Mercurial > repos > iuc > mothur_classify_tree
diff classify.tree.xml @ 4:b48b0dd9b75e draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
| author | iuc |
|---|---|
| date | Wed, 14 Feb 2018 09:35:32 -0500 |
| parents | 61b024f58c48 |
| children | f350dab14d28 |
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--- a/classify.tree.xml Fri Sep 08 13:05:48 2017 -0400 +++ b/classify.tree.xml Wed Feb 14 09:35:32 2018 -0500 @@ -7,34 +7,35 @@ <expand macro="stdio"/> <expand macro="version_command"/> <command><![CDATA[ - @SHELL_OPTIONS@ +@SHELL_OPTIONS@ - ## create symlinks to input datasets - ln -s "$tree" tree.dat && - ln -s "$name" name.dat && - ln -s "$group" group.dat && - ln -s "$taxonomy" taxonomy.dat && +## create symlinks to input datasets +ln -s '$tree' tree.dat && +ln -s '$name' name.dat && +ln -s '$group' group.dat && +ln -s '$taxonomy' taxonomy.dat && - echo 'classify.tree( - tree=tree.dat, - #if $name - name=name.dat, - #end if - #if $group: - group=group.dat, - #end if - taxonomy=taxonomy.dat - )' - | sed 's/ //g' ## mothur trips over whitespace - | mothur - | tee mothur.out.log +echo 'classify.tree( + tree=tree.dat, + #if $name + name=name.dat, + #end if + #if $group: + group=group.dat, + #end if + taxonomy=taxonomy.dat +)' +| sed 's/ //g' ## mothur trips over whitespace +| mothur +| tee mothur.out.log ]]></command> <inputs> - <param name="taxonomy" type="data" format="mothur.ref.taxonomy" optional="true" label="taxonomy - Taxonomy to screen"/> - <param name="tree" type="data" format="txt" label="tree - Sequences to filter"/> - <param name="name" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference file"/> - <param name="group" type="data" format="mothur.groups" optional="true" label="group - Sequences Group reference"/> - <param name="cutoff" type="integer" value="51" min="51" max="100" optional="true" label="cutoff - consensus confidence threshold" help="The default is 51, meaning 51%. Cutoff cannot be below 51"/> + <param argument="taxonomy" type="data" format="mothur.ref.taxonomy" optional="true" label="taxonomy - Taxonomy to screen"/> + <param argument="tree" type="data" format="txt" label="tree - Sequences to filter"/> + <param argument="name" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference file"/> + <param argument="group" type="data" format="mothur.groups" optional="true" label="group - Sequences Group reference"/> + <param argument="cutoff" type="integer" value="51" min="51" max="100" optional="true" label="cutoff - consensus confidence threshold" + help="The default is 51, meaning 51%. Cutoff cannot be below 51"/> </inputs> <outputs> <expand macro="logfile-output"/> @@ -50,8 +51,7 @@ <expand macro="logfile-test"/> </test> </tests> - <help> -<![CDATA[ + <help><![CDATA[ @MOTHUR_OVERVIEW@ @@ -76,7 +76,7 @@ .. _classify.tree: https://www.mothur.org/wiki/Classify.tree v.1.25.0: Trivial upgrade to Mothur 1.33 -]]> - </help> + + ]]></help> <expand macro="citations"/> </tool>