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comparison tagBed.xml @ 34:dde39ba9c031 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
author iuc
date Mon, 29 Apr 2019 05:55:48 -0400
parents 4f7a5ccd2ae9
children b28e0cfa7ba1
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33:87ee588b3d45 34:dde39ba9c031
1 <tool id="bedtools_tagbed" name="bedtools TagBed" version="@WRAPPER_VERSION@"> 1 <tool id="bedtools_tagbed" name="bedtools TagBed" version="@TOOL_VERSION@+galaxy1">
2 <description>tag BAM alignments based on overlaps with interval files</description> 2 <description>tag BAM alignments based on overlaps with interval files</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 <expand macro="stdio" /> 7 <expand macro="stdio" />
8 <command> 8 <command><![CDATA[
9 <![CDATA[ 9 bedtools tag
10 #set files = '" "'.join( [ str( $file ) for $file in $inputB ] ) 10 -i '${inputA}'
11 bedtools tag 11 -files
12 -i "${inputA}" 12 #for $file in $inputB
13 -files "${files}" 13 '$file'
14 -f $overlap 14 #end for
15 $strand 15 @OVERLAP@
16 -tag "${tag}" 16 $strand
17 $field 17 -tag '${tag}'
18 > "${output}" 18 $field
19 ]]> 19 > '${output}'
20 </command> 20 ]]></command>
21 <inputs> 21 <inputs>
22 <param name="inputA" format="bam" type="data" label="BAM file"/> 22 <param name="inputA" argument="-i" type="data" format="bam" label="BAM file"/>
23 <param name="inputB" format="@STD_BEDTOOLS_INPUTS@" multiple="True" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file" /> 23 <param name="inputB" argument="-files" type="data" format="@STD_BEDTOOLS_INPUTS@" multiple="true" label="@STD_BEDTOOLS_INPUT_LABEL@ file" />
24 <expand macro="strand2" /> 24 <expand macro="strand2" />
25 <expand macro="overlap" /> 25 <expand macro="overlap" fracof="the alignment"/>
26 <param name="tag" type="text" value="YB" label="Specify the tag to use" /> 26 <param argument="-tag" type="text" value="YB" label="Specify the tag to use" />
27 <param name="field" type="select" label="Field from the annotation files to populate tags?"> 27 <param name="field" type="select" label="Field from the annotation files to populate tags?">
28 <option value="-labels" selected="True">Labels</option> 28 <option value="-labels" selected="true">Labels</option>
29 <option value="-scores">Scores</option> 29 <option value="-scores">Scores</option>
30 <option value="-names">Names</option> 30 <option value="-names">Names</option>
31 <option value="-labels -intervals">Intervals</option> 31 <option value="-labels -intervals">Intervals</option>
32 </param> 32 </param>
33 </inputs> 33 </inputs>
34 <outputs> 34 <outputs>
35 <data format="bam" name="output"/> 35 <data name="output" format="bam" />
36 </outputs> 36 </outputs>
37 <tests> 37 <tests>
38 <test> 38 <test>
39 <param name="inputA" value="srma_in3.bam" ftype="bam" /> 39 <param name="inputA" value="srma_in3.bam" ftype="bam" />
40 <param name="inputB" value="tagBed1.bed" ftype="bed" /> 40 <param name="inputB" value="tagBed1.bed" ftype="bed" />
41 <param name="field" value="-names" /> 41 <param name="field" value="-names" />
42 <output name="output" file="tagBed_result1.bam" ftype="bam" /> 42 <output name="output" file="tagBed_result1.bam" ftype="bam" />
43 </test> 43 </test>
44 </tests> 44 </tests>
45 <help> 45 <help><![CDATA[
46 <![CDATA[
47 **What it does** 46 **What it does**
48 47
49 Annotates a BAM file based on overlaps with multiple @STD_BEDTOOLS_INPUT_LABEL@ files on the intervals in an input bam file 48 Annotates a BAM file based on overlaps with multiple @STD_BEDTOOLS_INPUT_LABEL@ files on the intervals in an input bam file
50 49
51 @REFERENCES@ 50 @REFERENCES@
52 ]]> 51 ]]></help>
53 </help>
54 <expand macro="citations" /> 52 <expand macro="citations" />
55 </tool> 53 </tool>