Mercurial > repos > iuc > bamtools_split_ref

annotate bamtools_split_ref.xml @ 4:9b8feb118f9e 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/main/tool_collections/bamtools/bamtools_split commit 5ebe920838ab3c36e93d620c479df17f43f8e336
author iuc
date Fri, 15 Mar 2024 13:49:30 +0000
parents 9b520009db81
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
3
9b520009db81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split commit 862f05b5053f55def8007194a702019418697cb5
iuc
parents: 1
diff changeset
1 <tool id="bamtools_split_ref" name="Split BAM by reference" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.09">
9b520009db81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split commit 862f05b5053f55def8007194a702019418697cb5
iuc
parents: 1
diff changeset
2 <description>into a dataset list collection</description>
0
09470ab960f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 1cacd14cfb2429fefa91fdd05c82d2e36d23283a"
iuc
parents:
diff changeset
3 <macros>
09470ab960f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 1cacd14cfb2429fefa91fdd05c82d2e36d23283a"
iuc
parents:
diff changeset
4 <import>macros.xml</import>
09470ab960f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 1cacd14cfb2429fefa91fdd05c82d2e36d23283a"
iuc
parents:
diff changeset
5 </macros>
4
9b8feb118f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split commit 5ebe920838ab3c36e93d620c479df17f43f8e336
iuc
parents: 3
diff changeset
6 <expand macro="xrefs"/>
1
9dbf707bebb0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split_ref commit a14db40361bcb2ee608bccd9222e1654aaea3324-dirty
iuc
parents: 0
diff changeset
7 <expand macro="requirements">
9dbf707bebb0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split_ref commit a14db40361bcb2ee608bccd9222e1654aaea3324-dirty
iuc
parents: 0
diff changeset
8 <requirement type="package" version="1.16.1">samtools</requirement>
9dbf707bebb0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split_ref commit a14db40361bcb2ee608bccd9222e1654aaea3324-dirty
iuc
parents: 0
diff changeset
9 </expand>
9dbf707bebb0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split_ref commit a14db40361bcb2ee608bccd9222e1654aaea3324-dirty
iuc
parents: 0
diff changeset
10 <command><![CDATA[
9dbf707bebb0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split_ref commit a14db40361bcb2ee608bccd9222e1654aaea3324-dirty
iuc
parents: 0
diff changeset
11 ln -s '${input_bam}' localbam.bam &&
9dbf707bebb0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split_ref commit a14db40361bcb2ee608bccd9222e1654aaea3324-dirty
iuc
parents: 0
diff changeset
12 ln -s '${input_bam.metadata.bam_index}' 'localbam.bam.bai' &&
9dbf707bebb0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split_ref commit a14db40361bcb2ee608bccd9222e1654aaea3324-dirty
iuc
parents: 0
diff changeset
13 samtools view -bH localbam.bam --no-PG -o header.bam &&
9dbf707bebb0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split_ref commit a14db40361bcb2ee608bccd9222e1654aaea3324-dirty
iuc
parents: 0
diff changeset
14 bamtools split -reference
9dbf707bebb0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split_ref commit a14db40361bcb2ee608bccd9222e1654aaea3324-dirty
iuc
parents: 0
diff changeset
15 -in localbam.bam
9dbf707bebb0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split_ref commit a14db40361bcb2ee608bccd9222e1654aaea3324-dirty
iuc
parents: 0
diff changeset
16 -stub split_bam
9dbf707bebb0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split_ref commit a14db40361bcb2ee608bccd9222e1654aaea3324-dirty
iuc
parents: 0
diff changeset
17 && (IFS=',';
9dbf707bebb0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split_ref commit a14db40361bcb2ee608bccd9222e1654aaea3324-dirty
iuc
parents: 0
diff changeset
18 for i in \$REFS_FROM_BAM_METADATA;
9dbf707bebb0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split_ref commit a14db40361bcb2ee608bccd9222e1654aaea3324-dirty
iuc
parents: 0
diff changeset
19 do FN=`printf "split_bam.REF_%s.bam" "\$i"`;
9dbf707bebb0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split_ref commit a14db40361bcb2ee608bccd9222e1654aaea3324-dirty
iuc
parents: 0
diff changeset
20 if [ ! -f \$FN ]; then cp header.bam "\$FN"; fi;
9dbf707bebb0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split_ref commit a14db40361bcb2ee608bccd9222e1654aaea3324-dirty
iuc
parents: 0
diff changeset
21 done)
9dbf707bebb0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split_ref commit a14db40361bcb2ee608bccd9222e1654aaea3324-dirty
iuc
parents: 0
diff changeset
22 && cp '$c1' galaxy.json
9dbf707bebb0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split_ref commit a14db40361bcb2ee608bccd9222e1654aaea3324-dirty
iuc
parents: 0
diff changeset
23 ]]></command>
9dbf707bebb0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split_ref commit a14db40361bcb2ee608bccd9222e1654aaea3324-dirty
iuc
parents: 0
diff changeset
24 <environment_variables>
9dbf707bebb0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split_ref commit a14db40361bcb2ee608bccd9222e1654aaea3324-dirty
iuc
parents: 0
diff changeset
25 <environment_variable name="REFS_FROM_BAM_METADATA">#import re
9dbf707bebb0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split_ref commit a14db40361bcb2ee608bccd9222e1654aaea3324-dirty
iuc
parents: 0
diff changeset
26 ## need to extract ref names from Galaxy's safe string representation
9dbf707bebb0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split_ref commit a14db40361bcb2ee608bccd9222e1654aaea3324-dirty
iuc
parents: 0
diff changeset
27 #set $ref_list = [$re.sub('^.*__sq__(.+)__sq__.*$','\\1',n) if n.find('__sq__') >= 0 else n for n in str($input_bam.metadata.reference_names).split(',')]
9dbf707bebb0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split_ref commit a14db40361bcb2ee608bccd9222e1654aaea3324-dirty
iuc
parents: 0
diff changeset
28 #if str($refs) != 'None'
9dbf707bebb0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split_ref commit a14db40361bcb2ee608bccd9222e1654aaea3324-dirty
iuc
parents: 0
diff changeset
29 #set $refs_selected = set(str($refs).split(","))
9dbf707bebb0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split_ref commit a14db40361bcb2ee608bccd9222e1654aaea3324-dirty
iuc
parents: 0
diff changeset
30 ## sort the selected refs by their order in the bam metadata
9dbf707bebb0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split_ref commit a14db40361bcb2ee608bccd9222e1654aaea3324-dirty
iuc
parents: 0
diff changeset
31 #echo ','.join([r for r in $ref_list if r in refs_selected])
9dbf707bebb0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split_ref commit a14db40361bcb2ee608bccd9222e1654aaea3324-dirty
iuc
parents: 0
diff changeset
32 #else
9dbf707bebb0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split_ref commit a14db40361bcb2ee608bccd9222e1654aaea3324-dirty
iuc
parents: 0
diff changeset
33 #echo ','.join($ref_list)
9dbf707bebb0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split_ref commit a14db40361bcb2ee608bccd9222e1654aaea3324-dirty
iuc
parents: 0
diff changeset
34 #end if
9dbf707bebb0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split_ref commit a14db40361bcb2ee608bccd9222e1654aaea3324-dirty
iuc
parents: 0
diff changeset
35 </environment_variable>
9dbf707bebb0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split_ref commit a14db40361bcb2ee608bccd9222e1654aaea3324-dirty
iuc
parents: 0
diff changeset
36 </environment_variables>
9dbf707bebb0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split_ref commit a14db40361bcb2ee608bccd9222e1654aaea3324-dirty
iuc
parents: 0
diff changeset
37 <configfiles>
9dbf707bebb0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split_ref commit a14db40361bcb2ee608bccd9222e1654aaea3324-dirty
iuc
parents: 0
diff changeset
38 <configfile name="c1">#import re
9dbf707bebb0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split_ref commit a14db40361bcb2ee608bccd9222e1654aaea3324-dirty
iuc
parents: 0
diff changeset
39 ## need to extract ref names from Galaxy's safe string representation
9dbf707bebb0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split_ref commit a14db40361bcb2ee608bccd9222e1654aaea3324-dirty
iuc
parents: 0
diff changeset
40 #set $ref_list = [$re.sub('^.*__sq__(.+)__sq__.*$','\\1',n) if n.find('__sq__') >= 0 else n for n in str($input_bam.metadata.reference_names).split(',')]
9dbf707bebb0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split_ref commit a14db40361bcb2ee608bccd9222e1654aaea3324-dirty
iuc
parents: 0
diff changeset
41 #if str($refs) != 'None'
9dbf707bebb0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split_ref commit a14db40361bcb2ee608bccd9222e1654aaea3324-dirty
iuc
parents: 0
diff changeset
42 #set $refs_selected = set(str($refs).split(","))
9dbf707bebb0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split_ref commit a14db40361bcb2ee608bccd9222e1654aaea3324-dirty
iuc
parents: 0
diff changeset
43 #set $ref_list = [r for r in $ref_list if r in refs_selected]
9dbf707bebb0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split_ref commit a14db40361bcb2ee608bccd9222e1654aaea3324-dirty
iuc
parents: 0
diff changeset
44 #end if
9dbf707bebb0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split_ref commit a14db40361bcb2ee608bccd9222e1654aaea3324-dirty
iuc
parents: 0
diff changeset
45 #set $elems = [{'name': '%s: %s' % ($input_bam.name, r), 'filename': 'split_bam.REF_%s.bam' % r, 'dbkey': str($input_bam.dbkey)} for r in $ref_list]
9dbf707bebb0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split_ref commit a14db40361bcb2ee608bccd9222e1654aaea3324-dirty
iuc
parents: 0
diff changeset
46 #import json
9dbf707bebb0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split_ref commit a14db40361bcb2ee608bccd9222e1654aaea3324-dirty
iuc
parents: 0
diff changeset
47 #echo json.dumps({'output_bams': {'elements': $elems}})</configfile>
9dbf707bebb0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split_ref commit a14db40361bcb2ee608bccd9222e1654aaea3324-dirty
iuc
parents: 0
diff changeset
48 </configfiles>
0
09470ab960f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 1cacd14cfb2429fefa91fdd05c82d2e36d23283a"
iuc
parents:
diff changeset
49 <inputs>
09470ab960f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 1cacd14cfb2429fefa91fdd05c82d2e36d23283a"
iuc
parents:
diff changeset
50 <param name="input_bam" type="data" format="bam" label="BAM dataset to split by reference"/>
09470ab960f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 1cacd14cfb2429fefa91fdd05c82d2e36d23283a"
iuc
parents:
diff changeset
51 <param name="refs" type="select" optional="True" multiple="True" label="Select references (chromosomes and contigs) you would like to restrict bam to" >
09470ab960f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 1cacd14cfb2429fefa91fdd05c82d2e36d23283a"
iuc
parents:
diff changeset
52 <help><![CDATA[Click and type in the box above to see options. You can select multiple entries.
09470ab960f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 1cacd14cfb2429fefa91fdd05c82d2e36d23283a"
iuc
parents:
diff changeset
53 If "No options available" is displayed, you need to re-detect metadata on the input dataset.
09470ab960f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 1cacd14cfb2429fefa91fdd05c82d2e36d23283a"
iuc
parents:
diff changeset
54 ]]></help>
09470ab960f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 1cacd14cfb2429fefa91fdd05c82d2e36d23283a"
iuc
parents:
diff changeset
55 <options>
09470ab960f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 1cacd14cfb2429fefa91fdd05c82d2e36d23283a"
iuc
parents:
diff changeset
56 <filter type="data_meta" ref="input_bam" key="reference_names" />
09470ab960f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 1cacd14cfb2429fefa91fdd05c82d2e36d23283a"
iuc
parents:
diff changeset
57 </options>
09470ab960f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 1cacd14cfb2429fefa91fdd05c82d2e36d23283a"
iuc
parents:
diff changeset
58 </param>
09470ab960f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 1cacd14cfb2429fefa91fdd05c82d2e36d23283a"
iuc
parents:
diff changeset
59 </inputs>
09470ab960f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 1cacd14cfb2429fefa91fdd05c82d2e36d23283a"
iuc
parents:
diff changeset
60 <outputs>
1
9dbf707bebb0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split_ref commit a14db40361bcb2ee608bccd9222e1654aaea3324-dirty
iuc
parents: 0
diff changeset
61 <collection name="output_bams" type="list">
9dbf707bebb0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split_ref commit a14db40361bcb2ee608bccd9222e1654aaea3324-dirty
iuc
parents: 0
diff changeset
62 <discover_datasets from_provided_metadata="true" ext="bam" visible="false" />
0
09470ab960f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 1cacd14cfb2429fefa91fdd05c82d2e36d23283a"
iuc
parents:
diff changeset
63 </collection>
09470ab960f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 1cacd14cfb2429fefa91fdd05c82d2e36d23283a"
iuc
parents:
diff changeset
64 </outputs>
09470ab960f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 1cacd14cfb2429fefa91fdd05c82d2e36d23283a"
iuc
parents:
diff changeset
65 <tests>
09470ab960f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 1cacd14cfb2429fefa91fdd05c82d2e36d23283a"
iuc
parents:
diff changeset
66 <test>
1
9dbf707bebb0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split_ref commit a14db40361bcb2ee608bccd9222e1654aaea3324-dirty
iuc
parents: 0
diff changeset
67 <param name="input_bam" ftype="bam" value="bamtools-input2.bam" />
9dbf707bebb0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split_ref commit a14db40361bcb2ee608bccd9222e1654aaea3324-dirty
iuc
parents: 0
diff changeset
68 <output_collection name="output_bams" type="list" count="25">
9dbf707bebb0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split_ref commit a14db40361bcb2ee608bccd9222e1654aaea3324-dirty
iuc
parents: 0
diff changeset
69 <element name="bamtools-input2.bam: chrM" file="bamtools_input2.header.bam" ftype="bam" />
9dbf707bebb0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split_ref commit a14db40361bcb2ee608bccd9222e1654aaea3324-dirty
iuc
parents: 0
diff changeset
70 <element name="bamtools-input2.bam: chr1" file="bamtools_input2.chr1" ftype="bam" />
9dbf707bebb0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split_ref commit a14db40361bcb2ee608bccd9222e1654aaea3324-dirty
iuc
parents: 0
diff changeset
71 <element name="bamtools-input2.bam: chr21" file="bamtools_input2.chr21.bam" ftype="bam" />
9dbf707bebb0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split_ref commit a14db40361bcb2ee608bccd9222e1654aaea3324-dirty
iuc
parents: 0
diff changeset
72 </output_collection>
9dbf707bebb0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split_ref commit a14db40361bcb2ee608bccd9222e1654aaea3324-dirty
iuc
parents: 0
diff changeset
73 </test>
9dbf707bebb0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split_ref commit a14db40361bcb2ee608bccd9222e1654aaea3324-dirty
iuc
parents: 0
diff changeset
74 <test>
9dbf707bebb0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split_ref commit a14db40361bcb2ee608bccd9222e1654aaea3324-dirty
iuc
parents: 0
diff changeset
75 <param name="input_bam" ftype="bam" value="bamtools-input2.bam" />
9dbf707bebb0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split_ref commit a14db40361bcb2ee608bccd9222e1654aaea3324-dirty
iuc
parents: 0
diff changeset
76 <param name="refs" value="chrM,chr1,chr21" />
9dbf707bebb0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split_ref commit a14db40361bcb2ee608bccd9222e1654aaea3324-dirty
iuc
parents: 0
diff changeset
77 <output_collection name="output_bams" type="list" count="3">
9dbf707bebb0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split_ref commit a14db40361bcb2ee608bccd9222e1654aaea3324-dirty
iuc
parents: 0
diff changeset
78 <element name="bamtools-input2.bam: chrM" file="bamtools_input2.header.bam" ftype="bam" />
9dbf707bebb0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split_ref commit a14db40361bcb2ee608bccd9222e1654aaea3324-dirty
iuc
parents: 0
diff changeset
79 <element name="bamtools-input2.bam: chr1" file="bamtools_input2.chr1" ftype="bam" />
9dbf707bebb0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split_ref commit a14db40361bcb2ee608bccd9222e1654aaea3324-dirty
iuc
parents: 0
diff changeset
80 <element name="bamtools-input2.bam: chr21" file="bamtools_input2.chr21.bam" ftype="bam" />
0
09470ab960f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 1cacd14cfb2429fefa91fdd05c82d2e36d23283a"
iuc
parents:
diff changeset
81 </output_collection>
09470ab960f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 1cacd14cfb2429fefa91fdd05c82d2e36d23283a"
iuc
parents:
diff changeset
82 </test>
09470ab960f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 1cacd14cfb2429fefa91fdd05c82d2e36d23283a"
iuc
parents:
diff changeset
83 </tests>
09470ab960f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 1cacd14cfb2429fefa91fdd05c82d2e36d23283a"
iuc
parents:
diff changeset
84 <help>
09470ab960f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 1cacd14cfb2429fefa91fdd05c82d2e36d23283a"
iuc
parents:
diff changeset
85 **What is does**
09470ab960f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 1cacd14cfb2429fefa91fdd05c82d2e36d23283a"
iuc
parents:
diff changeset
86
1
9dbf707bebb0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split_ref commit a14db40361bcb2ee608bccd9222e1654aaea3324-dirty
iuc
parents: 0
diff changeset
87 BAMTools split is a utility for splitting BAM files. It is based on the BAMtools suite of tools by Derek Barnett (https://github.com/pezmaster31/bamtools).
0
09470ab960f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 1cacd14cfb2429fefa91fdd05c82d2e36d23283a"
iuc
parents:
diff changeset
88
09470ab960f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 1cacd14cfb2429fefa91fdd05c82d2e36d23283a"
iuc
parents:
diff changeset
89 -----
09470ab960f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 1cacd14cfb2429fefa91fdd05c82d2e36d23283a"
iuc
parents:
diff changeset
90
09470ab960f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 1cacd14cfb2429fefa91fdd05c82d2e36d23283a"
iuc
parents:
diff changeset
91 **How it works**
09470ab960f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 1cacd14cfb2429fefa91fdd05c82d2e36d23283a"
iuc
parents:
diff changeset
92
1
9dbf707bebb0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split_ref commit a14db40361bcb2ee608bccd9222e1654aaea3324-dirty
iuc
parents: 0
diff changeset
93 Split alignments by reference name into a dataset list collection. The collection will be in the same order as the input BAM references and will consist of as many elements as there are references selected or listed in the input BAM header.
0
09470ab960f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 1cacd14cfb2429fefa91fdd05c82d2e36d23283a"
iuc
parents:
diff changeset
94
1
9dbf707bebb0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split_ref commit a14db40361bcb2ee608bccd9222e1654aaea3324-dirty
iuc
parents: 0
diff changeset
95 .. class:: warningmark
0
09470ab960f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 1cacd14cfb2429fefa91fdd05c82d2e36d23283a"
iuc
parents:
diff changeset
96
3
9b520009db81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split commit 862f05b5053f55def8007194a702019418697cb5
iuc
parents: 1
diff changeset
97 In cases of unfinished genomes with very large number of reference sequences (scaffolds) this could generate a collection with thousands (if not millions) of elements.
0
09470ab960f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 1cacd14cfb2429fefa91fdd05c82d2e36d23283a"
iuc
parents:
diff changeset
98
09470ab960f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 1cacd14cfb2429fefa91fdd05c82d2e36d23283a"
iuc
parents:
diff changeset
99 -----
09470ab960f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 1cacd14cfb2429fefa91fdd05c82d2e36d23283a"
iuc
parents:
diff changeset
100
09470ab960f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 1cacd14cfb2429fefa91fdd05c82d2e36d23283a"
iuc
parents:
diff changeset
101 .. class:: infomark
09470ab960f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 1cacd14cfb2429fefa91fdd05c82d2e36d23283a"
iuc
parents:
diff changeset
102
09470ab960f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 1cacd14cfb2429fefa91fdd05c82d2e36d23283a"
iuc
parents:
diff changeset
103 **More information**
09470ab960f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 1cacd14cfb2429fefa91fdd05c82d2e36d23283a"
iuc
parents:
diff changeset
104
09470ab960f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 1cacd14cfb2429fefa91fdd05c82d2e36d23283a"
iuc
parents:
diff changeset
105 Additional information about BAMtools can be found at https://github.com/pezmaster31/bamtools/wiki
09470ab960f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 1cacd14cfb2429fefa91fdd05c82d2e36d23283a"
iuc
parents:
diff changeset
106
09470ab960f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 1cacd14cfb2429fefa91fdd05c82d2e36d23283a"
iuc
parents:
diff changeset
107 </help>
09470ab960f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 1cacd14cfb2429fefa91fdd05c82d2e36d23283a"
iuc
parents:
diff changeset
108 <citations>
09470ab960f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 1cacd14cfb2429fefa91fdd05c82d2e36d23283a"
iuc
parents:
diff changeset
109 <citation type="doi">10.1093/bioinformatics/btr174</citation>
09470ab960f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 1cacd14cfb2429fefa91fdd05c82d2e36d23283a"
iuc
parents:
diff changeset
110 </citations>
09470ab960f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 1cacd14cfb2429fefa91fdd05c82d2e36d23283a"
iuc
parents:
diff changeset
111 </tool>