Mercurial > repos > iuc > mothur_sens_spec
view sens.spec.xml @ 4:084dc4e8caae draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit be5c8af076296a53959fc3ed2b82d92dc7607eeb
author | iuc |
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date | Mon, 23 Apr 2018 09:25:57 -0400 |
parents | edde8e7c2946 |
children | ddda05cfccb4 |
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<tool profile="16.07" id="mothur_sens_spec" name="Sens.spec" version="@WRAPPER_VERSION@.0"> <description>Determine the quality of OTU assignment</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 '$otu' otu.dat && ln -s '$matrix.dist' matrix.dist.dat && #if str($matrix.method_name.method) == "count" : ln -s '$matrix.method_name.count' matrix.method_name.count.dat && #else ln -s '$matrix.method_name.names' matrix.method_name.names.dat && #end if echo 'sens.spec( list=otu.dat, #if str($matrix.format) == "phylip": phylip=matrix.dist.dat, #else column=matrix.dist.dat, #end if #if str($matrix.method_name.method) == "count" : count=matrix.method_name.count.dat, #else names=matrix.method_name.names.dat, #end if #if $label: label=${ str($label).replace(",","-") }, #end if #if $label: label=${ str($label).replace(",","-") }, #end if precision=$precision, cutoff=$cutoff )' | sed 's/ //g' ## mothur trips over whitespace | mothur | tee mothur.out.log ]]></command> <inputs> <conditional name="matrix"> <param name="format" type="select" label="Select a Distance Matrix Format" help=""> <option value="column">Pairwise Column Matrix </option> <option value="phylip">Phylip Distance Matrix</option> </param> <when value="column"> <param name="dist" type="data" format="mothur.pair.dist" label="column - Distance Matrix"/> <conditional name="method_name"> <param name="method" type="select" label="Select a Method" help=""> <option value="count">count file associated with your distance matrix.</option> <option value="name">name file associated with your distance matrix. </option> </param> <when value="count"> <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/> </when> <when value="name"> <param name="names" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/> </when> </conditional> </when> <when value="phylip"> <param name="dist" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/> </when> </conditional> <param name="otu" type="data" format="mothur.list" label="list - OTU List"/> <param name="dist" type="data" format="mothur.dist,phylip,tabular" label="phylip,column - Distance Matrix"/> <param name="label" type="select" optional="true" label="label - Select OTU Labels to include" multiple="true" help="By default all are included if no selection is made."> <options> <filter type="data_meta" ref="otu" key="labels"/> </options> </param> <param name="precision" type="integer" value="100" min="0" optional="true" label="precision - Precision for rounding distance values"/> <param name="cutoff" type="float" value="-1" label="cutoff - Distance Cutoff threshold - ignored if not > 0" help="Ignore pairwise distances larger than this, a common value would be 0.10"/> <expand macro="param-savelog"/> </inputs> <outputs> <expand macro="logfile-output"/> <data name="sensspec" format="tabular" from_work_dir="otu*.sensspec" label="${tool.name} on ${on_string}: sensspec"/> </outputs> <tests> <test> <param name="count" value="amazon.count_table"/> <param name="otu" value="amazon.an.list" ftype="mothur.list"/> <param name="dist" value="amazon.dist" ftype="mothur.dist"/> <output name="sensspec" md5="720789a7ef4da26928a61161279d7344" ftype="tabular"/> <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> <test> <param name="count" value="amazon.count_table"/> <param name="names" value="amazon.names"/> <param name="otu" value="amazon.an.list" ftype="mothur.list"/> <param name="dist" value="amazon.dist" ftype="mothur.dist"/> <param name="cutoff" value="0.10"/> <param name="label" value="0.03,0.05,0.22"/> <output name="sensspec" md5="3992dec1d799ec3a061b3ef713a58382" ftype="tabular"/> <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> </tests> <help><![CDATA[ @MOTHUR_OVERVIEW@ **Command Documentation** The sens.spec_ command takes a list_ and either a column_ or phylip_ distance matrix to determine the quality of OTU assignment. .. _list: https://www.mothur.org/wiki/List_file .. _column: https://www.mothur.org/wiki/Column-formatted_distance_matrix .. _phylip: https://www.mothur.org/wiki/Phylip-formatted_distance_matrix .. _sens.spec: https://www.mothur.org/wiki/Sens.spec ]]></help> <expand macro="citations"/> </tool>