Mercurial > repos > iuc > macs2

annotate macs2_bdgbroadcall.xml @ 63:25e46cf1ee36 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e8307adcc6ee9245fa2bb9ecb6de1cbe008dc2c3"
author iuc
date Sat, 02 Apr 2022 21:36:50 +0000
parents 1ac88e46ee0f
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
63
25e46cf1ee36 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e8307adcc6ee9245fa2bb9ecb6de1cbe008dc2c3"
iuc
parents: 62
diff changeset
1 <tool id="macs2_bdgbroadcall" name="MACS2 bdgbroadcall" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
33
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
2 <description>Call broad peaks from bedGraph output</description>
62
1ac88e46ee0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 53
diff changeset
3 <expand macro="bio_tools"/>
36
8c8ae1e19b10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents: 33
diff changeset
4 <macros>
8c8ae1e19b10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents: 33
diff changeset
5 <import>macs2_macros.xml</import>
8c8ae1e19b10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents: 33
diff changeset
6 </macros>
33
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
7 <expand macro="requirements">
51
61d2f23acfb8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4583af716424e402e1f99e2181cfb954f565f681
iuc
parents: 49
diff changeset
8 <requirement type="package" version="4.1.3">gawk</requirement>
33
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
9 </expand>
36
8c8ae1e19b10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents: 33
diff changeset
10 <expand macro="stdio" />
33
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
11 <expand macro="version_command" />
53
8f6b37d29df5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 586ecaebf9e6020fac2674fbda368e293d1c9bc2
iuc
parents: 51
diff changeset
12 <command><![CDATA[
8f6b37d29df5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 586ecaebf9e6020fac2674fbda368e293d1c9bc2
iuc
parents: 51
diff changeset
13 @home_dir@
33
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
14 macs2 bdgbroadcall
49
1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 36
diff changeset
15 --ifile '${ infile }'
1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 36
diff changeset
16 --cutoff-peak '${ cutoffpeak }'
1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 36
diff changeset
17 --cutoff-link '${ cutofflink }'
1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 36
diff changeset
18 --min-length '${ minlen }'
1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 36
diff changeset
19 --lvl1-max-gap '${ LVL1MAXGAP }'
1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 36
diff changeset
20 --lvl2-max-gap '${ LVL2MAXGAP }'
33
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
21 --ofile "macs2_bdgbroadcall.bdg"
49
1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 36
diff changeset
22 &&
1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 36
diff changeset
23 awk '!/^track name/' "macs2_bdgbroadcall.bdg" > '${ outfile }'
53
8f6b37d29df5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 586ecaebf9e6020fac2674fbda368e293d1c9bc2
iuc
parents: 51
diff changeset
24 ]]></command>
33
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
25 <inputs>
49
1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 36
diff changeset
26 <param name="infile" type="data" format="bedgraph" label="bedGraph generated MACS" />
36
8c8ae1e19b10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents: 33
diff changeset
27 <param name="cutoffpeak" type="float" label="Cutoff for peaks" value="2.0"
49
1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 36
diff changeset
28 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 (--cutoff)"/>
36
8c8ae1e19b10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents: 33
diff changeset
29 <param name="cutofflink" type="float" label="Cutoff for peaks" value="1.0"
49
1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 36
diff changeset
30 help=" Cutoff for linking regions/low abundance regions depending on which method you used for score track. If the file contains qvalue scores from MACS2, score 1 means qvalue 0.1, and score 0.3 means qvalue 0.5. Default=1 (--cutoff-link)"/>
36
8c8ae1e19b10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents: 33
diff changeset
31 <param name="minlen" type="integer" label="Minimum length of peak" value="200"
49
1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 36
diff changeset
32 help="It is recommended to set it as d value. Default=200 (--min-length)" />
36
8c8ae1e19b10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents: 33
diff changeset
33 <param name="LVL1MAXGAP" type="integer" label="Maximum gap between significant peaks" value="30"
49
1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 36
diff changeset
34 help="It is recommended to set it to tag size. Default=30 (--lvl1-max-gap)" />
36
8c8ae1e19b10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents: 33
diff changeset
35 <param name="LVL2MAXGAP" type="integer" label="Maximum linking between significant peaks" value="800"
49
1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 36
diff changeset
36 help="It is recommended to set it to 4 times of d value. Default=800 (--lvl2-max-gap)" />
33
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
37 </inputs>
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
38 <outputs>
49
1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 36
diff changeset
39 <data name="outfile" format="interval" label="${tool.name} on ${on_string}" />
33
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
40 </outputs>
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
41 <tests>
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
42 <test>
49
1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 36
diff changeset
43 <param name="infile" value="bdgbroadcall_input.bdg" ftype="bedgraph" />
33
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
44 <param name="cutoffpeak" value="2.0"/>
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
45 <param name="cutofflink" value="1.0"/>
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
46 <param name="minlen" value="200"/>
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
47 <param name="LVL1MAXGAP" value="30"/>
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
48 <param name="LVL2MAXGAP" value="800"/>
49
1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 36
diff changeset
49 <output name="outfile" file="bdgbroadcall_output.bdg"/>
33
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
50 </test>
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
51 </tests>
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
52 <help>
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
53 **What it does**
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
54
49
1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 36
diff changeset
55 This is **bdgbroadcall** utility from the MACS2_ Package. It is designed to call broad peaks (e.g., histone) from bedGraph datasets generated with MACS2.
1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 36
diff changeset
56
1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 36
diff changeset
57 .. _MACS2: https://github.com/taoliu/MACS
1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 36
diff changeset
58
33
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
59
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
60 @citation@
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
61 </help>
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
62 <expand macro="citations" />
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
63 </tool>