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view seq.error.xml @ 1:29fa3670faa5 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 721531d2e9fd1e208a3fba8cfbe5dcd572599ca2
author | iuc |
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date | Tue, 05 Sep 2017 17:12:13 -0400 |
parents | 45af9683de29 |
children | a5418319c97a |
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<tool profile="16.07" id="mothur_seq_error" name="Seq.error" version="@WRAPPER_VERSION@.0"> <description>assess error rates in sequencing data</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 "$fasta_in" fasta_in.dat && ln -s "$name_in" name_in.dat && ln -s "$count" count.dat && ln -s "$alignment.template" alignment.template.dat && #if $qual.use == "yes": ln -s "$qual.qfile_in" qfile_in.dat && ln -s "$qual.alignreport_in" alignreport_in.dat && #end if echo 'seq.error( fasta=fasta_in.dat, reference=alignment.template.dat, #if $name_in: name=name_in.dat, #end if #if $qual.use == "yes": qfile=qfile_in.dat, report=alignreport_in.dat, #end if #if $threshold: threshold=$threshold, #end if ignorechimeras=$ignorechimeras, #if $count: count=count.dat, #end if #if $fasta_in.is_of_type('mothur.align') aligned=T, #else aligned=F, #end if processors='\${GALAXY_SLOTS:-8}' )' | sed 's/ //g' ## mothur trips over whitespace | mothur | tee mothur.out.log ]]></command> <inputs> <param name="fasta_in" type="data" format="mothur.align,fasta" label="fasta - Candidate Sequences" help="sequences must be aligned"/> <conditional name="alignment"> <param name="source" type="select" label="Select Reference Template from" help=""> <option value="ref">Cached Reference</option> <option value="history">Your History</option> </param> <when value="ref"> <param name="template" type="select" label="reference - Select an alignment database" help=""> <options from_data_table="mothur_aligndb"/> </param> </when> <when value="history"> <param name="template" type="data" format="mothur.align,fasta" label="reference - Reference to align with" help=""/> </when> </conditional> <param name="name_in" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/> <conditional name="qual"> <param name="use" type="select" label="Include a quality file and an alignment report as inputs" help=""> <option value="no">No</option> <option value="yes">Yes</option> </param> <when value="yes"> <param name="qfile_in" type="data" format="qual" label="qfile - Fasta Quality"/> <param name="alignreport_in" type="data" format="mothur.align.report" label="alignreport - Align Report"/> </when> <when value="no"/> </conditional> <param name="count" type="data" format="mothur.count_table" optional="true" label="count table"/> <param name="threshold" type="float" value="" min="0" max="1" optional="true" label="threshold - error rate at which to report (default 1.)"/> <param name="ignorechimeras" type="boolean" truevalue="true" falsevalue="false" checked="true" label="ignorechimeras - "/> </inputs> <outputs> <expand macro="logfile-output"/> <data name="summary_out" format="tabular" from_work_dir="fasta_in*.error.summary" label="${tool.name} on ${on_string}: error.summary"> <filter>'summary' in output_sel</filter> </data> <data name="seq_out" format="fasta" from_work_dir="fasta_in*.error.seq" label="${tool.name} on ${on_string}: error.seq"> <filter>'seq' in output_sel</filter> </data> <data name="seq_forward_out" format="tabular" from_work_dir="fasta_in*.error.seq.forward" label="${tool.name} on ${on_string}: error.seq.forward"> <filter>'seq_forward' in output_sel</filter> </data> <data name="seq_reverse_out" format="tabular" from_work_dir="fasta_in*.error.seq.reverse" label="${tool.name} on ${on_string}: error.seq.reverse"> <filter>'seq_reverse' in output_sel</filter> </data> <data name="chimera_out" format="tabular" from_work_dir="fasta_in*.error.chimera" label="${tool.name} on ${on_string}: error.chimera"> <filter>'chimera' in output_sel</filter> </data> <data name="count_out" format="tabular" from_work_dir="fasta_in*.error.count" label="${tool.name} on ${on_string}: error.count"> <filter>'count' in output_sel</filter> </data> <data name="matrix_out" format="tabular" from_work_dir="fasta_in*.error.matrix" label="${tool.name} on ${on_string}: error.matrix"> <filter>'matrix' in output_sel</filter> </data> <data name="quality_out" format="tabular" from_work_dir="fasta_in*.error.quality" label="${tool.name} on ${on_string}: error.quality"> <filter>qual['use'] == 'yes' and 'quality' in output_sel</filter> </data> <data name="qual_forward_out" format="tabular" from_work_dir="fasta_in*.error.qual.forward" label="${tool.name} on ${on_string}: error.qual.forward"> <filter>qual['use'] == 'yes' and 'qual_forward' in output_sel</filter> </data> <data name="qual_reverse_out" format="tabular" from_work_dir="fasta_in*.error.qual.reverse" label="${tool.name} on ${on_string}: error.qual.reverse"> <filter>qual['use'] == 'yes' and 'qual_reverse' in output_sel</filter> </data> <data name="ref_query_out" format="mothur.align" from_work_dir="fasta_in*.error.ref" label="${tool.name} on ${on_string}: error.ref-query"> <filter>'ref_query' in output_sel</filter> </data> </outputs> <tests> <test><!--test with all outputs and no qual file--> <param name="fasta_in" value="amazon.align_head" ftype="mothur.align"/> <param name="template" value="HMP_MOCK.v35.align" ftype="mothur.align"/> <param name="source" value="history"/> <param name="output_sel" value="summary,seq,seq_forward,seq_reverse,chimera,count,matrix,ref_query"/> <output name="chimera_out" md5="9faf0da7d724a1db5e0d8f5fcb72b486"/> <output name="count_out" md5="9aea787346ad6a1c496aa1d77262a487"/> <output name="matrix_out" md5="b7d9bbf3cdf363b41551e31c0b460a47"/> <output name="ref_query_out" md5="42b42eb4c6bc2705ded2c697a757106f"/> <output name="seq_out" md5="5a884846a8d94b8482c2935d2e7e43e6"/> <output name="seq_forward_out" md5="92a24ef3155bc050ae4fd31bab43cf92"/> <output name="seq_reverse_out" md5="92a24ef3155bc050ae4fd31bab43cf92"/> <output name="summary_out" md5="04abbbd6aa82f084e4a3bd51c4ce98e6"/> <expand macro="logfile-test"/> </test> <test><!--test with qual file and all outputs --> <param name="fasta_in" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head" ftype="mothur.align"/> <param name="template" value="HMP_MOCK.v35.align" ftype="mothur.align"/> <param name="source" value="history"/> <param name="output_sel" value="summary,seq,seq_forward,seq_reverse,chimera,count,matrix,ref_query,quality,qual_forward,qual_reverse"/> <param name="use" value="yes"/> <param name="qfile_in" value="Mock_S280_L001_R1_001_small.trim.contigs.qual"/> <param name="alignreport_in" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align.report"/> <output name="chimera_out" md5="78e586f1a1362fd98808d7725d786caa"/> <output name="count_out" md5="ee987c7b5dc90d4d3a0ef55d817cc540"/> <output name="matrix_out" md5="6b9310b4acd95c560cd062b620b35826"/> <output name="ref_query_out" md5="dd569264c5a4628079de3ef828766e90"/> <output name="quality_out" md5="844b50d6642381a7f434b8182b9307da"/> <output name="qual_forward_out" md5="371fc760fc51b5adf10044fc26c1bbb8"/> <output name="qual_reverse_out" md5="81f17617ba99cac5807e454a626eb006"/> <output name="seq_out" md5="69a8ec131df0b1d4d95eaeb04e057941"/> <output name="seq_forward_out" md5="dbcbbefdc83c2a7c045e3930850cdbd9"/> <output name="seq_reverse_out" md5="5618b1e431306ec1275f1572d6c0c2fc"/> <output name="summary_out" md5="d33bddf9b112f2f3a80b38cf7ac50e6a"/> <expand macro="logfile-test"/> </test> </tests> <help> <![CDATA[ @MOTHUR_OVERVIEW@ **Command Documentation** The seq.error_ command evaluates error rate for sequences by comparing to the fasta-formatted template_alignment_. This is demonstrated in https://www.mothur.org/wiki/Schloss_SOP#Error_analysis .. _template_alignment: https://www.mothur.org/wiki/Alignment_database .. _seq.error: https://www.mothur.org/wiki/Seq.error ]]> </help> <expand macro="citations"/> </tool>