Mercurial > repos > iuc > bam_to_scidx

annotate bam_to_scidx.xml @ 4:b737f6d83f48 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author iuc
date Fri, 13 Jan 2017 10:25:43 -0500
parents 11fc60f0e942
children 408520e1ae1a
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
4
b737f6d83f48 Uploaded
iuc
parents: 3
diff changeset
1 <tool id="bam_to_scidx" name="Convert BAM to ScIdx" version="1.0.1">
0
741b8af6386c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit dfaab7cbfdee82c9fe4ff34ce02b42fc456b9db9
iuc
parents:
diff changeset
2 <description></description>
1
ebbf2a6a4c55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit f33b04533bca91242b8a0a4077e1d593f5a874e0
iuc
parents: 0
diff changeset
3 <requirements>
4
b737f6d83f48 Uploaded
iuc
parents: 3
diff changeset
4 <requirement type="package" version="8.0.112">openjdk</requirement>
1
ebbf2a6a4c55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit f33b04533bca91242b8a0a4077e1d593f5a874e0
iuc
parents: 0
diff changeset
5 </requirements>
2
bd79c4d39af0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit d12fc0b2960551d8659d7079e15a3d4e214786b3
iuc
parents: 1
diff changeset
6 <stdio>
bd79c4d39af0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit d12fc0b2960551d8659d7079e15a3d4e214786b3
iuc
parents: 1
diff changeset
7 <!-- Anything other than zero is an error -->
bd79c4d39af0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit d12fc0b2960551d8659d7079e15a3d4e214786b3
iuc
parents: 1
diff changeset
8 <exit_code range=":-1" />
bd79c4d39af0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit d12fc0b2960551d8659d7079e15a3d4e214786b3
iuc
parents: 1
diff changeset
9 <exit_code range="1:" />
bd79c4d39af0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit d12fc0b2960551d8659d7079e15a3d4e214786b3
iuc
parents: 1
diff changeset
10 <!-- Check stderr in case the return code has not been set -->
bd79c4d39af0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit d12fc0b2960551d8659d7079e15a3d4e214786b3
iuc
parents: 1
diff changeset
11 <regex match="Error:" />
bd79c4d39af0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit d12fc0b2960551d8659d7079e15a3d4e214786b3
iuc
parents: 1
diff changeset
12 <regex match="Exception:" />
bd79c4d39af0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit d12fc0b2960551d8659d7079e15a3d4e214786b3
iuc
parents: 1
diff changeset
13 </stdio>
0
741b8af6386c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit dfaab7cbfdee82c9fe4ff34ce02b42fc456b9db9
iuc
parents:
diff changeset
14 <command>
741b8af6386c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit dfaab7cbfdee82c9fe4ff34ce02b42fc456b9db9
iuc
parents:
diff changeset
15 <![CDATA[
3
11fc60f0e942 Uploaded
iuc
parents: 2
diff changeset
16 ln -s "${input_bam}" "localbam.bam" &&
11fc60f0e942 Uploaded
iuc
parents: 2
diff changeset
17 ln -f -s "${input_bam.metadata.bam_index}" "localbam.bam.bai" &&
11fc60f0e942 Uploaded
iuc
parents: 2
diff changeset
18 java -jar $__tool_directory__/BAMtoscIDX.jar -b localbam.bam -i localbam.bam.bai -p $require_proper_mate_pairing -r $read -m $min_insert_size -M $max_insert_size -o "$output" 1>/dev/null
0
741b8af6386c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit dfaab7cbfdee82c9fe4ff34ce02b42fc456b9db9
iuc
parents:
diff changeset
19 ]]>
741b8af6386c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit dfaab7cbfdee82c9fe4ff34ce02b42fc456b9db9
iuc
parents:
diff changeset
20 </command>
741b8af6386c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit dfaab7cbfdee82c9fe4ff34ce02b42fc456b9db9
iuc
parents:
diff changeset
21 <inputs>
741b8af6386c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit dfaab7cbfdee82c9fe4ff34ce02b42fc456b9db9
iuc
parents:
diff changeset
22 <param name="input_bam" type="data" format="bam" label="BAM file" />
741b8af6386c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit dfaab7cbfdee82c9fe4ff34ce02b42fc456b9db9
iuc
parents:
diff changeset
23 <param name="require_proper_mate_pairing" type="select" label="Require proper mate-pairing?" help="Required if filtering by insert size for single-end Reqd 1 (below)." >
741b8af6386c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit dfaab7cbfdee82c9fe4ff34ce02b42fc456b9db9
iuc
parents:
diff changeset
24 <option value="1" selected="True">Yes</option>
741b8af6386c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit dfaab7cbfdee82c9fe4ff34ce02b42fc456b9db9
iuc
parents:
diff changeset
25 <option value="0">No</option>
741b8af6386c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit dfaab7cbfdee82c9fe4ff34ce02b42fc456b9db9
iuc
parents:
diff changeset
26 </param>
741b8af6386c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit dfaab7cbfdee82c9fe4ff34ce02b42fc456b9db9
iuc
parents:
diff changeset
27 <param name="read" type="select" label="Read to output">
741b8af6386c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit dfaab7cbfdee82c9fe4ff34ce02b42fc456b9db9
iuc
parents:
diff changeset
28 <option value="0" selected="True">Read1</option>
741b8af6386c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit dfaab7cbfdee82c9fe4ff34ce02b42fc456b9db9
iuc
parents:
diff changeset
29 <option value="1">Read2</option>
741b8af6386c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit dfaab7cbfdee82c9fe4ff34ce02b42fc456b9db9
iuc
parents:
diff changeset
30 <option value="2">Combined</option>
741b8af6386c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit dfaab7cbfdee82c9fe4ff34ce02b42fc456b9db9
iuc
parents:
diff changeset
31 </param>
741b8af6386c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit dfaab7cbfdee82c9fe4ff34ce02b42fc456b9db9
iuc
parents:
diff changeset
32 <param name="min_insert_size" type="integer" value="" optional="True" min="0" label="Minimum insert size to output" help="Will not filter out single-end Read 1 unless proper mate-pairing is required (above)."/>
741b8af6386c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit dfaab7cbfdee82c9fe4ff34ce02b42fc456b9db9
iuc
parents:
diff changeset
33 <param name="max_insert_size" type="integer" value="" optional="True" min="0" label="Maximum insert size to output" help="Will not filter out single-end Read 1 unless proper mate-pairing is required (above)." />
741b8af6386c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit dfaab7cbfdee82c9fe4ff34ce02b42fc456b9db9
iuc
parents:
diff changeset
34 </inputs>
741b8af6386c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit dfaab7cbfdee82c9fe4ff34ce02b42fc456b9db9
iuc
parents:
diff changeset
35 <outputs>
741b8af6386c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit dfaab7cbfdee82c9fe4ff34ce02b42fc456b9db9
iuc
parents:
diff changeset
36 <data name="output" format="scidx" />
741b8af6386c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit dfaab7cbfdee82c9fe4ff34ce02b42fc456b9db9
iuc
parents:
diff changeset
37 </outputs>
741b8af6386c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit dfaab7cbfdee82c9fe4ff34ce02b42fc456b9db9
iuc
parents:
diff changeset
38 <tests>
741b8af6386c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit dfaab7cbfdee82c9fe4ff34ce02b42fc456b9db9
iuc
parents:
diff changeset
39 <test>
741b8af6386c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit dfaab7cbfdee82c9fe4ff34ce02b42fc456b9db9
iuc
parents:
diff changeset
40 <param name="input_bam" value="input.bam" ftype="bam" />
741b8af6386c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit dfaab7cbfdee82c9fe4ff34ce02b42fc456b9db9
iuc
parents:
diff changeset
41 <param name="require_proper_mate_pairing" value="1" />
741b8af6386c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit dfaab7cbfdee82c9fe4ff34ce02b42fc456b9db9
iuc
parents:
diff changeset
42 <param name="read" value="0" />
1
ebbf2a6a4c55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit f33b04533bca91242b8a0a4077e1d593f5a874e0
iuc
parents: 0
diff changeset
43 <output name="output" file="output.scidx" lines_diff="1" ftype="scidx" compare="contains" />
0
741b8af6386c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit dfaab7cbfdee82c9fe4ff34ce02b42fc456b9db9
iuc
parents:
diff changeset
44 </test>
741b8af6386c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit dfaab7cbfdee82c9fe4ff34ce02b42fc456b9db9
iuc
parents:
diff changeset
45 </tests>
741b8af6386c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit dfaab7cbfdee82c9fe4ff34ce02b42fc456b9db9
iuc
parents:
diff changeset
46 <help>
741b8af6386c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit dfaab7cbfdee82c9fe4ff34ce02b42fc456b9db9
iuc
parents:
diff changeset
47
741b8af6386c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit dfaab7cbfdee82c9fe4ff34ce02b42fc456b9db9
iuc
parents:
diff changeset
48 **What it does**
741b8af6386c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit dfaab7cbfdee82c9fe4ff34ce02b42fc456b9db9
iuc
parents:
diff changeset
49
741b8af6386c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit dfaab7cbfdee82c9fe4ff34ce02b42fc456b9db9
iuc
parents:
diff changeset
50 Converts BAM data to ScIdx, the Strand-specific coordinate count format, which is used by tools within
741b8af6386c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit dfaab7cbfdee82c9fe4ff34ce02b42fc456b9db9
iuc
parents:
diff changeset
51 the Chip-exo Galaxy flavor. ScIdx files are 1-based. The format consists of 5 columns: the chromosome,
741b8af6386c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit dfaab7cbfdee82c9fe4ff34ce02b42fc456b9db9
iuc
parents:
diff changeset
52 the position of the genomic coordinate, the number of tags on the forward strand, the number of tags on
741b8af6386c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit dfaab7cbfdee82c9fe4ff34ce02b42fc456b9db9
iuc
parents:
diff changeset
53 the reverse strand and the number of total tags on the position. With pair-end reads, only the 5’ end of
741b8af6386c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit dfaab7cbfdee82c9fe4ff34ce02b42fc456b9db9
iuc
parents:
diff changeset
54 READ1 will be used to create the ScIdx data file. Tools that use this format include GeneTrack and MultiGPS.
741b8af6386c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit dfaab7cbfdee82c9fe4ff34ce02b42fc456b9db9
iuc
parents:
diff changeset
55
741b8af6386c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit dfaab7cbfdee82c9fe4ff34ce02b42fc456b9db9
iuc
parents:
diff changeset
56 -----
741b8af6386c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit dfaab7cbfdee82c9fe4ff34ce02b42fc456b9db9
iuc
parents:
diff changeset
57
741b8af6386c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit dfaab7cbfdee82c9fe4ff34ce02b42fc456b9db9
iuc
parents:
diff changeset
58 **Options**
741b8af6386c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit dfaab7cbfdee82c9fe4ff34ce02b42fc456b9db9
iuc
parents:
diff changeset
59
741b8af6386c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit dfaab7cbfdee82c9fe4ff34ce02b42fc456b9db9
iuc
parents:
diff changeset
60 * **Require proper mate-pairing?** - Select **Yes** to require proper mate paring. Filtering by insert size parameters will not filter out single-end Read 1 unless proper mate-pairing is required.
741b8af6386c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit dfaab7cbfdee82c9fe4ff34ce02b42fc456b9db9
iuc
parents:
diff changeset
61 * **Minimum insert size to output** - Insert size below the minimum will be filtered from the results, but single-end Read 1 will not be filtered unless proper mate-pairing is required.
741b8af6386c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit dfaab7cbfdee82c9fe4ff34ce02b42fc456b9db9
iuc
parents:
diff changeset
62 * **Maximum insert size to output** - Insert size above the maximum will be filtered from the results, but single-end Read 1 will not be filtered unless proper mate-pairing is required.
741b8af6386c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit dfaab7cbfdee82c9fe4ff34ce02b42fc456b9db9
iuc
parents:
diff changeset
63
741b8af6386c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit dfaab7cbfdee82c9fe4ff34ce02b42fc456b9db9
iuc
parents:
diff changeset
64 </help>
741b8af6386c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit dfaab7cbfdee82c9fe4ff34ce02b42fc456b9db9
iuc
parents:
diff changeset
65 <citations>
741b8af6386c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit dfaab7cbfdee82c9fe4ff34ce02b42fc456b9db9
iuc
parents:
diff changeset
66 <citation type="bibtex">
741b8af6386c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit dfaab7cbfdee82c9fe4ff34ce02b42fc456b9db9
iuc
parents:
diff changeset
67 @unpublished{None,
741b8af6386c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit dfaab7cbfdee82c9fe4ff34ce02b42fc456b9db9
iuc
parents:
diff changeset
68 author = {Lai, William},
741b8af6386c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit dfaab7cbfdee82c9fe4ff34ce02b42fc456b9db9
iuc
parents:
diff changeset
69 title = {None},
741b8af6386c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit dfaab7cbfdee82c9fe4ff34ce02b42fc456b9db9
iuc
parents:
diff changeset
70 year = {None},
741b8af6386c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit dfaab7cbfdee82c9fe4ff34ce02b42fc456b9db9
iuc
parents:
diff changeset
71 eprint = {None},
741b8af6386c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit dfaab7cbfdee82c9fe4ff34ce02b42fc456b9db9
iuc
parents:
diff changeset
72 url = {http://www.huck.psu.edu/content/research/independent-centers-excellence/center-for-eukaryotic-gene-regulation}
741b8af6386c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit dfaab7cbfdee82c9fe4ff34ce02b42fc456b9db9
iuc
parents:
diff changeset
73 }</citation>
741b8af6386c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit dfaab7cbfdee82c9fe4ff34ce02b42fc456b9db9
iuc
parents:
diff changeset
74 </citations>
741b8af6386c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit dfaab7cbfdee82c9fe4ff34ce02b42fc456b9db9
iuc
parents:
diff changeset
75 </tool>