Mercurial > repos > iuc > mothur_get_mimarkspackage
diff get.mimarkspackage.xml @ 2:74a93a1ec22c draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
author | iuc |
---|---|
date | Tue, 20 Mar 2018 22:25:46 -0400 |
parents | ad446a792958 |
children | 6c54b38dd0da |
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--- a/get.mimarkspackage.xml Tue Sep 05 16:56:28 2017 -0400 +++ b/get.mimarkspackage.xml Tue Mar 20 22:25:46 2018 -0400 @@ -7,23 +7,23 @@ <expand macro="stdio"/> <expand macro="version_command"/> <command><![CDATA[ - @SHELL_OPTIONS@ +@SHELL_OPTIONS@ - ## create symlinks to input datasets - ln -s "$input.infile" input.infile.dat && +## create symlinks to input datasets +ln -s '$input.infile' input.infile.dat && - echo 'get.mimarkspackage( - #if $input.filetype == "group": - group=input.infile.dat, - #elif $input.filetype == "oligos": - oligos=input.infile.dat, - #end if - package=$package, - requiredonly=$requiredonly - )' - | sed 's/ //g' ## mothur trips over whitespace - | mothur - | tee mothur.out.log +echo 'get.mimarkspackage( + #if $input.filetype == "group": + group=input.infile.dat, + #elif $input.filetype == "oligos": + oligos=input.infile.dat, + #end if + package=$package, + requiredonly=$requiredonly +)' +| sed 's/ //g' ## mothur trips over whitespace +| mothur +| tee mothur.out.log ]]></command> <inputs> <conditional name="input"> @@ -55,6 +55,7 @@ <option value="waterc">waterc</option> </param> <param name="requiredonly" type="boolean" truevalue="true" falsevalue="false" checked="false" label="requiredonly - used to indicate you only want the required mimarks fields printed. Default=false"/> + <expand macro="param-savelog"/> </inputs> <outputs> <expand macro="logfile-output"/> @@ -65,6 +66,7 @@ <param name="filetype" value="group"/> <param name="infile" value="amazon.groups" ftype="mothur.groups"/> <output name="package_out" md5="8e97dbe732b257494b796d23a3688d5a" ftype="tabular"/> + <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> <test><!-- test with oligos --> @@ -73,11 +75,11 @@ <param name="package" value="human_associated"/> <param name="requiredonly" value="true"/> <output name="package_out" md5="975cd41eb9a97725795c582dc7e903a3" ftype="tabular"/> + <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> </tests> - <help> -<![CDATA[ + <help><![CDATA[ @MOTHUR_OVERVIEW@ @@ -87,8 +89,7 @@ .. _get.mimarkspackage: https://www.mothur.org/wiki/Get.mimarkspackage -]]> - </help> + ]]></help> <citations> <citation type="doi">10.1128/AEM.01541-09</citation> </citations>