Mercurial > repos > iuc > macs2
annotate macs2_bdgpeakcall.xml @ 18:640d3af5d833 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e8307adcc6ee9245fa2bb9ecb6de1cbe008dc2c3"
author | iuc |
---|---|
date | Sat, 02 Apr 2022 21:37:38 +0000 |
parents | acbd3fb47f90 |
children | 86e2413cf3f8 |
rev | line source |
---|---|
18
640d3af5d833
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e8307adcc6ee9245fa2bb9ecb6de1cbe008dc2c3"
iuc
parents:
9
diff
changeset
|
1 <tool id="macs2_bdgpeakcall" name="MACS2 bdgpeakcall" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01"> |
0 | 2 <description>Call peaks from bedGraph output</description> |
18
640d3af5d833
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e8307adcc6ee9245fa2bb9ecb6de1cbe008dc2c3"
iuc
parents:
9
diff
changeset
|
3 <expand macro="bio_tools"/> |
2
bfe57d6e0c4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 63955994af5090ec444c03c221df0012d5ae4e74
iuc
parents:
0
diff
changeset
|
4 <macros> |
bfe57d6e0c4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 63955994af5090ec444c03c221df0012d5ae4e74
iuc
parents:
0
diff
changeset
|
5 <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
|
6 </macros> |
5
beb902da6e5f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents:
2
diff
changeset
|
7 <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
|
8 <expand macro="stdio" /> |
0 | 9 <expand macro="version_command" /> |
9
acbd3fb47f90
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 586ecaebf9e6020fac2674fbda368e293d1c9bc2
iuc
parents:
5
diff
changeset
|
10 <command><![CDATA[ |
acbd3fb47f90
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 586ecaebf9e6020fac2674fbda368e293d1c9bc2
iuc
parents:
5
diff
changeset
|
11 @home_dir@ |
0 | 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 | 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 }' |
9
acbd3fb47f90
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 586ecaebf9e6020fac2674fbda368e293d1c9bc2
iuc
parents:
5
diff
changeset
|
20 ]]></command> |
0 | 21 <inputs> |
22 <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
|
23 <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
|
24 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
|
25 <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
|
26 <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
|
27 <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
|
28 <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 | 29 </inputs> |
30 <outputs> | |
5
beb902da6e5f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents:
2
diff
changeset
|
31 <data name="outfile" format="bedgraph" label="${tool.name} on ${on_string}" /> |
0 | 32 </outputs> |
33 <tests> | |
34 <test> | |
5
beb902da6e5f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents:
2
diff
changeset
|
35 <param name="infile" value="bdgpeakcall_input.bdg" ftype="bedgraph" /> |
0 | 36 <param name="cutoff" value="5.0"/> |
37 <param name="minlen" value="200"/> | |
38 <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
|
39 <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
|
40 <assert_contents> |
beb902da6e5f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents:
2
diff
changeset
|
41 <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
|
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 </output> |
beb902da6e5f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents:
2
diff
changeset
|
44 </test> |
beb902da6e5f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents:
2
diff
changeset
|
45 <test> |
beb902da6e5f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents:
2
diff
changeset
|
46 <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
|
47 <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
|
48 <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
|
49 <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
|
50 <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
|
51 <output name="outfile" file="bdgpeakcall_output_cutoff.bdg"/> |
0 | 52 </test> |
53 </tests> | |
54 <help> | |
5
beb902da6e5f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents:
2
diff
changeset
|
55 <![CDATA[ |
0 | 56 **What it does** |
57 | |
5
beb902da6e5f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents:
2
diff
changeset
|
58 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
|
59 |
beb902da6e5f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents:
2
diff
changeset
|
60 .. _MACS2: https://github.com/taoliu/MACS |
0 | 61 |
62 | |
63 @citation@ | |
5
beb902da6e5f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents:
2
diff
changeset
|
64 ]]> |
0 | 65 </help> |
66 <expand macro="citations" /> | |
67 </tool> |