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comparison bedpeToBam.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
comparison
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33:87ee588b3d45 34:dde39ba9c031
1 <tool id="bedtools_bedpetobam" name="bedtools BEDPE to BAM" version="@WRAPPER_VERSION@"> 1 <tool id="bedtools_bedpetobam" name="bedtools BEDPE to BAM" version="@TOOL_VERSION@">
2 <description>converter</description> 2 <description>converter</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 bedpetobam
10 bedtools bedpetobam 10 -mapq $mapq
11 -mapq $mapq 11 -i '$input'
12 -i '$input' 12 -g @GENOME_FILE@
13 -g @GENOME_FILE@ 13 > '$output'
14 > '$output' 14 ]]></command>
15 ]]>
16 </command>
17 <inputs> 15 <inputs>
18 <param name="input" format="bed,gff,vcf" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/> 16 <param name="input" argument="-i" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
19 <expand macro="input_conditional_genome_file" /> 17 <expand macro="input_conditional_genome_file" />
20 <param name="mapq" type="integer" value="255" 18 <param argument="-mapq" type="integer" value="255"
21 label="Set a mapping quality (SAM MAPQ field) value for all BED entries" 19 label="Set a mapping quality (SAM MAPQ field) value for all BED entries" />
22 help="(-mapq)" />
23 </inputs> 20 </inputs>
24 <outputs> 21 <outputs>
25 <data format="bam" name="output" metadata_source="input"/> 22 <data name="output" format="bam" metadata_source="input"/>
26 </outputs> 23 </outputs>
27 <tests> 24 <tests>
28 <test> 25 <test>
29 <param name="input" value="bedpeToBamBed1.bed" ftype="bed" /> 26 <param name="input" value="bedpeToBamBed1.bed" ftype="bed" />
30 <param name="genome_file_opts_selector" value="hist" /> 27 <param name="genome_file_opts_selector" value="hist" />
31 <param name="genome" value="mm9.len"/> 28 <param name="genome" value="mm9.len"/>
32 <output name="output" file="bedpeToBam_result1.bam" lines_diff="72" ftype="bam" /> 29 <output name="output" file="bedpeToBam_result1.bam" lines_diff="72" ftype="bam" />
33 </test> 30 </test>
34 </tests> 31 </tests>
35 <help> 32 <help><![CDATA[
36 <![CDATA[
37 **What it does** 33 **What it does**
38 34
39 Converts feature records to BAM format. 35 Converts feature records to BAM format.
40 36
41 .. class:: warningmark 37 .. class:: warningmark
42 38
43 BED files must be at least BED4 to create BAM (needs name field). 39 BED files must be at least BED4 to create BAM (needs name field).
44 40
45 @REFERENCES@ 41 @REFERENCES@
46 ]]> 42 ]]></help>
47 </help>
48 <expand macro="citations" /> 43 <expand macro="citations" />
49 </tool> 44 </tool>