Mercurial > repos > iuc > macs2

annotate macs2_predictd.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_predictd" name="MACS2 predictd" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
33
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
2 <description>Predict 'd' or fragment size from alignment results</description>
62
1ac88e46ee0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 61
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>
49
1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 47
diff changeset
7 <expand macro="requirements"/>
36
8c8ae1e19b10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents: 33
diff changeset
8 <expand macro="stdio" />
33
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
9 <expand macro="version_command" />
53
8f6b37d29df5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 586ecaebf9e6020fac2674fbda368e293d1c9bc2
iuc
parents: 49
diff changeset
10 <command><![CDATA[
8f6b37d29df5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 586ecaebf9e6020fac2674fbda368e293d1c9bc2
iuc
parents: 49
diff changeset
11 @home_dir@
33
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
12 macs2 predictd
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
13
49
1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 47
diff changeset
14 -i ${ ' '.join(["'%s'" % $x for $x in $infiles ]) }
1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 47
diff changeset
15 @tag_size@
1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 47
diff changeset
16 @effective_genome_size@
1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 47
diff changeset
17 --bw '${ band_width }'
1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 47
diff changeset
18 @mfold_command@
63
25e46cf1ee36 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e8307adcc6ee9245fa2bb9ecb6de1cbe008dc2c3"
iuc
parents: 62
diff changeset
19 --d-min $d_min
25e46cf1ee36 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e8307adcc6ee9245fa2bb9ecb6de1cbe008dc2c3"
iuc
parents: 62
diff changeset
20 @buffer_size@
33
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
21
49
1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 47
diff changeset
22 ## remove the timepoint and strip the output
1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 47
diff changeset
23 2>&1 | awk -F: '{print $4}' | awk '{$1=$1}1'
36
8c8ae1e19b10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents: 33
diff changeset
24
49
1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 47
diff changeset
25 > '${ outfile }'
1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 47
diff changeset
26
1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 47
diff changeset
27 &&
33
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
28
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
29 Rscript predictd
53
8f6b37d29df5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 586ecaebf9e6020fac2674fbda368e293d1c9bc2
iuc
parents: 49
diff changeset
30 ]]></command>
33
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
31 <inputs>
61
644444825ef9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e90e79e18362561d0060d2c162f1938feebdbc29
iuc
parents: 59
diff changeset
32 <param name="infiles" type="data" format="bam,bed" multiple="True"
49
1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 47
diff changeset
33 label="ChIP-seq alignment file"
1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 47
diff changeset
34 help="If multiple files are given, then they will all be read and combined. Note that pair-end data is not supposed to work with this command. (-i)" />
33
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
35 <expand macro="conditional_effective_genome_size" />
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
36 <expand macro="tag_size" />
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
37 <expand macro="band_width" />
49
1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 47
diff changeset
38 <expand macro="mfold_options" />
63
25e46cf1ee36 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e8307adcc6ee9245fa2bb9ecb6de1cbe008dc2c3"
iuc
parents: 62
diff changeset
39 <expand macro="fragment_size"/>
25e46cf1ee36 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e8307adcc6ee9245fa2bb9ecb6de1cbe008dc2c3"
iuc
parents: 62
diff changeset
40 <expand macro="buffer_size"/>
33
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
41 </inputs>
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
42
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
43 <outputs>
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
44 <data name="outfile" format="txt" label="${tool.name} on ${on_string} - d value" />
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
45 <data name="outfile_image" from_work_dir="predictd_model.pdf" format="pdf" label="${tool.name} on ${on_string} - X-correlation image" />
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
46 </outputs>
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
47 <tests>
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
48 <test>
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
49 <param name="infiles" value="Control_200K.bed,ChIP_200K.bed" ftype="bed" />
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
50 <param name="effective_genome_size_options_selector" value="user_defined" />
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
51 <param name="gsize" value="3300000000" />
49
1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 47
diff changeset
52 <param name="tsize" value=""/>
33
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
53 <param name="band_width" value="300"/>
49
1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 47
diff changeset
54 <param name="lower" value="5"/>
1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 47
diff changeset
55 <param name="upper" value="50"/>
63
25e46cf1ee36 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e8307adcc6ee9245fa2bb9ecb6de1cbe008dc2c3"
iuc
parents: 62
diff changeset
56 <assert_command>
25e46cf1ee36 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e8307adcc6ee9245fa2bb9ecb6de1cbe008dc2c3"
iuc
parents: 62
diff changeset
57 <has_text text="--buffer-size"/>
25e46cf1ee36 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e8307adcc6ee9245fa2bb9ecb6de1cbe008dc2c3"
iuc
parents: 62
diff changeset
58 <has_text text="--d-min"/>
25e46cf1ee36 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e8307adcc6ee9245fa2bb9ecb6de1cbe008dc2c3"
iuc
parents: 62
diff changeset
59 </assert_command>
59
ea526bc73f8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 30858afbdbe0223d07d2936a8469295bcbeda786
iuc
parents: 53
diff changeset
60 <output name="outfile">
ea526bc73f8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 30858afbdbe0223d07d2936a8469295bcbeda786
iuc
parents: 53
diff changeset
61 <assert_contents>
ea526bc73f8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 30858afbdbe0223d07d2936a8469295bcbeda786
iuc
parents: 53
diff changeset
62 <has_line line="# predicted fragment length is 284 bps" />
ea526bc73f8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 30858afbdbe0223d07d2936a8469295bcbeda786
iuc
parents: 53
diff changeset
63 </assert_contents>
ea526bc73f8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 30858afbdbe0223d07d2936a8469295bcbeda786
iuc
parents: 53
diff changeset
64 </output>
63
25e46cf1ee36 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e8307adcc6ee9245fa2bb9ecb6de1cbe008dc2c3"
iuc
parents: 62
diff changeset
65 <output name="outfile_image" file="predictd_on_ChIP_200K_and_Control_200K.pdf" compare="sim_size" ftype="pdf"/>
33
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
66 </test>
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
67 </tests>
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
68 <help>
49
1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 47
diff changeset
69 <![CDATA[
33
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
70 **What it does**
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
71
49
1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 47
diff changeset
72 This is **predictd** utility from the MACS2_ Package. It predicts the *d* value or fragment size from alignment results.
33
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
73
49
1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 47
diff changeset
74 .. _MACS2: https://github.com/taoliu/MACS
33
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
75
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
76 @citation@
49
1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 47
diff changeset
77 ]]>
1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 47
diff changeset
78
33
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
79 </help>
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
80 <expand macro="citations" />
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
81 </tool>