Mercurial > repos > iuc > mothur_consensus_seqs
diff consensus.seqs.xml @ 2:4f4de4518aca draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
author | iuc |
---|---|
date | Tue, 20 Mar 2018 21:59:24 -0400 |
parents | 82a5c9700e76 |
children |
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--- a/consensus.seqs.xml Tue Sep 05 16:52:22 2017 -0400 +++ b/consensus.seqs.xml Tue Mar 20 21:59:24 2018 -0400 @@ -7,37 +7,37 @@ <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 && - #if $perotu.use == "yes": - ln -s "$perotu.otu" perotu.otu.dat && - #end if +## create symlinks to input datasets +ln -s '$fasta' fasta.dat && +ln -s '$name' name.dat && +ln -s '$count' count.dat && +#if $perotu.use == "yes": + ln -s '$perotu.otu' perotu.otu.dat && +#end if - echo 'consensus.seqs( - fasta=fasta.dat - #if $name: - ,name=name.dat - #end if - #if $cutoff: - ,cutoff=$cutoff - #end if - #if $perotu.use == "yes": - ,list=perotu.otu.dat - #if $perotu.label: - ,label=${ str($perotu.label).replace(",","-") } - #end if - #end if - #if $count: - ,count=count.dat - #end if - )' - | sed 's/ //g' ## mothur trips over whitespace - | mothur - | tee mothur.out.log +echo 'consensus.seqs( + fasta=fasta.dat + #if $name: + ,name=name.dat + #end if + #if $cutoff: + ,cutoff=$cutoff + #end if + #if $perotu.use == "yes": + ,list=perotu.otu.dat + #if $perotu.label: + ,label=${ str($perotu.label).replace(",","-") } + #end if + #end if + #if $count: + ,count=count.dat + #end if +)' +| sed 's/ //g' ## mothur trips over whitespace +| mothur +| tee mothur.out.log ]]></command> <inputs> <param name="fasta" type="data" format="mothur.align" label="fasta - Sequences to Bin" help="Sequences must be aligned"/> @@ -55,8 +55,10 @@ </when> <when value="no"/> </conditional> - <param name="cutoff" type="integer" value="" optional="True" min="1" max="100" label="Cutoff - set a percentage of sequences that support the base" help="For example: cutoff=95 would return the base that was supported by at least 95% of sequences. Must be between 1 and 100. Optional"/> + <param name="cutoff" type="integer" value="" optional="True" min="1" max="100" label="Cutoff - set a percentage of sequences that support the base" + help="For example: cutoff=95 would return the base that was supported by at least 95% of sequences. Must be between 1 and 100. Optional"/> <param name="count" type="data" format="mothur.count_table" optional="true" label="Count - a count table" help="this file can be generated by count.seqs"/> + <expand macro="param-savelog"/> </inputs> <outputs> <expand macro="logfile-output"/> @@ -84,6 +86,7 @@ <param name="fasta" value="amazon.align_head" ftype="mothur.align"/> <output name="summary" md5="61a0e170a8b881135421afd0cea8305a" ftype="tabular"/> <output name="cons_fasta" md5="82f3475b61f240eba09597a409364c04" ftype="mothur.align"/> + <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> <test><!-- test with list file --> @@ -101,11 +104,11 @@ <output_collection name="consensussummaries" count="3"> <element name="0.30" md5="d595234c6018dfcc1465e59d35d59205" ftype="tabular"/> </output_collection> + <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> </tests> - <help> -<![CDATA[ + <help><![CDATA[ @MOTHUR_OVERVIEW@ @@ -114,7 +117,7 @@ The consensus.seqs_ command can be used in 2 ways: create a consensus sequence from a fastafile, or with a listfile create a consensus sequence for each otu. Sequences must be aligned. .. _consensus.seqs: https://www.mothur.org/wiki/Consensus.seqs -]]> - </help> + + ]]></help> <expand macro="citations"/> </tool>