Mercurial > repos > sanbi-uwc > mothur_test
diff tools/mothur/shhh.seqs.xml @ 0:ee4fee239fe7 draft default tip
planemo upload commit 68a4fd4cc5332c57ac39bef73db224425af0706c-dirty
author | sanbi-uwc |
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date | Fri, 03 Jun 2016 09:32:47 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/mothur/shhh.seqs.xml Fri Jun 03 09:32:47 2016 -0400 @@ -0,0 +1,64 @@ +<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="version_command"/> + <command detect_errors="aggressive"><![CDATA[ + echo 'shhh.seqs( + fasta=$fasta, + name=$name, + #if $group: + group=$group, + #end if + sigma=$sigma, + processors='\${GALAXY_SLOTS:-8}' + )' + | sed 's/ //g' ## mothur trips over whitespace + | mothur && + + ## move output files to correct destination + prefix="$fasta" && + mv mothur.*.logfile "$logfile" && + mv \${prefix%.dat}*.shhh_seqs.fasta "$shhh_fasta" && + mv \${prefix%.dat}*.shhh_seqs.names "$shhh_names" && + mv \${prefix%.dat}*.shhh_seqs.map "$shhh_map" + ]]></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> + <data name="logfile" format="txt" label="${tool.name} on ${on_string}: logfile"/> + <data name="shhh_fasta" format_source="fasta" label="${tool.name} on ${on_string}: shhh.fasta"/> + <data name="shhh_names" format="mothur.names" label="${tool.name} on ${on_string}: shhh.names"/> + <data name="shhh_map" format="txt" label="${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 Documenation** + +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: http://www.mothur.org/wiki/Shhh.seqs + +]]> + </help> + <expand macro="citations"/> +</tool>