Mercurial > repos > rnateam > cmsearch_deoverlap
comparison cmsearch-deoverlap.xml @ 1:3fd3be28a04c draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap commit a9df96eec1bfb4e4d61926b02e8847babd1187ad-dirty
| author | rnateam |
|---|---|
| date | Mon, 18 Mar 2024 09:34:56 +0000 |
| parents | 54b16c794341 |
| children | 874ad23526a0 |
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| 0:54b16c794341 | 1:3fd3be28a04c |
|---|---|
| 1 <tool id="cmsearch_deoverlap" name="CMsearch deoverlap" version="0.08+galaxy0" profile="21.05"> | 1 <tool id="cmsearch_deoverlap" name="CMsearch deoverlap" version="0.08+galaxy1" profile="21.05"> |
| 2 <description>removes lower scoring overlaps from cmsearch results</description> | 2 <description>removes lower scoring overlaps from cmsearch results</description> |
| 3 <requirements> | 3 <requirements> |
| 4 <requirement type="package" version="5.26">perl</requirement> | 4 <requirement type="package" version="5.26">perl</requirement> |
| 5 </requirements> | 5 </requirements> |
| 6 <command><![CDATA[ | 6 <command><![CDATA[ |
| 11 #if $maxkeep: | 11 #if $maxkeep: |
| 12 $maxkeep | 12 $maxkeep |
| 13 #end if | 13 #end if |
| 14 #if $dirty: | 14 #if $dirty: |
| 15 $dirty && | 15 $dirty && |
| 16 mv *.sort '$matches_sort' | 16 sed 's/[:blank:]+/,/g' cmsearch_matches.sort > cmsearch_matches.sort.tabular && |
| 17 mv cmsearch_matches.sort.tabular '$matches_sort' | |
| 17 #end if | 18 #end if |
| 18 && | 19 && |
| 19 mv *.deoverlapped '$deoverlapped_matches' | 20 sed 's/[:blank:]+/,/g' cmsearch_matches.deoverlapped > cmsearch_matches.deoverlapped.tabular && |
| 21 mv cmsearch_matches.deoverlapped.tabular '$deoverlapped_matches' | |
| 20 | 22 |
| 21 ]]></command> | 23 ]]></command> |
| 22 <inputs> | 24 <inputs> |
| 23 <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"/> | 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"/> |
| 24 <param name="cmsearch_matches" type="data" format="tabular" label="The tabular result file from cmsearch"/> | 26 <param name="cmsearch_matches" type="data" format="tabular" label="The tabular result file from cmsearch"/> |