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comparison bedToBam.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 3e38c9b3214f
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33:87ee588b3d45 34:dde39ba9c031
1 <tool id="bedtools_bedtobam" name="bedtools BED to BAM" version="@WRAPPER_VERSION@"> 1 <tool id="bedtools_bedtobam" name="bedtools BED 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 bedtobam
10 bedtools bedtobam 10 $bed12
11 $bed12 11 -mapq $mapq
12 -mapq $mapq 12 -g @GENOME_FILE@
13 -g @GENOME_FILE@ 13 -i '$input'
14 -i '$input' 14 > '$output'
15 > '$output' 15 ]]></command>
16 ]]>
17 </command>
18 <inputs> 16 <inputs>
19 <param format="bed" name="input" type="data" label="Convert the following BED file to BAM"/> 17 <param name="input" argument="-i" type="data" format="bed" label="Convert the following BED file to BAM"/>
20 <param name="bed12" type="boolean" truevalue="-bed12" falsevalue="" checked="false" 18 <param argument="-bed12" type="boolean" truevalue="-bed12" falsevalue="" checked="false"
21 label="Indicate that the input BED file is in BED12 (a.k.a 'blocked' BED) format" 19 label="Indicate that the input BED file is in BED12 (a.k.a 'blocked' BED) format"
22 help="If Selected, bedToBam will convert blocked BED features (e.g., gene annotaions) into 'spliced' BAM alignments by creating an appropriate CIGAR string. (-bed12)"/> 20 help="If Selected, bedToBam will convert blocked BED features (e.g., gene annotaions) into 'spliced' BAM alignments by creating an appropriate CIGAR string"/>
23 <expand macro="input_conditional_genome_file" /> 21 <expand macro="input_conditional_genome_file" />
24 <param name="mapq" type="integer" value="255" 22 <param argument="-mapq" type="integer" value="255"
25 label="Set a mapping quality (SAM MAPQ field) value for all BED entries" help="(-mapq)"/> 23 label="Set a mapping quality (SAM MAPQ field) value for all BED entries" />
26 </inputs> 24 </inputs>
27 <outputs> 25 <outputs>
28 <data format="bam" name="output" metadata_source="input" label="${input.name} (as BAM)"/> 26 <data name="output" format="bam" metadata_source="input" label="${input.name} (as BAM)"/>
29 </outputs> 27 </outputs>
30 <tests> 28 <tests>
31 <test> 29 <test>
32 <param name="input" value="bedToBam1.bed" ftype="bed" /> 30 <param name="input" value="bedToBam1.bed" ftype="bed" />
33 <param name="genome_file_opts_selector" value="hist" /> 31 <param name="genome_file_opts_selector" value="hist" />
34 <param name="genome" value="mm9_chr1.len" ftype="tabular" /> 32 <param name="genome" value="mm9_chr1.len" ftype="tabular" />
35 <output name="output" file="bedToBam_result.bam" lines_diff="4" ftype="bam" /> 33 <output name="output" file="bedToBam_result.bam" lines_diff="4" ftype="bam" />
36 </test> 34 </test>
37 </tests> 35 </tests>
38 <help> 36 <help><![CDATA[
39 <![CDATA[
40 **What it does** 37 **What it does**
41 38
42 bedToBam converts features in a feature file to BAM format. This is useful as an efficient means of storing large genome annotations in a compact, indexed format for visualization purposes. 39 bedToBam converts features in a feature file to BAM format. This is useful as an efficient means of storing large genome annotations in a compact, indexed format for visualization purposes.
43 40
44 @REFERENCES@ 41 @REFERENCES@
45 ]]> 42 ]]></help>
46 </help>
47 <expand macro="citations" /> 43 <expand macro="citations" />
48 </tool> 44 </tool>