Mercurial > repos > sanbi-uwc > mothur_test
diff tools/mothur/seq.error.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/seq.error.xml Fri Jun 03 09:32:47 2016 -0400 @@ -0,0 +1,206 @@ +<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="version_command"/> + <command detect_errors="aggressive"><![CDATA[ + echo 'seq.error( + fasta=$fasta_in, + reference=$alignment.template, + #if $name_in: + name=$name_in, + #end if + #if $qual.use == "yes": + qfile=$qfile_in, + report=$alignreport_in, + #end if + #if $threshold: + threshold=$threshold, + #end if + ignorechimeras=$ignorechimeras, + #if $count: + count=$count, + #end if + processors='\${GALAXY_SLOTS:-8}' + )' + | sed 's/ //g' ## mothur trips over whitespace + | mothur && + + ## move output files to correct destination + prefix="$fasta_in" + && mv mothur.*.logfile "$logfile" + #if 'summary' in str($output_sel).split(','): + && mv \${prefix%.dat}*.error.summary "$summary_out" + #end if + #if 'seq' in str($output_sel).split(','): + && mv \${prefix%.dat}*.error.seq "$seq_out" + #end if + #if 'seq_forward' in str($output_sel).split(','): + && mv \${prefix%.dat}*.error.seq.forward "$seq_forward_out" + #end if + #if 'seq_reverse' in str($output_sel).split(','): + && mv \${prefix%.dat}*.error.seq.reverse "$seq_reverse_out" + #end if + #if 'chimera' in str($output_sel).split(','): + && mv \${prefix%.dat}*.error.chimera "$chimera_out" + #end if + #if 'count' in str($output_sel).split(','): + && mv \${prefix%.dat}*.error.count "$count_out" + #end if + #if 'matrix' in str($output_sel).split(','): + && mv \${prefix%.dat}*.error.matrix "$matrix_out" + #end if + #if 'ref_query' in str($output_sel).split(','): + && mv \${prefix%.dat}*.error.ref "$ref_query_out" + #end if + + #if $qual.use == "yes": + #if 'quality' in str($output_sel).split(','): + && mv \${prefix%.dat}*.error.quality "$quality_out" + #end if + #if 'qual_forward' in str($output_sel).split(','): + && mv \${prefix%.dat}*.error.qual.forward "$qual_forward_out" + #end if + #if 'qual_reverse' in str($output_sel).split(','): + && mv \${prefix%.dat}*.error.qual.reverse "$qual_reverse_out" + #end if + #end if + ]]></command> + <inputs> + <param name="fasta_in" type="data" format="mothur.align" 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" 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="The count parameter allows you to provide a count file associated with your fasta file, so you can include the redundant sequences in your error analysis"/> + <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 - "/> + <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 name="logfile" format="txt" label="${tool.name} on ${on_string}: logfile"/> + <data name="summary_out" format="tabular" label="${tool.name} on ${on_string}: error.summary"> + <filter>'summary' in output_sel</filter> + </data> + <data name="seq_out" format="fasta" label="${tool.name} on ${on_string}: error.seq"> + <filter>'seq' in output_sel</filter> + </data> + <data name="seq_forward_out" format="tabular" label="${tool.name} on ${on_string}: error.seq.forward"> + <filter>'seq_forward' in output_sel</filter> + </data> + <data name="seq_reverse_out" format="tabular" label="${tool.name} on ${on_string}: error.seq.reverse"> + <filter>'seq_reverse' in output_sel</filter> + </data> + <data name="chimera_out" format="tabular" label="${tool.name} on ${on_string}: error.chimera"> + <filter>'chimera' in output_sel</filter> + </data> + <data name="count_out" format="tabular" label="${tool.name} on ${on_string}: error.count"> + <filter>'count' in output_sel</filter> + </data> + <data name="matrix_out" format="tabular" label="${tool.name} on ${on_string}: error.matrix"> + <filter>'matrix' in output_sel</filter> + </data> + <data name="quality_out" format="tabular" label="${tool.name} on ${on_string}: error.quality"> + <filter>qual['use'] == 'yes' and 'quality' in output_sel</filter> + </data> + <data name="qual_forward_out" format="tabular" label="${tool.name} on ${on_string}: error.qual.forward"> + <filter>qual['use'] == 'yes' and 'qual_forward' in output_sel</filter> + </data> + <data name="qual_reverse_out" format="tabular" label="${tool.name} on ${on_string}: error.qual.reverse"> + <filter>qual['use'] == 'yes' and 'qual_reverse' in output_sel</filter> + </data> + <data name="ref_query_out" format="mothur.align" label="${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 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> + <expand macro="citations"/> +</tool>