Mercurial > repos > iuc > bamtools_split_ref

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split commit 7d29261847d2514a1ac4246e0b8bff1d32463434
author iuc
date Wed, 11 Feb 2026 14:31:36 +0000
parents 9b8feb118f9e
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5
f66e109710bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split commit 7d29261847d2514a1ac4246e0b8bff1d32463434
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1 <tool id="bamtools_split_ref" name="Split BAM by reference" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
3
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2 <description>into a dataset list collection</description>
0
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3 <macros>
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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"
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5 </macros>
4
9b8feb118f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split commit 5ebe920838ab3c36e93d620c479df17f43f8e336
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6 <expand macro="xrefs"/>
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7 <expand macro="requirements"/>
1
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8 <command><![CDATA[
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9 ln -s '${input_bam}' localbam.bam &&
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10 ln -s '${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
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11 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
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12 bamtools split -reference
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13 -in localbam.bam
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14 -stub split_bam
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15 && (IFS=',';
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16 for i in \$REFS_FROM_BAM_METADATA;
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17 do FN=`printf "split_bam.REF_%s.bam" "\$i"`;
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18 if [ ! -f \$FN ]; then cp header.bam "\$FN"; fi;
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19 done)
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20 && cp '$c1' galaxy.json
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21 ]]></command>
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22 <environment_variables>
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23 <environment_variable name="REFS_FROM_BAM_METADATA">#import re
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24 ## need to extract ref names from Galaxy's safe string representation
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25 #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
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26 #if str($refs) != 'None'
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27 #set $refs_selected = set(str($refs).split(","))
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28 ## sort the selected refs by their order in the bam metadata
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29 #echo ','.join([r for r in $ref_list if r in refs_selected])
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30 #else
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31 #echo ','.join($ref_list)
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32 #end if
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33 </environment_variable>
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34 </environment_variables>
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35 <configfiles>
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36 <configfile name="c1"><![CDATA[#import re
1
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37 ## need to extract ref names from Galaxy's safe string representation
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38 #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(',')]
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39 #if str($refs) != 'None'
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40 #set $refs_selected = set(str($refs).split(","))
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41 #set $ref_list = [r for r in $ref_list if r in refs_selected]
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42 #end if
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43 #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]
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44 #import json
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45 #echo json.dumps({'output_bams': {'elements': $elems}})]]></configfile>
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46 </configfiles>
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47 <inputs>
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48 <param name="input_bam" type="data" format="bam" label="BAM dataset to split by reference"/>
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49 <param name="refs" type="select" optional="True" multiple="True" label="Select references (chromosomes and contigs) you would like to restrict bam to" >
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50 <help><![CDATA[Click and type in the box above to see options. You can select multiple entries.
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51 If "No options available" is displayed, you need to re-detect metadata on the input dataset.
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52 ]]></help>
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53 <options>
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54 <filter type="data_meta" ref="input_bam" key="reference_names" />
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55 </options>
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56 </param>
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57 </inputs>
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58 <outputs>
1
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59 <collection name="output_bams" type="list">
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60 <discover_datasets from_provided_metadata="true" ext="bam" visible="false" />
0
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61 </collection>
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62 </outputs>
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63 <tests>
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64 <test>
1
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65 <param name="input_bam" ftype="bam" value="bamtools-input2.bam" />
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66 <output_collection name="output_bams" type="list" count="25">
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67 <element name="bamtools-input2.bam: chrM" file="bamtools_input2.header.bam" ftype="bam" />
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68 <element name="bamtools-input2.bam: chr1" file="bamtools_input2.chr1" ftype="bam" />
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69 <element name="bamtools-input2.bam: chr21" file="bamtools_input2.chr21.bam" ftype="bam" />
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70 </output_collection>
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71 </test>
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72 <test>
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73 <param name="input_bam" ftype="bam" value="bamtools-input2.bam" />
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74 <param name="refs" value="chrM,chr1,chr21" />
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75 <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
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76 <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
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77 <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
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78 <element name="bamtools-input2.bam: chr21" file="bamtools_input2.chr21.bam" ftype="bam" />
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09470ab960f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 1cacd14cfb2429fefa91fdd05c82d2e36d23283a"
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79 </output_collection>
09470ab960f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 1cacd14cfb2429fefa91fdd05c82d2e36d23283a"
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80 </test>
09470ab960f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 1cacd14cfb2429fefa91fdd05c82d2e36d23283a"
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81 </tests>
09470ab960f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 1cacd14cfb2429fefa91fdd05c82d2e36d23283a"
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82 <help>
09470ab960f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 1cacd14cfb2429fefa91fdd05c82d2e36d23283a"
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83 **What is does**
09470ab960f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 1cacd14cfb2429fefa91fdd05c82d2e36d23283a"
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84
1
9dbf707bebb0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split_ref commit a14db40361bcb2ee608bccd9222e1654aaea3324-dirty
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85 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
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86
09470ab960f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 1cacd14cfb2429fefa91fdd05c82d2e36d23283a"
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87 -----
09470ab960f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 1cacd14cfb2429fefa91fdd05c82d2e36d23283a"
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88
09470ab960f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 1cacd14cfb2429fefa91fdd05c82d2e36d23283a"
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89 **How it works**
09470ab960f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 1cacd14cfb2429fefa91fdd05c82d2e36d23283a"
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90
1
9dbf707bebb0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split_ref commit a14db40361bcb2ee608bccd9222e1654aaea3324-dirty
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91 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.
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09470ab960f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 1cacd14cfb2429fefa91fdd05c82d2e36d23283a"
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92
1
9dbf707bebb0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split_ref commit a14db40361bcb2ee608bccd9222e1654aaea3324-dirty
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93 .. class:: warningmark
0
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94
3
9b520009db81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split commit 862f05b5053f55def8007194a702019418697cb5
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95 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
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96
09470ab960f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 1cacd14cfb2429fefa91fdd05c82d2e36d23283a"
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97 -----
09470ab960f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 1cacd14cfb2429fefa91fdd05c82d2e36d23283a"
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98
09470ab960f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 1cacd14cfb2429fefa91fdd05c82d2e36d23283a"
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99 .. class:: infomark
09470ab960f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 1cacd14cfb2429fefa91fdd05c82d2e36d23283a"
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100
09470ab960f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 1cacd14cfb2429fefa91fdd05c82d2e36d23283a"
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101 **More information**
09470ab960f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 1cacd14cfb2429fefa91fdd05c82d2e36d23283a"
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102
09470ab960f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 1cacd14cfb2429fefa91fdd05c82d2e36d23283a"
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103 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"
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104
09470ab960f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 1cacd14cfb2429fefa91fdd05c82d2e36d23283a"
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105 </help>
09470ab960f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 1cacd14cfb2429fefa91fdd05c82d2e36d23283a"
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106 <citations>
09470ab960f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 1cacd14cfb2429fefa91fdd05c82d2e36d23283a"
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107 <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"
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108 </citations>
09470ab960f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 1cacd14cfb2429fefa91fdd05c82d2e36d23283a"
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109 </tool>