Mercurial > repos > iuc > pairtools_dedup
view dedup.xml @ 4:55a53b5e308d draft
planemo upload for repository https://github.com/open2c/pairtools commit 162c595b19e442f40be4c2f5434b20b56ade52d4
author | iuc |
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date | Tue, 30 Apr 2024 12:02:29 +0000 |
parents | f8c1d2a93d43 |
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<tool id="pairtools_dedup" name="Pairtools dedup" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@" profile="23.2" license="MIT"> <description>Find and remove PCR/optical duplicates</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ pairtools dedup '$pairs_path' -o '$output_dedup_pairs' #if $output_dups: --output-dups '$output_dups_pairs' #end if $mark_dups #if $output_stats: --output-stats '$dedup_pairs_stats' #end if --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 pairs file" help="Input triu-flipped sorted .pairs or .pairsam file"/> <param argument="--mark-dups" type="boolean" truevalue="--mark-dups" falsevalue="" checked="True" label="Duplicate pairs are marked as DD in pair_type and as a duplicate in the SAM entries"/> <param argument="--output-dups" type="boolean" truevalue="--output-dups" falsevalue="" checked="False" label="Output file for duplicate pairs"/> <param argument="--output-stats" type="boolean" truevalue="--output-stats" falsevalue="" checked="False" label="Output file for duplicate statistics"/> </inputs> <outputs> <data name="output_dedup_pairs" format_source="pairs_path" label="${tool.name} on ${on_string}: Deduplicated Pairs"/> <data name="output_dups_pairs" format_source="pairs_path" label="${tool.name} on ${on_string}: Duplicate Pairs"> <filter>output_dups</filter> </data> <data name="dedup_pairs_stats" format="tabular" label="${tool.name} on ${on_string}: Deduplicated stats"> <filter>output_stats</filter> </data> </outputs> <tests> <!--Test 01 with default parameters--> <test expect_num_outputs="1"> <param name="pairs_path" value="output_sorted_pairs.pairsam"/> <output name="output_dedup_pairs" file="output_dedup_pairs.pairsam" lines_diff="20"/> </test> <!--Test 02 mark_dups enabled and output_dups--> <test expect_num_outputs="2"> <param name="pairs_path" value="output_sorted_pairs.pairsam"/> <param name="mark_dups" value="true"></param> <param name="output_dups" value="true"></param> <output name="output_dedup_pairs" file="output_dedup_pairs_markdups.pairsam" lines_diff="20"/> <output name="output_dups_pairs" file="output_dups_pairs_markdups.pairsam" lines_diff="20"/> </test> <!--Test 03 mark_dups and output_stats enabled--> <test expect_num_outputs="2"> <param name="pairs_path" value="output_sorted_pairs.pairsam"/> <param name="mark_dups" value="true"></param> <param name="output_stats" value="true"></param> <output name="output_dedup_pairs" file="output_dedup_pairs_markdups.pairsam" lines_diff="20"/> <output name="dedup_pairs_stats" file="output_dedup_pairs.stats" lines_diff="20"/> </test> </tests> <help><![CDATA[ **Pairtools dedup** Find PCR/optical duplicates in an upper-triangular flipped sorted pairs/pairsam file. Allow for a +/-N bp mismatch at each side of duplicated molecules. ]]></help> <expand macro="citations"/> <expand macro="creator"/> </tool>