Mercurial > repos > iuc > mothur_sub_sample
diff sub.sample.xml @ 2:46d13e8c60ba draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
| author | iuc |
|---|---|
| date | Tue, 20 Mar 2018 22:24:53 -0400 |
| parents | be6c106b1960 |
| children | 2986f7b01e74 |
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--- a/sub.sample.xml Tue Sep 05 16:57:21 2017 -0400 +++ b/sub.sample.xml Tue Mar 20 22:24:53 2018 -0400 @@ -7,64 +7,64 @@ <expand macro="stdio"/> <expand macro="version_command"/> <command><![CDATA[ - @SHELL_OPTIONS@ +@SHELL_OPTIONS@ - ## create symlinks to input datasets - ln -s "$input.otu" input_otu.dat && - ln -s "$count" count.dat && - ln -s "$taxonomy" taxonomy.dat && - #if $input.format == "fasta": - ln -s "$input.name_in" input_name_in.dat && - #end if - #if ($input.format == "fasta" or $input.format == "list") and $input.use_group.to_filter == "yes": - ln -s "$input.use_group.group_in" input_use_group_group_in.dat && - #end if +## create symlinks to input datasets +ln -s '$input.otu' input_otu.dat && +ln -s '$count' count.dat && +ln -s '$taxonomy' taxonomy.dat && +#if $input.format == "fasta": + ln -s '$input.name_in' input_name_in.dat && +#end if +#if ($input.format == "fasta" or $input.format == "list") and $input.use_group.to_filter == "yes": + ln -s '$input.use_group.group_in' input_use_group_group_in.dat && +#end if - echo 'sub.sample( - #if $input.format == "fasta": - fasta=input_otu.dat - #if $input.name_in: - ,name=input_name_in.dat - #end if - #else - #if $input.format == "list": - list=input_otu.dat - #elif $input.format == "sabund": - sabund=input_otu.dat - #elif $input.format == "rabund": - rabund=input_otu.dat - #elif $input.format == "shared": - shared=input_otu.dat - #if $input.groups: - ,groups=${ str($input.groups).replace(",","-") } - #end if - #end if - #if $input.label: - ,label=${ str($input.label).replace(",","-") } - #end if +echo 'sub.sample( + #if $input.format == "fasta": + fasta=input_otu.dat + #if $input.name_in: + ,name=input_name_in.dat + #end if + #else + #if $input.format == "list": + list=input_otu.dat + #elif $input.format == "sabund": + sabund=input_otu.dat + #elif $input.format == "rabund": + rabund=input_otu.dat + #elif $input.format == "shared": + shared=input_otu.dat + #if $input.groups: + ,groups=${ str($input.groups).replace(",","-") } #end if - #if $input.format == "fasta" or $input.format == "list": - #if $input.use_group.to_filter == "yes": - ,group=input_use_group_group_in.dat - #if $input.use_group.groups: - ,groups=${ str($input.use_group.groups).replace(",","-") } - #end if - ,persample=$input.use_group.persample - #end if + #end if + #if $input.label: + ,label=${ str($input.label).replace(",","-") } + #end if + #end if + #if $input.format == "fasta" or $input.format == "list": + #if $input.use_group.to_filter == "yes": + ,group=input_use_group_group_in.dat + #if $input.use_group.groups: + ,groups=${ str($input.use_group.groups).replace(",","-") } #end if - #if $count: - ,count=count.dat - #end if - #if $taxonomy: - ,taxonomy=taxonomy.dat - #end if - #if $size: - ,size=$size - #end if - )' - | sed 's/ //g' ## mothur trips over whitespace - | mothur - | tee mothur.out.log + ,persample=$input.use_group.persample + #end if + #end if + #if $count: + ,count=count.dat + #end if + #if $taxonomy: + ,taxonomy=taxonomy.dat + #end if + #if $size: + ,size=$size + #end if +)' +| sed 's/ //g' ## mothur trips over whitespace +| mothur +| tee mothur.out.log ]]></command> <inputs> <conditional name="input"> @@ -144,6 +144,7 @@ <param name="size" type="integer" value="" min="1" optional="true" label="size - If set, the number of samples to pick"/> <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/> <param name="taxonomy" type="data" format="mothur.seq.taxonomy,mothur.ref.taxonomy" optional="true" label="taxonomy - allows a taxonomy file"/> + <expand macro="param-savelog"/> </inputs> <outputs> <expand macro="logfile-output"/> @@ -186,6 +187,7 @@ </assert_contents> </element> </output_collection> + <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> <test><!-- test with list and group file and label select--> @@ -203,6 +205,7 @@ </assert_contents> </element> </output_collection> + <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> <test><!-- test with fasta and taxonomy --> @@ -219,6 +222,7 @@ <has_line_matching expression="^U[0-9]+\tBacteria.*$"/> </assert_contents> </output> + <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> <test><!-- test with fasta and group file and name file --> @@ -243,6 +247,7 @@ <has_line_matching expression="^U[0-9]+\tU[0-9]+$"/> </assert_contents> </output> + <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> <test><!-- test with shared --> @@ -260,6 +265,7 @@ </assert_contents> </element> </output_collection> + <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> <test><!-- test with rabund --> @@ -271,6 +277,7 @@ <has_text text="0.55"/> </assert_contents> </output> + <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> <test><!-- test with sabund --> @@ -282,11 +289,11 @@ <has_text text="0.55"/> </assert_contents> </output> + <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> </tests> - <help> -<![CDATA[ + <help><![CDATA[ @MOTHUR_OVERVIEW@ @@ -300,7 +307,6 @@ .. _sabund: https://www.mothur.org/wiki/Sabund_file .. _sub.sample: https://www.mothur.org/wiki/Sub.sample -]]> - </help> + ]]></help> <expand macro="citations"/> </tool>