Mercurial > repos > iuc > bedtools
view bedpeToBam.xml @ 34:dde39ba9c031 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
author | iuc |
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date | Mon, 29 Apr 2019 05:55:48 -0400 |
parents | 4f7a5ccd2ae9 |
children | b28e0cfa7ba1 |
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<tool id="bedtools_bedpetobam" name="bedtools BEDPE to BAM" version="@TOOL_VERSION@"> <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" argument="-i" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/> <expand macro="input_conditional_genome_file" /> <param argument="-mapq" type="integer" value="255" label="Set a mapping quality (SAM MAPQ field) value for all BED entries" /> </inputs> <outputs> <data name="output" format="bam" 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>