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comparison sambamba.xml @ 3:de833cc76a8e draft default tip

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 1b6bff4ab8aaac8a247f603648f63bbadb02e1fe"
author artbio
date Thu, 30 Dec 2021 17:44:31 +0000
parents 7ad3484aa5db
children
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2:7ad3484aa5db 3:de833cc76a8e
1 <tool id="sambamba_sample_or_filter" name="Sample or Filter BAM" version="0.7.1+galaxy0"> 1 <tool id="sambamba_sample_or_filter" name="Sample, Slice or Filter BAM" version="0.7.1+galaxy1">
2 <description> 2 <description>
3 on flags, fields, and tags using Sambamba 3 on flags, fields, and tags using Sambamba
4 </description> 4 </description>
5 <requirements> 5 <requirements>
6 <requirement type="package" version="0.7.1">sambamba</requirement> 6 <requirement type="package" version="0.7.1">sambamba</requirement>
24 #else if $sambamba_options.selector == 'sample' 24 #else if $sambamba_options.selector == 'sample'
25 sambamba view -h -t \${GALAXY_SLOTS:-4} -f '$sambamba_options.format' 25 sambamba view -h -t \${GALAXY_SLOTS:-4} -f '$sambamba_options.format'
26 --subsampling-seed='$sambamba_options.seed' 26 --subsampling-seed='$sambamba_options.seed'
27 -s '$sambamba_options.fraction' 27 -s '$sambamba_options.fraction'
28 -o '$outfile' input.bam 28 -o '$outfile' input.bam
29 29 #end if
30 #else 30
31 sambamba slice -o '$outfile' input.bam $sambamba_options.region 31 #if $sambamba_options.selector == 'slice'
32 #if $sambamba_options.slice.slice_format == 'text'
33 sambamba slice -o '$outfile' input.bam $sambamba_options.slice.region
34 #else
35 sambamba slice --regions $sambamba_options.slice.bed_file -o '$outfile' input.bam
36 #end if
32 #end if 37 #end if
33 ]]></command> 38 ]]></command>
34 <inputs> 39 <inputs>
35 <param name="input" type="data" format="bam" label="BAM or SAM input file(s)"/> 40 <param name="input" type="data" format="bam" label="BAM or SAM input file(s)"/>
36 <conditional name="sambamba_options"> 41 <conditional name="sambamba_options">
62 </help> 67 </help>
63 </param> 68 </param>
64 </when> 69 </when>
65 70
66 <when value="slice"> 71 <when value="slice">
67 <param name="region" type="text" size="40" label="Region in format chr:beg-end"> 72 <conditional name="slice">
68 <help> 73 <param name="slice_format" type="select" label="specify in text field or a bed file">
69 Regions can be specified as 'chr2' (the whole chr2), 'chr2:1000000' 74 <option value="text">Specify in the region field</option>
70 (region starting from 1,000,000bp) or 'chr2:1,000,000-2,000,000' 75 <option value="bed" selected="true">BED file</option>
71 (region between 1,000,000 and 2,000,000bp including the end points). 76 </param>
72 The coordinates are 1-based. NOTE that sambamba slice only outputs 77 <when value="bed">
73 BAM-format datasets. 78 <param name="bed_file" type="data" format="bed" label="BED file"
74 </help> 79 help="The coordinates are 0-based. NOTE that sambamba slice only outputs BAM-format datasets."/>
75 </param> 80 </when>
81 <when value="text">
82 <param name="region" type="text" size="40" label="Region(s) in space-separated format chr:start-end">
83 <help>
84 Regions can be specified as 'chr2' (the whole chr2), 'chr2:1000000'
85 (region starting from 1,000,000bp) or 'chr2:1,000,000-2,000,000'
86 (region between 1,000,000 and 2,000,000bp including the end points).
87 The coordinates are 1-based. NOTE that sambamba slice only outputs
88 BAM-format datasets.
89 </help>
90 </param>
91 </when>
92 </conditional>
76 </when> 93 </when>
77 94
78 <when value="sample"> 95 <when value="sample">
79 <param name="format" type="select" label="format of the tool output"> 96 <param name="format" type="select" label="format of the tool output">
80 <option value="bam">BAM</option> 97 <option value="bam">BAM</option>
129 <output name="outfile" file="c1215_fixmate_region-filtered.sam" ftype="sam" lines_diff="2"/> 146 <output name="outfile" file="c1215_fixmate_region-filtered.sam" ftype="sam" lines_diff="2"/>
130 </test> 147 </test>
131 <test> 148 <test>
132 <param name="input" value="c1215_fixmate.bam" ftype="bam" /> 149 <param name="input" value="c1215_fixmate.bam" ftype="bam" />
133 <param name="selector" value="slice" /> 150 <param name="selector" value="slice" />
151 <param name="slice_format" value="text" />
134 <param name="query" value='' /> 152 <param name="query" value='' />
135 <param name="region" value="AL096846:1000-2000 AL096846:4000-5000" /> 153 <param name="region" value="AL096846:1000-2000 AL096846:4000-5000" />
154 <output name="outfile" file="c1215_fixmate_region-sliced.bam" ftype="bam"/>
155 </test>
156 <test>
157 <param name="input" value="c1215_fixmate.bam" ftype="bam" />
158 <param name="selector" value="slice" />
159 <param name="slice_format" value="bed" />
160 <param name="query" value='' />
161 <param name="bed_file" value="regions.bed" />
136 <output name="outfile" file="c1215_fixmate_region-sliced.bam" ftype="bam"/> 162 <output name="outfile" file="c1215_fixmate_region-sliced.bam" ftype="bam"/>
137 </test> 163 </test>
138 <test> 164 <test>
139 <param name="input" value="ex1_header.sam" ftype="sam" /> 165 <param name="input" value="ex1_header.sam" ftype="sam" />
140 <param name="selector" value="sample" /> 166 <param name="selector" value="sample" />