Mercurial > repos > iuc > mothur_get_label
diff get.label.xml @ 4:2db0ca9ce0d9 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
| author | iuc |
|---|---|
| date | Wed, 14 Feb 2018 09:26:19 -0500 |
| parents | 6d082f402534 |
| children | 5d5df87a14d5 |
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--- a/get.label.xml Fri Sep 08 12:57:08 2017 -0400 +++ b/get.label.xml Wed Feb 14 09:26:19 2018 -0500 @@ -7,29 +7,29 @@ <expand macro="stdio"/> <expand macro="version_command"/> <command><![CDATA[ - @SHELL_OPTIONS@ +@SHELL_OPTIONS@ - ## create symlinks to input datasets - ln -s "$otu" otu.dat && +## create symlinks to input datasets +ln -s '$otu' otu.dat && - echo 'get.label( - #if $otu.is_of_type("mothur.rabund"): - rabund=otu.dat - #elif $otu.is_of_type("mothur.sabund"): - sabund=otu.dat - #else - list=otu.dat - #end if - )' - | sed 's/ //g' ## mothur trips over whitespace - | mothur - | tee mothur.out.log && +echo 'get.label( + #if $otu.is_of_type("mothur.rabund"): + rabund=otu.dat + #elif $otu.is_of_type("mothur.sabund"): + sabund=otu.dat + #else + list=otu.dat + #end if +)' +| sed 's/ //g' ## mothur trips over whitespace +| mothur +| tee mothur.out.log && - ## parse relevant output from logfile to file - cat mothur.*.logfile - | head -n-3 - | sed '1,29d' - > "$labels_list" +## parse relevant output from logfile to file +cat mothur.*.logfile +| head -n-3 +| sed '1,30d' +> '$labels_list' ]]></command> <inputs> <param name="otu" type="data" format="mothur.list,mothur.sabund,mothur.rabund" label="Input file. May be shared, sabund or rabund file"/> @@ -55,8 +55,7 @@ <expand macro="logfile-test"/> </test> </tests> - <help> -<![CDATA[ + <help><![CDATA[ @MOTHUR_OVERVIEW@ @@ -67,7 +66,7 @@ .. _get.label: https://www.mothur.org/wiki/Get.label v.1.20.0: Updated to Mothur 1.33 -]]> - </help> + + ]]></help> <expand macro="citations"/> </tool>