annotate macs2_filterdup.xml @ 17:424aefbd7777 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e90e79e18362561d0060d2c162f1938feebdbc29
author iuc
date Thu, 25 Apr 2019 17:49:05 -0400
parents acbd3fb47f90
children 640d3af5d833
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
17
424aefbd7777 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e90e79e18362561d0060d2c162f1938feebdbc29
iuc
parents: 9
diff changeset
1 <tool id="macs2_filterdup" name="MACS2 filterdup" version="@VERSION_STRING@.1">
0
fe62ba547975 Uploaded
iuc
parents:
diff changeset
2 <description>Remove duplicate reads at the same position</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>
2
bfe57d6e0c4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 63955994af5090ec444c03c221df0012d5ae4e74
iuc
parents: 0
diff changeset
6 <expand macro="requirements" />
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" />
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="version_command" />
5
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 2
diff changeset
9 <command><![CDATA[
9
acbd3fb47f90 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 586ecaebf9e6020fac2674fbda368e293d1c9bc2
iuc
parents: 5
diff changeset
10 @home_dir@
0
fe62ba547975 Uploaded
iuc
parents:
diff changeset
11 macs2 filterdup
5
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 2
diff changeset
12 -i '${ infile }'
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 2
diff changeset
13 -o '${ outfile }'
0
fe62ba547975 Uploaded
iuc
parents:
diff changeset
14 --format '${ infile.extension.upper() }'
fe62ba547975 Uploaded
iuc
parents:
diff changeset
15 @effective_genome_size@
fe62ba547975 Uploaded
iuc
parents:
diff changeset
16 @tag_size@
5
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 2
diff changeset
17 --pvalue '${ pvalue }'
0
fe62ba547975 Uploaded
iuc
parents:
diff changeset
18 #if str( $keep_dup_options.keep_dup_options_selector ) == "user":
5
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 2
diff changeset
19 --keep-dup '${ keep_dup_options.user_keepdup }'
0
fe62ba547975 Uploaded
iuc
parents:
diff changeset
20 #else
5
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 2
diff changeset
21 --keep-dup '${ keep_dup_options.keep_dup_options_selector }'
0
fe62ba547975 Uploaded
iuc
parents:
diff changeset
22 #end if
5
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 2
diff changeset
23 ]]>
0
fe62ba547975 Uploaded
iuc
parents:
diff changeset
24 </command>
fe62ba547975 Uploaded
iuc
parents:
diff changeset
25 <inputs>
17
424aefbd7777 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e90e79e18362561d0060d2c162f1938feebdbc29
iuc
parents: 9
diff changeset
26 <param name="infile" type="data" format="bam,bed" label="Sequencing alignment file" />
0
fe62ba547975 Uploaded
iuc
parents:
diff changeset
27 <expand macro="conditional_effective_genome_size" />
fe62ba547975 Uploaded
iuc
parents:
diff changeset
28 <expand macro="tag_size" />
5
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 2
diff changeset
29 <param name="pvalue" type="text" value="1e-5" label="Pvalue cutoff for binomial distribution test" help="Default=1e-5 (--pvalue)" />
0
fe62ba547975 Uploaded
iuc
parents:
diff changeset
30 <expand macro="keep_duplicates" />
fe62ba547975 Uploaded
iuc
parents:
diff changeset
31
fe62ba547975 Uploaded
iuc
parents:
diff changeset
32 </inputs>
fe62ba547975 Uploaded
iuc
parents:
diff changeset
33 <outputs>
fe62ba547975 Uploaded
iuc
parents:
diff changeset
34 <data name="outfile" format="bed" label="${tool.name} on ${on_string}" />
fe62ba547975 Uploaded
iuc
parents:
diff changeset
35 </outputs>
fe62ba547975 Uploaded
iuc
parents:
diff changeset
36 <tests>
fe62ba547975 Uploaded
iuc
parents:
diff changeset
37 <test>
fe62ba547975 Uploaded
iuc
parents:
diff changeset
38 <param name="infile" value="ChIP_200K_w_dups.bed" ftype="bed"/>
fe62ba547975 Uploaded
iuc
parents:
diff changeset
39 <param name="pvalue" value="1e-5"/>
fe62ba547975 Uploaded
iuc
parents:
diff changeset
40 <param name="keep_dup_options_selector" value="auto"/>
fe62ba547975 Uploaded
iuc
parents:
diff changeset
41 <param name="effective_genome_size_options_selector" value="user_defined" />
fe62ba547975 Uploaded
iuc
parents:
diff changeset
42 <param name="gsize" value="3300000000" />
fe62ba547975 Uploaded
iuc
parents:
diff changeset
43 <output name="outfile" file="filterdup_on_ChIP_200K_w_dups.bed"/>
fe62ba547975 Uploaded
iuc
parents:
diff changeset
44 </test>
fe62ba547975 Uploaded
iuc
parents:
diff changeset
45 </tests>
fe62ba547975 Uploaded
iuc
parents:
diff changeset
46 <help>
5
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 2
diff changeset
47 <![CDATA[
0
fe62ba547975 Uploaded
iuc
parents:
diff changeset
48 **What it does**
fe62ba547975 Uploaded
iuc
parents:
diff changeset
49
5
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 2
diff changeset
50 This is **filterdup** utility from the MACS2_ Package. It removes duplicate reads and converts results to BED format.
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 2
diff changeset
51
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 2
diff changeset
52 .. _MACS2: https://github.com/taoliu/MACS
0
fe62ba547975 Uploaded
iuc
parents:
diff changeset
53
fe62ba547975 Uploaded
iuc
parents:
diff changeset
54 @citation@
5
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 2
diff changeset
55 ]]>
0
fe62ba547975 Uploaded
iuc
parents:
diff changeset
56 </help>
fe62ba547975 Uploaded
iuc
parents:
diff changeset
57 <expand macro="citations" />
fe62ba547975 Uploaded
iuc
parents:
diff changeset
58 </tool>