Mercurial > repos > iuc > mothur_shhh_seqs
diff shhh.seqs.xml @ 0:fddd81ee5cd4 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author | iuc |
---|---|
date | Fri, 19 May 2017 05:07:22 -0400 |
parents | |
children | c54bf33450d7 |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/shhh.seqs.xml Fri May 19 05:07:22 2017 -0400 @@ -0,0 +1,66 @@ +<tool profile="16.07" id="mothur_shhh_seqs" name="Shhh.seqs" version="@WRAPPER_VERSION@.0"> + <description>Denoise program (Quince SeqNoise)</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <expand macro="stdio"/> + <expand macro="version_command"/> + <command><![CDATA[ + @SHELL_OPTIONS@ + + ## create symlinks to input datasets + ln -s "$fasta" fasta.dat && + ln -s "$name" name.dat && + ln -s "$group" group.dat && + + echo 'shhh.seqs( + fasta=fasta.dat, + name=name.dat, + #if $group: + group=group.dat, + #end if + sigma=$sigma, + 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" label="fasta - Sequences" help=""/> + <param name="name" type="data" format="mothur.names" label="name - Sequences Name reference"/> + <param name="group" type="data" format="mothur.groups" optional="true" label="group - Sequences Name reference"/> + <param name="sigma" type="float" value=".01" min="0.0" max="1.0" label="sigma" help="default .01"/> + </inputs> + <outputs> + <expand macro="logfile-output"/> + <data name="shhh_fasta" format_source="fasta" from_work_dir="fasta*.shhh_seqs.fasta" label="${tool.name} on ${on_string}: shhh.fasta"/> + <data name="shhh_names" format="mothur.names" from_work_dir="fasta*.shhh_seqs.names" label="${tool.name} on ${on_string}: shhh.names"/> + <data name="shhh_map" format="txt" from_work_dir="fasta*.shhh_seqs.map" label="${tool.name} on ${on_string}: shhh.map"/> + </outputs> + <tests> + <test> + <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head" ftype="mothur.align"/> + <param name="name" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head.names"/> + <output name="shhh_fasta" md5="0169152fa33b588cabf3c3b932cc6018" ftype="mothur.align"/> + <output name="shhh_names" md5="f3bc939b899d91f7cf3b822c5a822805" ftype="mothur.names"/> + <output name="shhh_map" md5="0bcfe53ec754878ca5f6a126114671e1" ftype="txt"/> + <expand macro="logfile-test"/> + </test> + </tests> + <help> +<![CDATA[ + +@MOTHUR_OVERVIEW@ + +**Command Documentation** + +The shhh.seqs_ command is a mothur-based rewrite of Chris Quince's sequence denoting program, SeqNoise. Schloss prefers pre.cluster for this operation. + +.. _shhh.seqs: https://www.mothur.org/wiki/Shhh.seqs + +]]> + </help> + <expand macro="citations"/> +</tool>