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comparison bedToBam.xml @ 32:b0d5e752c0c5 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit a78ca56350b1fcf9d7de2a1112155c9bd0844348
author iuc
date Tue, 05 Sep 2017 09:51:56 -0400
parents a2d4c30ba2f9
children ac2040a5e6ff
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31:cb98f29aa1dc 32:b0d5e752c0c5
1 <tool id="bedtools_bedtobam" name="BED to BAM" version="@WRAPPER_VERSION@.0"> 1 <tool id="bedtools_bedtobam" name="BED to BAM" version="@WRAPPER_VERSION@.1">
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" />
8 <command> 8 <command>
9 <![CDATA[ 9 <![CDATA[
10 bedtools bedtobam 10 bedtools bedtobam
11 $bed12 11 $bed12
12 -mapq $mapq 12 -mapq $mapq
13 -g $genome 13 -g @GENOME_FILE@
14 -i '$input' 14 -i '$input'
15 > '$output' 15 > '$output'
16 ]]> 16 ]]>
17 </command> 17 </command>
18 <inputs> 18 <inputs>
19 <param format="bed" name="input" type="data" label="Convert the following BED file to BAM"/> 19 <param format="bed" name="input" type="data" label="Convert the following BED file to BAM"/>
20 <param name="bed12" type="boolean" truevalue="-bed12" falsevalue="" checked="false" 20 <param name="bed12" type="boolean" truevalue="-bed12" falsevalue="" checked="false"
21 label="Indicate that the input BED file is in BED12 (a.k.a 'blocked' BED) format" 21 label="Indicate that the input BED file is in BED12 (a.k.a 'blocked' BED) format"
22 help="If Selected, bedToBam will convert blocked BED features (e.g., gene annotaions) into 'spliced' BAM alignments by creating an appropriate CIGAR string. (-bed12)"/> 22 help="If Selected, bedToBam will convert blocked BED features (e.g., gene annotaions) into 'spliced' BAM alignments by creating an appropriate CIGAR string. (-bed12)"/>
23 <expand macro="genome" /> 23 <expand macro="input_conditional_genome_file" />
24 <param name="mapq" type="integer" value="255" 24 <param name="mapq" type="integer" value="255"
25 label="Set a mapping quality (SAM MAPQ field) value for all BED entries" help="(-mapq)"/> 25 label="Set a mapping quality (SAM MAPQ field) value for all BED entries" help="(-mapq)"/>
26 </inputs> 26 </inputs>
27 <outputs> 27 <outputs>
28 <data format="bam" name="output" metadata_source="input" label="${input.name} (as BAM)"/> 28 <data format="bam" name="output" metadata_source="input" label="${input.name} (as BAM)"/>
29 </outputs> 29 </outputs>
30 <tests> 30 <tests>
31 <test> 31 <test>
32 <param name="input" value="bedToBam1.bed" ftype="bed" /> 32 <param name="input" value="bedToBam1.bed" ftype="bed" />
33 <param name="genome_file_opts_selector" value="hist" />
33 <param name="genome" value="mm9_chr1.len" ftype="tabular" /> 34 <param name="genome" value="mm9_chr1.len" ftype="tabular" />
34 <output name="output" file="bedToBam_result.bam" lines_diff="4" ftype="bam" /> 35 <output name="output" file="bedToBam_result.bam" lines_diff="4" ftype="bam" />
35 </test> 36 </test>
36 </tests> 37 </tests>
37 <help> 38 <help>