Mercurial > repos > iuc > mothur_summary_seqs
diff summary.seqs.xml @ 2:d68125f75fc2 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
author | iuc |
---|---|
date | Tue, 20 Mar 2018 21:59:09 -0400 |
parents | 9377122cc144 |
children | 600c14c6dcc5 |
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--- a/summary.seqs.xml Tue Sep 05 17:16:26 2017 -0400 +++ b/summary.seqs.xml Tue Mar 20 21:59:09 2018 -0400 @@ -7,31 +7,32 @@ <expand macro="stdio"/> <expand macro="version_command"/> <command><![CDATA[ - @SHELL_OPTIONS@ +@SHELL_OPTIONS@ - ## create symlinks to input datasets - ln -s "$fasta" fasta.dat && - ln -s "$name" name.dat && - ln -s "$count" count.dat && +## create symlinks to input datasets +ln -s '$fasta' fasta.dat && +ln -s '$name' name.dat && +ln -s '$count' count.dat && - echo 'summary.seqs( - fasta=fasta.dat, - #if $name: - name=name.dat, - #end if - #if $count: - count=count.dat, - #end if - processors='\${GALAXY_SLOTS:-8}' - )' - | sed 's/ //g' ## mothur trips over whitespace - | mothur - | tee mothur.out.log +echo 'summary.seqs( + fasta=fasta.dat, + #if $name: + name=name.dat, + #end if + #if $count: + count=count.dat, + #end if + processors='\${GALAXY_SLOTS:-8}' +)' +| sed 's/ //g' ## mothur trips over whitespace +| mothur +| tee mothur.out.log ]]></command> <inputs> <param name="fasta" type="data" format="fasta,mothur.align" label="fasta - Dataset"/> <param name="name" type="data" format="mothur.names" label="name - Names" optional="true"/> <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="The count file is similar to the name file in that it is used to represent the number of duplicate sequences for a given representative sequence. "/> + <expand macro="param-savelog"/> </inputs> <outputs> <expand macro="logfile-output"/> @@ -41,23 +42,25 @@ <test> <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.fasta"/> <output name="out_summary" file="Mock_S280_L001_R1_001_small.trim.contigs.summary" ftype="mothur.summary"/> + <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> <test><!-- test names input --> <param name="fasta" value="amazon.unique.fasta"/> <param name="name" value="amazon.names"/> <output name="out_summary" md5="b8a53926f64434291d232d2736da8293" ftype="mothur.summary"/> + <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> <test><!-- test count input --> <param name="fasta" value="amazon.unique.fasta"/> <param name="count" value="amazon.count_table"/> <output name="out_summary" md5="b8a53926f64434291d232d2736da8293" ftype="mothur.summary"/> + <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> </tests> - <help> -<![CDATA[ + <help><![CDATA[ @MOTHUR_OVERVIEW@ @@ -67,7 +70,7 @@ .. _summary.seqs: https://www.mothur.org/wiki/Summary.seqs -]]> - </help> + + ]]></help> <expand macro="citations"/> </tool>