Mercurial > repos > iuc > mothur_count_seqs
diff count.seqs.xml @ 3:448f43db98c4 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
| author | iuc |
|---|---|
| date | Wed, 14 Feb 2018 09:52:51 -0500 |
| parents | cb4e005b8e8d |
| children | 4649b8f719a2 |
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--- a/count.seqs.xml Tue Sep 05 16:11:47 2017 -0400 +++ b/count.seqs.xml Wed Feb 14 09:52:51 2018 -0500 @@ -7,27 +7,26 @@ <expand macro="stdio"/> <expand macro="version_command"/> <command><![CDATA[ - @SHELL_OPTIONS@ +@SHELL_OPTIONS@ - ## create symlinks to input datasets - ln -s "$name" name.dat && - #if $grouping.use == "yes": - ln -s "$grouping.group" grouping.group.dat && - #end if +## create symlinks to input datasets +ln -s '$name' name.dat && +#if $grouping.use == "yes": + ln -s '$grouping.group' grouping.group.dat && +#end if - echo 'count.seqs( - name=name.dat, - #if $grouping.use == "yes": - group=grouping.group.dat, - #if $grouping.groups: - groups=${ str($grouping.groups).replace(",","-") }, - #end if - #end if - large=$large - )' - | sed 's/ //g' ## mothur trips over whitespace - | mothur - | tee mothur.out.log +echo 'count.seqs( + #if $grouping.use == "yes": + group=grouping.group.dat, + #if $grouping.groups: + groups=${ str($grouping.groups).replace(",","-") }, + #end if + #end if + name=name.dat +)' +| sed 's/ //g' ## mothur trips over whitespace +| mothur +| tee mothur.out.log ]]></command> <inputs> <param name="name" type="data" format="mothur.names" label="name - Sequences Name reference"/> @@ -47,7 +46,6 @@ </when> <when value="no"/> </conditional> - <param name="large" type="boolean" checked="false" truevalue="true" falsevalue="false" label="large - Datasets are large and may not fit in RAM"/> </inputs> <outputs> <expand macro="logfile-output"/> @@ -83,8 +81,7 @@ <expand macro="logfile-test"/> </test> </tests> - <help> -<![CDATA[ + <help><![CDATA[ @MOTHUR_OVERVIEW@ @@ -98,7 +95,7 @@ .. _count_table: https://www.mothur.org/wiki/Count_File v.1.21.0: Updated to Mothur 1.33 -]]> - </help> + + ]]></help> <expand macro="citations"/> </tool>