Mercurial > repos > iuc > bam_to_scidx
annotate bam_to_scidx.xml @ 1:ebbf2a6a4c55 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit f33b04533bca91242b8a0a4077e1d593f5a874e0
author | iuc |
---|---|
date | Tue, 19 Apr 2016 18:10:09 -0400 |
parents | 741b8af6386c |
children | bd79c4d39af0 |
rev | line source |
---|---|
0
741b8af6386c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit dfaab7cbfdee82c9fe4ff34ce02b42fc456b9db9
iuc
parents:
diff
changeset
|
1 <tool id="bam_to_scidx" name="Convert BAM to ScIdx" version="1.0.0"> |
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> |
ebbf2a6a4c55
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit f33b04533bca91242b8a0a4077e1d593f5a874e0
iuc
parents:
0
diff
changeset
|
4 <requirement type="package" version="8.0.45">java-jdk</requirement> |
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> |
0
741b8af6386c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit dfaab7cbfdee82c9fe4ff34ce02b42fc456b9db9
iuc
parents:
diff
changeset
|
6 <command> |
741b8af6386c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit dfaab7cbfdee82c9fe4ff34ce02b42fc456b9db9
iuc
parents:
diff
changeset
|
7 <![CDATA[ |
741b8af6386c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit dfaab7cbfdee82c9fe4ff34ce02b42fc456b9db9
iuc
parents:
diff
changeset
|
8 ln -f -s "${input_bam.metadata.bam_index}" "${input_bam}.bai" && |
741b8af6386c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit dfaab7cbfdee82c9fe4ff34ce02b42fc456b9db9
iuc
parents:
diff
changeset
|
9 java -jar $__tool_directory__/BAMtoscIDX.jar -b "$input_bam" -i "${input_bam}.bai" -p $require_proper_mate_pairing -r $read -m $min_insert_size -M $max_insert_size -o "$output" 1>/dev/null |
741b8af6386c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit dfaab7cbfdee82c9fe4ff34ce02b42fc456b9db9
iuc
parents:
diff
changeset
|
10 ]]> |
741b8af6386c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit dfaab7cbfdee82c9fe4ff34ce02b42fc456b9db9
iuc
parents:
diff
changeset
|
11 </command> |
741b8af6386c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit dfaab7cbfdee82c9fe4ff34ce02b42fc456b9db9
iuc
parents:
diff
changeset
|
12 <inputs> |
741b8af6386c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit dfaab7cbfdee82c9fe4ff34ce02b42fc456b9db9
iuc
parents:
diff
changeset
|
13 <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
|
14 <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
|
15 <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
|
16 <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
|
17 </param> |
741b8af6386c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit dfaab7cbfdee82c9fe4ff34ce02b42fc456b9db9
iuc
parents:
diff
changeset
|
18 <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
|
19 <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
|
20 <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
|
21 <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
|
22 </param> |
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="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
|
24 <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
|
25 </inputs> |
741b8af6386c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit dfaab7cbfdee82c9fe4ff34ce02b42fc456b9db9
iuc
parents:
diff
changeset
|
26 <outputs> |
741b8af6386c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit dfaab7cbfdee82c9fe4ff34ce02b42fc456b9db9
iuc
parents:
diff
changeset
|
27 <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
|
28 </outputs> |
741b8af6386c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit dfaab7cbfdee82c9fe4ff34ce02b42fc456b9db9
iuc
parents:
diff
changeset
|
29 <tests> |
741b8af6386c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit dfaab7cbfdee82c9fe4ff34ce02b42fc456b9db9
iuc
parents:
diff
changeset
|
30 <test> |
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 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
|
32 <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
|
33 <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
|
34 <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
|
35 </test> |
741b8af6386c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit dfaab7cbfdee82c9fe4ff34ce02b42fc456b9db9
iuc
parents:
diff
changeset
|
36 </tests> |
741b8af6386c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit dfaab7cbfdee82c9fe4ff34ce02b42fc456b9db9
iuc
parents:
diff
changeset
|
37 <help> |
741b8af6386c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit dfaab7cbfdee82c9fe4ff34ce02b42fc456b9db9
iuc
parents:
diff
changeset
|
38 |
741b8af6386c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit dfaab7cbfdee82c9fe4ff34ce02b42fc456b9db9
iuc
parents:
diff
changeset
|
39 **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
|
40 |
741b8af6386c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit dfaab7cbfdee82c9fe4ff34ce02b42fc456b9db9
iuc
parents:
diff
changeset
|
41 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
|
42 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
|
43 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
|
44 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
|
45 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
|
46 |
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 |
741b8af6386c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit dfaab7cbfdee82c9fe4ff34ce02b42fc456b9db9
iuc
parents:
diff
changeset
|
49 **Options** |
741b8af6386c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit dfaab7cbfdee82c9fe4ff34ce02b42fc456b9db9
iuc
parents:
diff
changeset
|
50 |
741b8af6386c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit dfaab7cbfdee82c9fe4ff34ce02b42fc456b9db9
iuc
parents:
diff
changeset
|
51 * **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
|
52 * **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
|
53 * **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
|
54 |
741b8af6386c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit dfaab7cbfdee82c9fe4ff34ce02b42fc456b9db9
iuc
parents:
diff
changeset
|
55 </help> |
741b8af6386c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit dfaab7cbfdee82c9fe4ff34ce02b42fc456b9db9
iuc
parents:
diff
changeset
|
56 <citations> |
741b8af6386c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit dfaab7cbfdee82c9fe4ff34ce02b42fc456b9db9
iuc
parents:
diff
changeset
|
57 <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
|
58 @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
|
59 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
|
60 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
|
61 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
|
62 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
|
63 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
|
64 }</citation> |
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 </tool> |