Mercurial > repos > iuc > pairtools_split
view split.xml @ 4:39df08e91cdf draft default tip
planemo upload for repository https://github.com/open2c/pairtools commit 13aa776596c927adff29d936740ac80f0e37375d
author | iuc |
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date | Tue, 21 May 2024 16:04:49 +0000 |
parents | bffcba7ce9b5 |
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<tool id="pairtools_split" name="Pairtools split" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@" profile="23.2" license="MIT"> <description>Split a pairsam file into pairs and SAM/BAM</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ pairtools split '$pairsam_path' --output-pairs '$output_pairs' --output-sam ./output.bam --nproc-in \${GALAXY_SLOTS:-4} --nproc-out \${GALAXY_SLOTS:-4} ]]></command> <inputs> <param name="pairsam_path" type="data" format="4dn_pairsam" label="Input 4dn pairsam file"/> </inputs> <outputs> <data name="output_pairs" format="4dn_pairs" label="${tool.name} on ${on_string}: Output Pairs" /> <data name="output_file" format="qname_sorted.bam" from_work_dir="output.bam" label="${tool.name} on ${on_string}: Output BAM" /> </outputs> <tests> <!--Test default parameters--> <test expect_num_outputs="2"> <param name="pairsam_path" value="output_dedup_pairs_markdups.pairsam"/> <output name="output_pairs" ftype="4dn_pairs" file="output_pairs_split.pairs" lines_diff="10"/> <output name="output_file" ftype="qname_sorted.bam" file="output_pairs_split.bam" lines_diff="20"/> </test> </tests> <help><![CDATA[ **Pairtools split** Restore a SAM/BAM file from SAM1 and SAM2 fields of a `pairsam` file. Create a `pairs` file without SAM1/SAM2 fields. ]]></help> <expand macro="citations"/> <expand macro="creator"/> </tool>