Mercurial > repos > rnateam > cmsearch_deoverlap
comparison cmsearch-deoverlap.xml @ 2:874ad23526a0 draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap commit fa7deee70d449c6ec1ae9eb42d01d283e9bee586
| author | rnateam |
|---|---|
| date | Mon, 18 Mar 2024 16:32:39 +0000 |
| parents | 3fd3be28a04c |
| children |
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| 1:3fd3be28a04c | 2:874ad23526a0 |
|---|---|
| 1 <tool id="cmsearch_deoverlap" name="CMsearch deoverlap" version="0.08+galaxy1" profile="21.05"> | 1 <tool id="cmsearch_deoverlap" name="CMsearch deoverlap" version="0.08+galaxy2" profile="21.05"> |
| 2 <description>removes lower scoring overlaps from cmsearch results</description> | 2 <description>removes lower scoring overlaps from cmsearch results</description> |
| 3 <xrefs> | |
| 4 <xref type="bio.tools">cmsearch-deoverlap</xref> | |
| 5 </xrefs> | |
| 3 <requirements> | 6 <requirements> |
| 4 <requirement type="package" version="5.26">perl</requirement> | 7 <requirement type="package" version="5.26">perl</requirement> |
| 8 <requirement type="package" version="4.8">sed</requirement> | |
| 5 </requirements> | 9 </requirements> |
| 6 <command><![CDATA[ | 10 <command><![CDATA[ |
| 7 ln -s '$clan_information' clan_info && | 11 ln -s '$clan_information' clan_info && |
| 8 ln -s '$cmsearch_matches' cmsearch_matches && | 12 ln -s '$cmsearch_matches' cmsearch_matches && |
| 9 LC_ALL=C perl '$__tool_directory__/cmsearch-deoverlap.pl' | 13 LC_ALL=C perl '$__tool_directory__/cmsearch-deoverlap.pl' |
| 11 #if $maxkeep: | 15 #if $maxkeep: |
| 12 $maxkeep | 16 $maxkeep |
| 13 #end if | 17 #end if |
| 14 #if $dirty: | 18 #if $dirty: |
| 15 $dirty && | 19 $dirty && |
| 16 sed 's/[:blank:]+/,/g' cmsearch_matches.sort > cmsearch_matches.sort.tabular && | 20 sed "s/[[:blank:]]\+/\t/g" cmsearch_matches.sort > cmsearch_matches.sort.tabular && |
| 17 mv cmsearch_matches.sort.tabular '$matches_sort' | 21 mv cmsearch_matches.sort.tabular '$matches_sort' |
| 18 #end if | 22 #end if |
| 19 && | 23 && |
| 20 sed 's/[:blank:]+/,/g' cmsearch_matches.deoverlapped > cmsearch_matches.deoverlapped.tabular && | 24 sed "s/[[:blank:]]\+/\t/g" cmsearch_matches.deoverlapped > cmsearch_matches.deoverlapped.tabular && |
| 21 mv cmsearch_matches.deoverlapped.tabular '$deoverlapped_matches' | 25 mv cmsearch_matches.deoverlapped.tabular '$deoverlapped_matches' |
| 22 | 26 |
| 23 ]]></command> | 27 ]]></command> |
| 24 <inputs> | 28 <inputs> |
| 25 <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"/> | 29 <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"/> |