Mercurial > repos > iuc > mothur_remove_dists
diff remove.dists.xml @ 5:9067f78ae9bd draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
| author | iuc |
|---|---|
| date | Wed, 14 Feb 2018 09:30:19 -0500 |
| parents | 27ab74145f55 |
| children | 6a4feed29ebc |
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--- a/remove.dists.xml Tue Sep 05 16:23:39 2017 -0400 +++ b/remove.dists.xml Wed Feb 14 09:30:19 2018 -0500 @@ -7,23 +7,23 @@ <expand macro="stdio"/> <expand macro="version_command"/> <command><![CDATA[ - @SHELL_OPTIONS@ +@SHELL_OPTIONS@ - ## create symlinks to input datasets - ln -s "$accnos" accnos.dat && - ln -s "$input.dist" input_dist.dat && +## create symlinks to input datasets +ln -s '$accnos' accnos.dat && +ln -s '$input.dist' input_dist.dat && - echo 'remove.dists( - accnos=accnos.dat, - #if $input.source == "phylip": - phylip=input_dist.dat - #else - column=input_dist.dat - #end if - )' - | sed 's/ //g' ## mothur trips over whitespace - | mothur - | tee mothur.out.log +echo 'remove.dists( + accnos=accnos.dat, + #if $input.source == "phylip": + phylip=input_dist.dat + #else + column=input_dist.dat + #end if +)' +| sed 's/ //g' ## mothur trips over whitespace +| mothur +| tee mothur.out.log ]]></command> <inputs> <conditional name="input"> @@ -32,13 +32,13 @@ <option value="phylip">Phylip Distance Matrix</option> </param> <when value="column"> - <param name="dist" type="data" format="mothur.pair.dist" label="column - Distance Matrix"/> + <param name="dist" argument="column" type="data" format="mothur.pair.dist" label="column - Distance Matrix"/> </when> <when value="phylip"> - <param name="dist" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/> + <param name="dist" argument="phylip" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/> </when> </conditional> - <param name="accnos" type="data" format="mothur.accnos" label="accnos - sort" help="format must be mothur.accnos"/> + <param argument="accnos" type="data" format="mothur.accnos" label="accnos - sort" help="format must be mothur.accnos"/> </inputs> <outputs> <expand macro="logfile-output"/> @@ -49,12 +49,17 @@ <param name="source" value="phylip"/> <param name="dist" value="98_sq_phylip_amazon.dist" ftype="mothur.square.dist"/> <param name="accnos" value="amazon.bad.accnos" ftype="mothur.accnos"/> - <output name="pick_dist" md5="ec444ddb897d21864a245e8645fcda33" ftype="mothur.square.dist"/> + <output name="pick_dist" ftype="mothur.square.dist"> + <assert_contents> + <expand macro="test-dist-format"/> + <has_text text="U68589"/> + <has_line_matching expression="^90$"/> + </assert_contents> + </output> <expand macro="logfile-test"/> </test> </tests> - <help> -<![CDATA[ + <help><![CDATA[ @MOTHUR_OVERVIEW@ @@ -64,7 +69,6 @@ .. _remove.dists: https://www.mothur.org/wiki/Remove.dists -]]> - </help> + ]]></help> <expand macro="citations"/> </tool>