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author | rnateam |
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date | Sat, 19 Aug 2023 05:37:02 +0000 |
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children | 3fd3be28a04c |
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<tool id="cmsearch_deoverlap" name="CMsearch deoverlap" version="0.08+galaxy0" profile="21.05"> <description>removes lower scoring overlaps from cmsearch results</description> <requirements> <requirement type="package" version="5.26">perl</requirement> </requirements> <command><![CDATA[ ln -s '$clan_information' clan_info && ln -s '$cmsearch_matches' cmsearch_matches && LC_ALL=C perl '$__tool_directory__/cmsearch-deoverlap.pl' --clanin clan_info cmsearch_matches #if $maxkeep: $maxkeep #end if #if $dirty: $dirty && mv *.sort '$matches_sort' #end if && mv *.deoverlapped '$deoverlapped_matches' ]]></command> <inputs> <param name="clan_information" type="data" format="txt" label="Clan information" help="Each row in the file contains an RNA clan and its corresponding family members"/> <param name="cmsearch_matches" type="data" format="tabular" label="The tabular result file from cmsearch"/> <param argument="--maxkeep" type="boolean" truevalue="--maxkeep" falsevalue="" label="Keep hits that only overlap with other hits that are not kept" help="If this option is not set, all hits with higher scoring overlap will be removed." /> <param argument="--dirty" type="boolean" truevalue="--dirty" falsevalue="" label="Keep the intermediate sorted tblout file"/> </inputs> <outputs> <data name="deoverlapped_matches" format="tabular" label="Deoverlapped matches" /> <data name="matches_sort" format="tabular" label="Sorted matches"> <filter>dirty</filter> </data> </outputs> <tests> <test expect_num_outputs="2"> <param name="clan_information" value="ribo.claninfo" /> <param name="cmsearch_matches" value="1.cmsearch.tblout" /> <param name="dirty" value="--dirty"/> <output name="deoverlapped_matches" file="1.cmsearch.tblout.deoverlapped" /> <output name="matches_sort" file="1.cmsearch.tblout.sort" /> </test> <test expect_num_outputs="1"> <param name="clan_information" value="ribo.claninfo" /> <param name="cmsearch_matches" value="1.cmsearch.tblout" /> <param name="dirty" value=""/> <output name="deoverlapped_matches" file="1.cmsearch.tblout.deoverlapped" /> </test> </tests> <help><![CDATA[ .. class:: infomark **What this tool does** This tool removes lower-scoring overlaps from cmsearch results. Given information about the clans and the cmsearch tbl output this tool returns a filtered cmsearch tbl output. **clan.info:** CL00111 SSU_rRNA_bacteria SSU_rRNA_archaea SSU_rRNA_eukarya SSU_rRNA_microsporidia SSU_trypano_mito CL00112 LSU_rRNA_archaea LSU_rRNA_bacteria LSU_rRNA_eukarya LSU_trypano_mito 5_8S_rRNA CL99999 5S_rRNA mtPerm-5S **cmsearch.tblout:** contig--2249925 - SSU_rRNA_bacteria RF00177 hmm 19 914 2 898 + - 6 0.50 5.7 638.4 1.1e-189 ! - contig--2255364 - SSU_rRNA_bacteria RF00177 hmm 325 1084 765 1 - - 6 0.52 3.9 624.0 2.5e-185 ! - contig--2369838 - SSU_rRNA_bacteria RF00177 hmm 90 938 20 855 + - 6 0.52 7.0 609.3 6.6e-181 ! - contig--2271497 - SSU_rRNA_bacteria RF00177 hmm 4 812 835 2 - - 6 0.51 5.0 597.5 2.5e-177 ! - contig--2369838 - SSU_rRNA_archaea RF01959 hmm 70 894 17 855 + - 6 0.52 5.4 346.7 9.9e-102 ! - **cmsearch.tblout.deoverlapped:** contig--2249925 - SSU_rRNA_bacteria RF00177 hmm 19 914 2 898 + - 6 0.50 5.7 638.4 1.1e-189 ! - contig--2255364 - SSU_rRNA_bacteria RF00177 hmm 325 1084 765 1 - - 6 0.52 3.9 624.0 2.5e-185 ! - contig--2271497 - SSU_rRNA_bacteria RF00177 hmm 4 812 835 2 - - 6 0.51 5.0 597.5 2.5e-177 ! - contig--2369838 - SSU_rRNA_bacteria RF00177 hmm 90 938 20 855 + - 6 0.52 7.0 609.3 6.6e-181 ! - ]]></help> <citations> <citation type="bibtex"> @software{nawrocki_nawrockiecmsearch_tblout_deoverlap_2019, title = {nawrockie/cmsearch\_tblout\_deoverlap}, url = {https://github.com/nawrockie/cmsearch_tblout_deoverlap}, abstract = {Script that removes lower scoring overlaps from cmsearch v1.1x --tblout files.}, author = {Nawrocki, Eric}, year = {2019}} </citation> </citations> </tool>