Mercurial > repos > jjohnson > mothur_toolsuite
view mothur/tools/mothur/seq.error.xml @ 33:d53b9eb16c2d
mothur_wrapper.py - convert_value needs to return a String
author | Jim Johnson <jj@umn.edu> |
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date | Wed, 11 Sep 2013 16:56:31 -0500 |
parents | 49058b1f8d3f |
children | 95d75b35e4d2 |
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<tool id="mothur_seq_error" name="Seq.error" version="1.22.0"> <description>assess error rates in sequencing data</description> <command interpreter="python"> mothur_wrapper.py #import re, os.path #set results = ["'^mothur.\S+\.logfile$:'" + $logfile.__str__] #if 'summary' in $output_sel.__str__.split(','): #set results = $results + ["'^\S+.error.summary$:'" + $summary_out.__str__] #end if #if 'seq' in $output_sel.__str__.split(','): #set results = $results + ["'^\S+.error.seq$:'" + $seq_out.__str__] #end if #if 'seq_forward' in $output_sel.__str__.split(','): #set results = $results + ["'^\S+.error.seq.forward$:'" + $seq_forward_out.__str__] #end if #if 'seq_reverse' in $output_sel.__str__.split(','): #set results = $results + ["'^\S+.error.seq.reverse$:'" + $seq_reverse_out.__str__] #end if #if 'chimera' in $output_sel.__str__.split(','): #set results = $results + ["'^\S+.error.chimera$:'" + $chimera_out.__str__] #end if #if 'count' in $output_sel.__str__.split(','): #set results = $results + ["'^\S+.error.count$:'" + $count_out.__str__] #end if #if 'matrix' in $output_sel.__str__.split(','): #set results = $results + ["'^\S+.error.matrix$:'" + $matrix_out.__str__] #end if #if 'ref_query' in $output_sel.__str__.split(','): #set results = $results + ["'^\S+.error.ref-query$:'" + $ref_query_out.__str__] #end if --cmd='seq.error' --outputdir='$logfile.extra_files_path' --fasta=$fasta_in --reference=$alignment.template #if $name_in.__str__ != "None" and len($name_in.__str__) > 0: --name=$name_in #end if #if $qual.use.__str__ == 'yes': --qfile=$qfile_in --alignreport=$alignreport_in #if 'quality' in $output_sel.__str__.split(','): #set results = $results + ["'^\S+.error.quality$:'" + $quality_out.__str__] #end if #if 'qual_forward' in $output_sel.__str__.split(','): #set results = $results + ["'^\S+.error.qual.forward$:'" + $qual_forward_out.__str__] #end if #if 'qual_reverse' in $output_sel.__str__.split(','): #set results = $results + ["'^\S+.error.qual.reverse$:'" + $qual_reverse_out.__str__] #end if #end if #if $threshold.__str__ != '': --threshold=$threshold #end if $ignorechimeras --result=#echo ','.join($results) --processors=8 </command> <inputs> <param name="fasta_in" type="data" format="align" label="fasta - Candiate Sequences"/> <conditional name="alignment"> <param name="source" type="select" label="Select Reference Template from" help=""> <option value="ref">Cached Reference</option> <option value="history">Your History</option> </param> <when value="ref"> <param name="template" type="select" label="reference - Select an alignment database " help=""> <options from_file="mothur_aligndb.loc"> <column name="name" index="0" /> <column name="value" index="1" /> </options> </param> </when> <when value="history"> <param name="template" type="data" format="align" label="reference - Reference to align with" help=""/> </when> </conditional> <param name="name_in" type="data" format="names" optional="true" label="name - Sequences Name reference"/> <conditional name="qual"> <param name="use" type="select" label="Include a quality file and an alignment report as inputs" help=""> <option value="no">No</option> <option value="yes">Yes</option> </param> <when value="yes"> <param name="qfile_in" type="data" format="qual" label="qfile - Fasta Quality"/> <param name="alignreport_in" type="data" format="align.report" label="alignreport - Align Report"/> </when> <when value="no"/> </conditional> <param name="threshold" type="float" value="" optional="true" label="threshold - error rate at which to report (default 1.)" help=""> <validator type="in_range" message="error rate threshold between 0. and 1." min="0.0" max="1.0"/> </param> <param name="ignorechimeras" type="boolean" truevalue="" falsevalue="--ignorechimeras=false" checked="true" label="ignorechimeras - " /> <param name="output_sel" type="select" multiple="true" display="checkboxes" label="Outputs as history datasets" > <option value="summary">error.summary</option> <option value="seq">error.seq</option> <option value="seq_forward">error.seq.forward</option> <option value="seq_reverse">error.seq.reverse</option> <option value="chimera">error.chimera</option> <option value="count">error.count</option> <option value="matrix">error.matrix</option> <option value="quality">error.quality</option> <option value="qual_forward">error.qual.forward</option> <option value="qual_reverse">error.qual.reverse</option> <option value="ref_query">error.ref-query</option> </param> </inputs> <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> <data format="tabular" name="summary_out" label="${tool.name} on ${on_string}: error.summary" > <filter>('summary' in output_sel)</filter> </data> <data format="fasta" name="seq_out" label="${tool.name} on ${on_string}: error.seq" > <filter>('seq' in output_sel)</filter> </data> <data format="tabular" name="seq_forward_out" label="${tool.name} on ${on_string}: error.seq.forward" > <filter>('seq_forward' in output_sel)</filter> </data> <data format="tabular" name="seq_reverse_out" label="${tool.name} on ${on_string}: error.seq.reverse" > <filter>('seq_reverse' in output_sel)</filter> </data> <data format="tabular" name="chimera_out" label="${tool.name} on ${on_string}: error.chimera" > <filter>('chimera' in output_sel)</filter> </data> <data format="tabular" name="count_out" label="${tool.name} on ${on_string}: error.count" > <filter>('count' in output_sel)</filter> </data> <data format="tabular" name="matrix_out" label="${tool.name} on ${on_string}: error.matrix" > <filter>('matrix' in output_sel)</filter> </data> <data format="tabular" name="quality_out" label="${tool.name} on ${on_string}: error.quality" > <filter>('quality' in output_sel)</filter> </data> <data format="tabular" name="qual_forward_out" label="${tool.name} on ${on_string}: error.qual.forward" > <filter>('qual_forward' in output_sel)</filter> </data> <data format="tabular" name="qual_reverse_out" label="${tool.name} on ${on_string}: error.qual.reverse" > <filter>('qual_reverse' in output_sel)</filter> </data> <data format="align" name="ref_query_out" label="${tool.name} on ${on_string}: error.ref-query" > <filter>('ref_query' in output_sel)</filter> </data> </outputs> <requirements> <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests> <help> **Mothur Overview** Mothur_, initiated by Dr. Patrick Schloss and his software development team in the Department of Microbiology and Immunology at The University of Michigan, provides bioinformatics for the microbial ecology community. .. _Mothur: http://www.mothur.org/wiki/Main_Page **Command Documenation** The seq.error_ command evaluates error rate for sequences by comparing to the fasta-formatted template_alignment_. This is demonstrated in http://www.mothur.org/wiki/Schloss_SOP#Error_analysis .. _template_alignment: http://www.mothur.org/wiki/Alignment_database .. _seq.error: http://www.mothur.org/wiki/Seq.error </help> </tool>