annotate macs2_predictd.xml @ 8:e8a060164e11 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
author iuc
date Wed, 27 Dec 2017 10:18:03 -0500
parents beb902da6e5f
children acbd3fb47f90
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
fe62ba547975 Uploaded
iuc
parents:
diff changeset
1 <tool id="macs2_predictd" name="MACS2 predictd" version="@VERSION_STRING@.0">
fe62ba547975 Uploaded
iuc
parents:
diff changeset
2 <description>Predict 'd' or fragment size from alignment results</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>
5
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 3
diff changeset
6 <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
7 <expand macro="stdio" />
0
fe62ba547975 Uploaded
iuc
parents:
diff changeset
8 <expand macro="version_command" />
fe62ba547975 Uploaded
iuc
parents:
diff changeset
9 <command>
5
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 3
diff changeset
10 <![CDATA[
0
fe62ba547975 Uploaded
iuc
parents:
diff changeset
11 macs2 predictd
fe62ba547975 Uploaded
iuc
parents:
diff changeset
12
5
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 3
diff changeset
13 -i ${ ' '.join(["'%s'" % $x for $x in $infiles ]) }
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 3
diff changeset
14 @tag_size@
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 3
diff changeset
15 @effective_genome_size@
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 3
diff changeset
16 --bw '${ band_width }'
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 3
diff changeset
17 @mfold_command@
0
fe62ba547975 Uploaded
iuc
parents:
diff changeset
18
5
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 3
diff changeset
19 ## remove the timepoint and strip the output
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 3
diff changeset
20 2>&1 | awk -F: '{print $4}' | awk '{$1=$1}1'
2
bfe57d6e0c4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 63955994af5090ec444c03c221df0012d5ae4e74
iuc
parents: 0
diff changeset
21
5
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 3
diff changeset
22 > '${ outfile }'
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 3
diff changeset
23
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 3
diff changeset
24 &&
0
fe62ba547975 Uploaded
iuc
parents:
diff changeset
25
fe62ba547975 Uploaded
iuc
parents:
diff changeset
26 Rscript predictd
5
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 3
diff changeset
27 ]]>
0
fe62ba547975 Uploaded
iuc
parents:
diff changeset
28 </command>
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: 3
diff changeset
30 <param name="infiles" type="data" format="bam,sam,bed" multiple="True"
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 3
diff changeset
31 label="ChIP-seq alignment file"
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 3
diff changeset
32 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)" />
0
fe62ba547975 Uploaded
iuc
parents:
diff changeset
33 <expand macro="conditional_effective_genome_size" />
fe62ba547975 Uploaded
iuc
parents:
diff changeset
34 <expand macro="tag_size" />
fe62ba547975 Uploaded
iuc
parents:
diff changeset
35 <expand macro="band_width" />
5
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 3
diff changeset
36 <expand macro="mfold_options" />
0
fe62ba547975 Uploaded
iuc
parents:
diff changeset
37 </inputs>
fe62ba547975 Uploaded
iuc
parents:
diff changeset
38
fe62ba547975 Uploaded
iuc
parents:
diff changeset
39 <outputs>
fe62ba547975 Uploaded
iuc
parents:
diff changeset
40 <data name="outfile" format="txt" label="${tool.name} on ${on_string} - d value" />
fe62ba547975 Uploaded
iuc
parents:
diff changeset
41 <data name="outfile_image" from_work_dir="predictd_model.pdf" format="pdf" label="${tool.name} on ${on_string} - X-correlation image" />
fe62ba547975 Uploaded
iuc
parents:
diff changeset
42 </outputs>
fe62ba547975 Uploaded
iuc
parents:
diff changeset
43 <tests>
fe62ba547975 Uploaded
iuc
parents:
diff changeset
44 <test>
fe62ba547975 Uploaded
iuc
parents:
diff changeset
45 <param name="infiles" value="Control_200K.bed,ChIP_200K.bed" ftype="bed" />
fe62ba547975 Uploaded
iuc
parents:
diff changeset
46 <param name="effective_genome_size_options_selector" value="user_defined" />
fe62ba547975 Uploaded
iuc
parents:
diff changeset
47 <param name="gsize" value="3300000000" />
5
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 3
diff changeset
48 <param name="tsize" value=""/>
0
fe62ba547975 Uploaded
iuc
parents:
diff changeset
49 <param name="band_width" value="300"/>
5
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 3
diff changeset
50 <param name="lower" value="5"/>
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 3
diff changeset
51 <param name="upper" value="50"/>
0
fe62ba547975 Uploaded
iuc
parents:
diff changeset
52 <output name="outfile" file="predictd_on_ChIP_200K_and_Control_200K.txt"/>
fe62ba547975 Uploaded
iuc
parents:
diff changeset
53 <output name="outfile_image" file="predictd_on_ChIP_200K_and_Control_200K.pdf" compare="sim_size"/>
fe62ba547975 Uploaded
iuc
parents:
diff changeset
54 </test>
fe62ba547975 Uploaded
iuc
parents:
diff changeset
55 </tests>
fe62ba547975 Uploaded
iuc
parents:
diff changeset
56 <help>
5
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 3
diff changeset
57 <![CDATA[
0
fe62ba547975 Uploaded
iuc
parents:
diff changeset
58 **What it does**
fe62ba547975 Uploaded
iuc
parents:
diff changeset
59
5
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 3
diff changeset
60 This is **predictd** utility from the MACS2_ Package. It predicts the *d* value or fragment size from alignment results.
0
fe62ba547975 Uploaded
iuc
parents:
diff changeset
61
5
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 3
diff changeset
62 .. _MACS2: https://github.com/taoliu/MACS
0
fe62ba547975 Uploaded
iuc
parents:
diff changeset
63
fe62ba547975 Uploaded
iuc
parents:
diff changeset
64 @citation@
5
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 3
diff changeset
65 ]]>
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 3
diff changeset
66
0
fe62ba547975 Uploaded
iuc
parents:
diff changeset
67 </help>
fe62ba547975 Uploaded
iuc
parents:
diff changeset
68 <expand macro="citations" />
fe62ba547975 Uploaded
iuc
parents:
diff changeset
69 </tool>