Mercurial > repos > iuc > mothur_homova
diff homova.xml @ 2:2ccbfa78b831 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
| author | iuc |
|---|---|
| date | Tue, 20 Mar 2018 21:58:39 -0400 |
| parents | d891666964ad |
| children | 68005ede9e6e |
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--- a/homova.xml Tue Sep 05 16:49:53 2017 -0400 +++ b/homova.xml Tue Mar 20 21:58:39 2018 -0400 @@ -7,24 +7,24 @@ <expand macro="stdio"/> <expand macro="version_command"/> <command><![CDATA[ - @SHELL_OPTIONS@ +@SHELL_OPTIONS@ - ## create symlinks to input datasets - ln -s "$dist" dist.dat && - ln -s "$design" design.dat && +## create symlinks to input datasets +ln -s '$dist' dist.dat && +ln -s '$design' design.dat && - echo 'homova( - phylip=dist.dat, - design=design.dat, - #if $sets: - sets=${ str($sets).replace(",","-") }, - #end if - iters=$iters, - alpha=$alpha - )' - | sed 's/ //g' ## mothur trips over whitespace - | mothur - | tee mothur.out.log +echo 'homova( + phylip=dist.dat, + design=design.dat, + #if $sets: + sets=${ str($sets).replace(",","-") }, + #end if + iters=$iters, + alpha=$alpha +)' +| sed 's/ //g' ## mothur trips over whitespace +| mothur +| tee mothur.out.log ]]></command> <inputs> <param name="dist" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/> @@ -36,6 +36,7 @@ <filter type="data_meta" ref="design" key="groups"/> </options> </param> + <expand macro="param-savelog"/> </inputs> <outputs> <expand macro="logfile-output"/> @@ -51,6 +52,7 @@ <has_text text="A-B"/> </assert_contents> </output> + <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> <test><!-- test with subsets --> @@ -63,11 +65,11 @@ <has_line_matching expression="A\t.*$"/> </assert_contents> </output> + <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> </tests> - <help> -<![CDATA[ + <help><![CDATA[ @MOTHUR_OVERVIEW@ @@ -90,7 +92,7 @@ .. _homova: https://www.mothur.org/wiki/Homova v.1.20.0: Updated to Mothur 1.33, added sets parameter -]]> - </help> + + ]]></help> <expand macro="citations"/> </tool>