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annotate bamtools_split_ref.xml @ 3:9b520009db81 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split commit 862f05b5053f55def8007194a702019418697cb5
author iuc
date Fri, 13 Jan 2023 12:17:49 +0000
parents 9dbf707bebb0
children 9b8feb118f9e
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9b520009db81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split commit 862f05b5053f55def8007194a702019418697cb5
iuc
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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
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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"
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3 <macros>
09470ab960f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 1cacd14cfb2429fefa91fdd05c82d2e36d23283a"
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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>
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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6 <expand macro="requirements">
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7 <requirement type="package" version="1.16.1">samtools</requirement>
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8 </expand>
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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9 <command><![CDATA[
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10 ln -s '${input_bam}' localbam.bam &&
9dbf707bebb0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split_ref commit a14db40361bcb2ee608bccd9222e1654aaea3324-dirty
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11 ln -s '${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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12 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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13 bamtools split -reference
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14 -in localbam.bam
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15 -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
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16 && (IFS=',';
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17 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
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18 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
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19 if [ ! -f \$FN ]; then cp header.bam "\$FN"; fi;
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20 done)
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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21 && 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
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22 ]]></command>
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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23 <environment_variables>
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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24 <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
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25 ## 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
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26 #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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27 #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
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28 #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
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29 ## sort the selected refs by their order in the bam metadata
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30 #echo ','.join([r for r in $ref_list if r in refs_selected])
9dbf707bebb0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split_ref commit a14db40361bcb2ee608bccd9222e1654aaea3324-dirty
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31 #else
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32 #echo ','.join($ref_list)
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33 #end if
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34 </environment_variable>
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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35 </environment_variables>
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36 <configfiles>
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37 <configfile name="c1">#import re
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38 ## need to extract ref names from Galaxy's safe string representation
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39 #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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40 #if str($refs) != 'None'
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41 #set $refs_selected = set(str($refs).split(","))
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42 #set $ref_list = [r for r in $ref_list if r in refs_selected]
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43 #end if
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44 #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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45 #import json
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46 #echo json.dumps({'output_bams': {'elements': $elems}})</configfile>
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47 </configfiles>
0
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48 <inputs>
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49 <param name="input_bam" type="data" format="bam" label="BAM dataset to split by reference"/>
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50 <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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51 <help><![CDATA[Click and type in the box above to see options. You can select multiple entries.
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52 If "No options available" is displayed, you need to re-detect metadata on the input dataset.
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53 ]]></help>
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54 <options>
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55 <filter type="data_meta" ref="input_bam" key="reference_names" />
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56 </options>
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57 </param>
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58 </inputs>
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59 <outputs>
1
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60 <collection name="output_bams" type="list">
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61 <discover_datasets from_provided_metadata="true" ext="bam" visible="false" />
0
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62 </collection>
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63 </outputs>
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64 <tests>
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65 <test>
1
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66 <param name="input_bam" ftype="bam" value="bamtools-input2.bam" />
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67 <output_collection name="output_bams" type="list" count="25">
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68 <element name="bamtools-input2.bam: chrM" file="bamtools_input2.header.bam" ftype="bam" />
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69 <element name="bamtools-input2.bam: chr1" file="bamtools_input2.chr1" ftype="bam" />
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70 <element name="bamtools-input2.bam: chr21" file="bamtools_input2.chr21.bam" ftype="bam" />
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71 </output_collection>
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72 </test>
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73 <test>
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74 <param name="input_bam" ftype="bam" value="bamtools-input2.bam" />
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75 <param name="refs" value="chrM,chr1,chr21" />
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76 <output_collection name="output_bams" type="list" count="3">
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77 <element name="bamtools-input2.bam: chrM" file="bamtools_input2.header.bam" ftype="bam" />
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78 <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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79 <element name="bamtools-input2.bam: chr21" file="bamtools_input2.chr21.bam" ftype="bam" />
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80 </output_collection>
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81 </test>
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82 </tests>
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83 <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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84 **What is does**
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85
1
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86 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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87
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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
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 **How it works**
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91
1
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92 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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93
1
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94 .. class:: warningmark
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95
3
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96 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.
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97
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98 -----
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99
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100 .. class:: infomark
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101
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102 **More information**
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103
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104 Additional information about BAMtools can be found at https://github.com/pezmaster31/bamtools/wiki
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105
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106 </help>
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107 <citations>
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108 <citation type="doi">10.1093/bioinformatics/btr174</citation>
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109 </citations>
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110 </tool>