name="minlen" value="200"/>
fe62ba547975 Uploaded
iuc
parents:
diff changeset
40 <param name="maxgap" value="30"/>
5
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 2
diff changeset
41 <output name="outfile">
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 2
diff changeset
42 <assert_contents>
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 2
diff changeset
43 <has_text text="chrV" />
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 2
diff changeset
44 </assert_contents>
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 2
diff changeset
45 </output>
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 2
diff changeset
46 </test>
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 2
diff changeset
47 <test>
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 2
diff changeset
48 <param name="infile" value="bdgpeakcall_input.bdg" ftype="bedgraph" />
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 2
diff changeset
49 <param name="cutoff" value="5.0"/>
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 2
diff changeset
50 <param name="minlen" value="200"/>
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 2
diff changeset
51 <param name="maxgap" value="30"/>
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 2
diff changeset
52 <param name="cutoff_analysis" value="true" />
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 2
diff changeset
53 <output name="outfile" file="bdgpeakcall_output_cutoff.bdg"/>
0
fe62ba547975 Uploaded
iuc
parents:
diff changeset
54 </test>
fe62ba547975 Uploaded
iuc
parents:
diff changeset
55 </tests>
fe62ba547975 Uploaded
iuc
parents:
diff changeset
56 <help>
5
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 2
diff changeset
57 <![CDATA[
0
fe62ba547975 Uploaded
iuc
parents:
diff changeset
58 **What it does**
fe62ba547975 Uploaded
iuc
parents:
diff changeset
59
5
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 2
diff changeset
60 This is **bdgpeakcall** utility from the MACS2_ Package. It calls peaks from bedGraph output.
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 2
diff changeset
61
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 2
diff changeset
62 .. _MACS2: https://github.com/taoliu/MACS
0
fe62ba547975 Uploaded
iuc
parents:
diff changeset
63
fe62ba547975 Uploaded
iuc
parents:
diff changeset
64
fe62ba547975 Uploaded
iuc
parents:
diff changeset
65 @citation@
5
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 2
diff changeset
66 ]]>
0
fe62ba547975 Uploaded
iuc
parents:
diff changeset
67 </help>
fe62ba547975 Uploaded
iuc
parents:
diff changeset
68 <expand macro="citations" />
fe62ba547975 Uploaded
iuc
parents:
diff changeset
69 </tool>