Mercurial > repos > iuc > bedtools
view bedpeToBam.xml @ 27:a33db97b220c draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 1ec398a9421f016b852fe59d46961c12321ee5c8
author | iuc |
---|---|
date | Tue, 15 May 2018 14:52:10 -0400 |
parents | 95a3b2c25bd1 |
children | 4f7a5ccd2ae9 |
line wrap: on
line source
<tool id="bedtools_bedpetobam" name="BEDPE to BAM" version="@WRAPPER_VERSION@.0"> <description>converter</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements" /> <expand macro="stdio" /> <command> <![CDATA[ bedtools bedpetobam -mapq $mapq -i '$input' -g @GENOME_FILE@ > '$output' ]]> </command> <inputs> <param name="input" format="bed,gff,vcf" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/> <expand macro="input_conditional_genome_file" /> <param name="mapq" type="integer" value="255" label="Set a mapping quality (SAM MAPQ field) value for all BED entries" help="(-mapq)" /> </inputs> <outputs> <data format="bam" name="output" metadata_source="input"/> </outputs> <tests> <test> <param name="input" value="bedpeToBamBed1.bed" ftype="bed" /> <param name="genome_file_opts_selector" value="hist" /> <param name="genome" value="mm9.len"/> <output name="output" file="bedpeToBam_result1.bam" lines_diff="72" ftype="bam" /> </test> </tests> <help> <![CDATA[ **What it does** Converts feature records to BAM format. .. class:: warningmark BED files must be at least BED4 to create BAM (needs name field). @REFERENCES@ ]]> </help> <expand macro="citations" /> </tool>