Mercurial > repos > iuc > pairtools_sort
view sort.xml @ 4:8cffb8fc34f0 draft
planemo upload for repository https://github.com/open2c/pairtools commit edb9fd7a6734203070b623876e76ce4a0a164ed9
author | iuc |
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date | Tue, 16 Apr 2024 12:50:39 +0000 |
parents | 9179bf8f4ae1 |
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<tool id="pairtools_sort" name="Pairtools sort" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@" profile="23.2" license="MIT"> <description>Sort a 4dn pairs/pairsam file</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ pairtools sort '$pairs_path' -o '$output_sorted_pairs' --nproc-in \${GALAXY_SLOTS:-4} --nproc-out \${GALAXY_SLOTS:-4} ]]></command> <inputs> <param name="pairs_path" type="data" format="4dn_pairs,4dn_pairsam" label="Input file" help="Input a 4dn pairs or pairsam file"/> </inputs> <outputs> <data name="output_sorted_pairs" format_source="pairs_path" label="${tool.name} on ${on_string}"> </data> </outputs> <tests> <!--Test default parameters with pairs file--> <test expect_num_outputs="1"> <param name="pairs_path" value="output_parsed_pairs_bam.pairs"/> <output name="output_sorted_pairs" file="output_sorted_pairs.pairs" lines_diff="10"/> </test> <!--Test default parameters with pairsam file--> <test expect_num_outputs="1"> <param name="pairs_path" value="output_dedup_pairs_markdups.pairsam"/> <output name="output_sorted_pairs" file="output_dedup_sorted.pairsam" lines_diff="10"/> </test> </tests> <help><![CDATA[ **Pairtools sort** Sort pairs in the lexicographic order along chrom1 and chrom2, in the numeric order along pos1 and pos2 and in the lexicographic order along pair_type. ]]></help> <expand macro="citations"/> <expand macro="creator"/> </tool>