annotate macs2_bdgbroadcall.xml @ 14:c16dbe4e2db2 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit c9c5c4dd15aed950ed9b43a294ce6c41f5732a23
author iuc
date Mon, 06 Aug 2018 10:41:57 -0400
parents acbd3fb47f90
children 640d3af5d833
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
fe62ba547975 Uploaded
iuc
parents:
diff changeset
1 <tool id="macs2_bdgbroadcall" name="MACS2 bdgbroadcall" version="@VERSION_STRING@.0">
fe62ba547975 Uploaded
iuc
parents:
diff changeset
2 <description>Call broad 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>
0
fe62ba547975 Uploaded
iuc
parents:
diff changeset
6 <expand macro="requirements">
7
f5d67c722d67 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4583af716424e402e1f99e2181cfb954f565f681
iuc
parents: 5
diff changeset
7 <requirement type="package" version="4.1.3">gawk</requirement>
0
fe62ba547975 Uploaded
iuc
parents:
diff changeset
8 </expand>
2
bfe57d6e0c4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 63955994af5090ec444c03c221df0012d5ae4e74
iuc
parents: 0
diff changeset
9 <expand macro="stdio" />
0
fe62ba547975 Uploaded
iuc
parents:
diff changeset
10 <expand macro="version_command" />
9
acbd3fb47f90 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 586ecaebf9e6020fac2674fbda368e293d1c9bc2
iuc
parents: 7
diff changeset
11 <command><![CDATA[
acbd3fb47f90 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 586ecaebf9e6020fac2674fbda368e293d1c9bc2
iuc
parents: 7
diff changeset
12 @home_dir@
0
fe62ba547975 Uploaded
iuc
parents:
diff changeset
13 macs2 bdgbroadcall
5
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 2
diff changeset
14 --ifile '${ infile }'
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 2
diff changeset
15 --cutoff-peak '${ cutoffpeak }'
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 2
diff changeset
16 --cutoff-link '${ cutofflink }'
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 2
diff changeset
17 --min-length '${ minlen }'
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 2
diff changeset
18 --lvl1-max-gap '${ LVL1MAXGAP }'
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 2
diff changeset
19 --lvl2-max-gap '${ LVL2MAXGAP }'
0
fe62ba547975 Uploaded
iuc
parents:
diff changeset
20 --ofile "macs2_bdgbroadcall.bdg"
5
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 2
diff changeset
21 &&
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 2
diff changeset
22 awk '!/^track name/' "macs2_bdgbroadcall.bdg" > '${ outfile }'
9
acbd3fb47f90 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 586ecaebf9e6020fac2674fbda368e293d1c9bc2
iuc
parents: 7
diff changeset
23 ]]></command>
0
fe62ba547975 Uploaded
iuc
parents:
diff changeset
24 <inputs>
5
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 2
diff changeset
25 <param name="infile" type="data" format="bedgraph" label="bedGraph generated MACS" />
2
bfe57d6e0c4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 63955994af5090ec444c03c221df0012d5ae4e74
iuc
parents: 0
diff changeset
26 <param name="cutoffpeak" type="float" label="Cutoff for peaks" value="2.0"
5
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 2
diff changeset
27 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)"/>
2
bfe57d6e0c4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 63955994af5090ec444c03c221df0012d5ae4e74
iuc
parents: 0
diff changeset
28 <param name="cutofflink" type="float" label="Cutoff for peaks" value="1.0"
5
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 2
diff changeset
29 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)"/>
2
bfe57d6e0c4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 63955994af5090ec444c03c221df0012d5ae4e74
iuc
parents: 0
diff changeset
30 <param name="minlen" type="integer" label="Minimum length of peak" value="200"
5
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 2
diff changeset
31 help="It is recommended to set it as d value. Default=200 (--min-length)" />
2
bfe57d6e0c4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 63955994af5090ec444c03c221df0012d5ae4e74
iuc
parents: 0
diff changeset
32 <param name="LVL1MAXGAP" type="integer" label="Maximum gap between significant peaks" 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
33 help="It is recommended to set it to tag size. Default=30 (--lvl1-max-gap)" />
2
bfe57d6e0c4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 63955994af5090ec444c03c221df0012d5ae4e74
iuc
parents: 0
diff changeset
34 <param name="LVL2MAXGAP" type="integer" label="Maximum linking between significant peaks" value="800"
5
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 2
diff changeset
35 help="It is recommended to set it to 4 times of d value. Default=800 (--lvl2-max-gap)" />
0
fe62ba547975 Uploaded
iuc
parents:
diff changeset
36 </inputs>
fe62ba547975 Uploaded
iuc
parents:
diff changeset
37 <outputs>
5
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 2
diff changeset
38 <data name="outfile" format="interval" label="${tool.name} on ${on_string}" />
0
fe62ba547975 Uploaded
iuc
parents:
diff changeset
39 </outputs>
fe62ba547975 Uploaded
iuc
parents:
diff changeset
40 <tests>
fe62ba547975 Uploaded
iuc
parents:
diff changeset
41 <test>
5
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 2
diff changeset
42 <param name="infile" value="bdgbroadcall_input.bdg" ftype="bedgraph" />
0
fe62ba547975 Uploaded
iuc
parents:
diff changeset
43 <param name="cutoffpeak" value="2.0"/>
fe62ba547975 Uploaded
iuc
parents:
diff changeset
44 <param name="cutofflink" value="1.0"/>
fe62ba547975 Uploaded
iuc
parents:
diff changeset
45 <param name="minlen" value="200"/>
fe62ba547975 Uploaded
iuc
parents:
diff changeset
46 <param name="LVL1MAXGAP" value="30"/>
fe62ba547975 Uploaded
iuc
parents:
diff changeset
47 <param name="LVL2MAXGAP" value="800"/>
5
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 2
diff changeset
48 <output name="outfile" file="bdgbroadcall_output.bdg"/>
0
fe62ba547975 Uploaded
iuc
parents:
diff changeset
49 </test>
fe62ba547975 Uploaded
iuc
parents:
diff changeset
50 </tests>
fe62ba547975 Uploaded
iuc
parents:
diff changeset
51 <help>
fe62ba547975 Uploaded
iuc
parents:
diff changeset
52 **What it does**
fe62ba547975 Uploaded
iuc
parents:
diff changeset
53
5
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 2
diff changeset
54 This is **bdgbroadcall** utility from the MACS2_ Package. It is designed to call broad peaks (e.g., histone) from bedGraph datasets generated with MACS2.
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 2
diff changeset
55
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 2
diff changeset
56 .. _MACS2: https://github.com/taoliu/MACS
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 2
diff changeset
57
0
fe62ba547975 Uploaded
iuc
parents:
diff changeset
58
fe62ba547975 Uploaded
iuc
parents:
diff changeset
59 @citation@
fe62ba547975 Uploaded
iuc
parents:
diff changeset
60 </help>
fe62ba547975 Uploaded
iuc
parents:
diff changeset
61 <expand macro="citations" />
fe62ba547975 Uploaded
iuc
parents:
diff changeset
62 </tool>