Mercurial > repos > iuc > macs2

annotate macs2_bdgdiff.xml @ 15:c33686854b19 draft

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 30858afbdbe0223d07d2936a8469295bcbeda786
author iuc
date Mon, 15 Oct 2018 06:49:16 -0400
parents 38769345062e
children 640d3af5d833
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
12
38769345062e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 09ef7ee96fadeef22273029ea23d1e140ce96737
iuc
parents: 9
diff changeset
1 <tool id="macs2_bdgdiff" name="MACS2 bdgdiff" version="@VERSION_STRING@.1" profile="17.09">
0
fe62ba547975 Uploaded
iuc
parents:
diff changeset
2 <description>Differential peak detection based on paired four bedgraph files</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>
5
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 4
diff changeset
6 <expand macro="requirements">
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 4
diff changeset
7 <requirement type="package" version="4.1.3">gawk</requirement>
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 4
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" />
bfe57d6e0c4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 63955994af5090ec444c03c221df0012d5ae4e74
iuc
parents: 0
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: 5
diff changeset
11 <command><![CDATA[
acbd3fb47f90 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 586ecaebf9e6020fac2674fbda368e293d1c9bc2
iuc
parents: 5
diff changeset
12 @home_dir@
0
fe62ba547975 Uploaded
iuc
parents:
diff changeset
13 macs2 bdgdiff
5
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 4
diff changeset
14 --t1 '${ t1 }'
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 4
diff changeset
15 --t2 '${ t2 }'
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 4
diff changeset
16 --c1 '${ c1 }'
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 4
diff changeset
17 --c2 '${ c2 }'
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 4
diff changeset
18 --cutoff '${ cutoff }'
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 4
diff changeset
19 --min-len '${ minlen }'
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 4
diff changeset
20 --depth1 '${ depth.depth1 }'
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 4
diff changeset
21 --depth2 '${ depth.depth2 }'
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 4
diff changeset
22 --max-gap '${ maxgap }'
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 4
diff changeset
23 -o c1.bed c2.bed both.bed &&
0
fe62ba547975 Uploaded
iuc
parents:
diff changeset
24
5
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 4
diff changeset
25 awk '!/^track name/' "c1.bed" > '${ output_cond1 }' &&
12
38769345062e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 09ef7ee96fadeef22273029ea23d1e140ce96737
iuc
parents: 9
diff changeset
26 awk '!/^track name/' "c2.bed" > '${ output_cond2 }' &&
5
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 4
diff changeset
27 awk '!/^track name/' "both.bed" > '${ output_both }'
9
acbd3fb47f90 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 586ecaebf9e6020fac2674fbda368e293d1c9bc2
iuc
parents: 5
diff changeset
28 ]]></command>
0
fe62ba547975 Uploaded
iuc
parents:
diff changeset
29 <inputs>
5
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 4
diff changeset
30 <param name="t1" type="data" format="bedgraph" label="BedGraph for Treatment experiment 1" />
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 4
diff changeset
31 <param name="t2" type="data" format="bedgraph" label="BedGraph for Treatment experiment 2" />
0
fe62ba547975 Uploaded
iuc
parents:
diff changeset
32
5
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 4
diff changeset
33 <param name="c1" type="data" format="bedgraph" label="BedGraph for Control experiment 1" />
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 4
diff changeset
34 <param name="c2" type="data" format="bedgraph" label="Bedgraph for Control experiment 2" />
0
fe62ba547975 Uploaded
iuc
parents:
diff changeset
35
5
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 4
diff changeset
36 <param name="cutoff" type="float" label="Cutoff of log10 likelihood ratio cutoff" value="1.0" help="Default=1.0 correspoinding to likelihood ratio of 1,000 (--cutoff)"/>
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 4
diff changeset
37 <param name="minlen" type="integer" label="Minimum length of differential region" value="200" help=" Try bigger value to remove small regions. Default=200 (--min-len)"/>
0
fe62ba547975 Uploaded
iuc
parents:
diff changeset
38
5
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 4
diff changeset
39 <section name="depth" title="Sequencing depth" expanded="True" help="Sequencing depths will be used to calculate scaling factor for each sample, to down-scale larger sample to the level of smaller one. For example, while comparing condition 1 (10 Million reads) and condition 2 (20 million reads), use --depth1 10 --depth2 20, then pileup value in bedGraph for condition 2 will be divided by 2.">
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 4
diff changeset
40 <param name="depth1" type="integer" value="1" label="Sequence depth of condition 1 in million reads" help="Default=1 (--depth1)" />
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 4
diff changeset
41 <param name="depth2" type="integer" value="1" label="Sequence depth of condition 2 in million reads" help="Default=1 (--depth2)" />
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 4
diff changeset
42 </section>
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 4
diff changeset
43 <param name="maxgap" type="integer" value="100" label="Maximum gap to merge nearby differential regions" help="Consider a wider gap for broad marks. Maximum gap should be smaller than minimum length. Default=100 (--max-gap)." />
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 4
diff changeset
44
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 4
diff changeset
45
0
fe62ba547975 Uploaded
iuc
parents:
diff changeset
46 </inputs>
fe62ba547975 Uploaded
iuc
parents:
diff changeset
47 <outputs>
5
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 4
diff changeset
48 <data name="output_cond1" format="bed" label="${tool.name} on ${on_string} (Condition 1)"/>
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 4
diff changeset
49 <data name="output_cond2" format="bed" label="${tool.name} on ${on_string} (Condition 2)"/>
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 4
diff changeset
50 <data name="output_both" format="bed" label="${tool.name} on ${on_string} (Common)"/>
0
fe62ba547975 Uploaded
iuc
parents:
diff changeset
51 </outputs>
fe62ba547975 Uploaded
iuc
parents:
diff changeset
52 <tests>
fe62ba547975 Uploaded
iuc
parents:
diff changeset
53 <test>
5
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 4
diff changeset
54 <param name="t1" value="bdgdiff_t1.bdg" ftype="bedgraph"/>
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 4
diff changeset
55 <param name="t2" value="bdgdiff_t2.bdg" ftype="bedgraph"/>
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 4
diff changeset
56 <param name="c1" value="bdgdiff_c1.bdg" ftype="bedgraph"/>
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 4
diff changeset
57 <param name="c2" value="bdgdiff_c2.bdg" ftype="bedgraph"/>
0
fe62ba547975 Uploaded
iuc
parents:
diff changeset
58 <param name="cutoff" value="1.0"/>
fe62ba547975 Uploaded
iuc
parents:
diff changeset
59 <param name="minlen" value="200"/>
5
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 4
diff changeset
60 <param name="depth1" value="10"/>
0
fe62ba547975 Uploaded
iuc
parents:
diff changeset
61 <param name="depth2" value="1"/>
fe62ba547975 Uploaded
iuc
parents:
diff changeset
62 <param name="maxgap" value="100"/>
12
38769345062e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 09ef7ee96fadeef22273029ea23d1e140ce96737
iuc
parents: 9
diff changeset
63 <output name="output_cond1" ftype="bed" value="bdgdiff_output_c1.bed"/>
38769345062e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 09ef7ee96fadeef22273029ea23d1e140ce96737
iuc
parents: 9
diff changeset
64 <output name="output_cond2">
5
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 4
diff changeset
65 <assert_contents>
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 4
diff changeset
66 <has_text text="c2.bed1" />
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 4
diff changeset
67 </assert_contents>
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 4
diff changeset
68 </output>
12
38769345062e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 09ef7ee96fadeef22273029ea23d1e140ce96737
iuc
parents: 9
diff changeset
69 <output name="output_both" ftype="bed" value="bdgdiff_output_both.bed"/>
0
fe62ba547975 Uploaded
iuc
parents:
diff changeset
70 </test>
fe62ba547975 Uploaded
iuc
parents:
diff changeset
71 </tests>
fe62ba547975 Uploaded
iuc
parents:
diff changeset
72 <help>
5
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 4
diff changeset
73 <![CDATA[
0
fe62ba547975 Uploaded
iuc
parents:
diff changeset
74 **What it does**
fe62ba547975 Uploaded
iuc
parents:
diff changeset
75
5
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 4
diff changeset
76 This is **bdgdiff** utility from the MACS2_ Package. It performs differential peak detection based on paired four bedgraph files.
0
fe62ba547975 Uploaded
iuc
parents:
diff changeset
77
5
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 4
diff changeset
78 .. _MACS2: https://github.com/taoliu/MACS
0
fe62ba547975 Uploaded
iuc
parents:
diff changeset
79
fe62ba547975 Uploaded
iuc
parents:
diff changeset
80 @citation@
5
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 4
diff changeset
81 ]]>
0
fe62ba547975 Uploaded
iuc
parents:
diff changeset
82 </help>
fe62ba547975 Uploaded
iuc
parents:
diff changeset
83 <expand macro="citations" />
fe62ba547975 Uploaded
iuc
parents:
diff changeset
84 </tool>