Mercurial > repos > iuc > mothur_make_shared
diff make.shared.xml @ 3:4ad0836d0ade draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
| author | iuc |
|---|---|
| date | Tue, 20 Mar 2018 21:57:06 -0400 |
| parents | c4b6d7acffbf |
| children |
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--- a/make.shared.xml Tue Sep 05 16:59:06 2017 -0400 +++ b/make.shared.xml Tue Mar 20 21:57:06 2018 -0400 @@ -7,43 +7,43 @@ <expand macro="stdio"/> <expand macro="version_command"/> <command><![CDATA[ - @SHELL_OPTIONS@ +@SHELL_OPTIONS@ - ## create symlinks to input datasets - ln -s "$intype.otu" intype_otu.dat && - #if $intype.infile == "otulist": - ln -s "$intype.group" intype_group.dat && - #end if +## create symlinks to input datasets +ln -s '$intype.otu' intype_otu.dat && +#if $intype.infile == "otulist": + ln -s '$intype.group' intype_group.dat && +#end if - echo 'make.shared( - #if $intype.infile == "biom": - biom=intype_otu.dat - #else - #if $intype.group.is_of_type("mothur.groups"): - group=intype_group.dat, - #elif $intype.group.is_of_type("mothur.count_table"): - count=intype_group.dat, - #end if - #if $intype.label: - label=${ str($intype.label).replace(",","-") }, - #end if - #if $intype.groups: - groups=${ str($intype.groups).replace(",","-") }, - #end if - list=intype_otu.dat - #end if - )' - | sed 's/ //g' ## mothur trips over whitespace - | mothur - | tee mothur.out.log && +echo 'make.shared( + #if $intype.infile == "biom": + biom=intype_otu.dat + #else + #if $intype.group.is_of_type("mothur.groups"): + group=intype_group.dat, + #elif $intype.group.is_of_type("mothur.count_table"): + count=intype_group.dat, + #end if + #if $intype.label: + label=${ str($intype.label).replace(",","-") }, + #end if + #if $intype.groups: + groups=${ str($intype.groups).replace(",","-") }, + #end if + list=intype_otu.dat + #end if +)' +| sed 's/ //g' ## mothur trips over whitespace +| mothur +| tee mothur.out.log && - ## move output files to correct destination - mv mothur.*.logfile "$logfile" && - #if $intype.infile == 'otulist' and $intype.groups: - mv intype_otu*.groups "$groupout" - #else - mv intype_otu*.shared "$shared" - #end if +## move output files to correct destination +mv mothur.*.logfile "$logfile" && +#if $intype.infile == 'otulist' and $intype.groups: + mv intype_otu*.groups "$groupout" +#else + mv intype_otu*.shared "$shared" +#end if ]]></command> <inputs> <conditional name="intype"> @@ -67,6 +67,7 @@ <param name="otu" type="data" format="biom1" label="Biom 1.0 file"/> </when> </conditional> + <expand macro="param-savelog"/> </inputs> <outputs> <expand macro="logfile-output"/> @@ -84,6 +85,7 @@ <param name="infile" value="biom"/> <param name="otu" value="example.biom"/> <output name="shared" md5="e44d5ca4e4a5dbc68e8219c5690aa156" ftype="mothur.shared"/> + <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> <test><!-- test with otu and group file--> @@ -91,6 +93,7 @@ <param name="otu" value="amazon.an.list" ftype="mothur.list"/> <param name="group" value="amazon.groups" ftype="mothur.groups"/> <output name="shared" file="amazon.an.shared" ftype="mothur.shared"/> + <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> <test><!-- test with label and group select--> @@ -103,11 +106,11 @@ <output_collection name="labelshares" count="3"> <element name="0.22" md5="592b4fb84412de47be18e64ef26b7a80" ftype="mothur.shared"/> </output_collection> + <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> </tests> - <help> -<![CDATA[ + <help><![CDATA[ @MOTHUR_OVERVIEW@ @@ -121,7 +124,7 @@ .. _shared: https://www.mothur.org/wiki/Shared_file .. _rabund: https://www.mothur.org/wiki/Rabund_file .. _make.shared: https://www.mothur.org/wiki/Make.shared -]]> - </help> + + ]]></help> <expand macro="citations"/> </tool>