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comparison seq.error.xml @ 1:b85d7c129afb draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
author iuc
date Thu, 18 May 2017 18:09:32 -0400
parents 3d74b329068b
children 5aa51a579879
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0:3d74b329068b 1:b85d7c129afb
2 <description>assess error rates in sequencing data</description> 2 <description>assess error rates in sequencing data</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <expand macro="stdio"/>
7 <expand macro="version_command"/> 8 <expand macro="version_command"/>
8 <command detect_errors="aggressive"><![CDATA[ 9 <command><![CDATA[
10 @SHELL_OPTIONS@
11
9 ## create symlinks to input datasets 12 ## create symlinks to input datasets
10 ln -s "$fasta_in" fasta_in.dat && 13 ln -s "$fasta_in" fasta_in.dat &&
11 ln -s "$name_in" name_in.dat && 14 ln -s "$name_in" name_in.dat &&
12 ln -s "$count" count.dat && 15 ln -s "$count" count.dat &&
13 ln -s "$alignment.template" alignment.template.dat && 16 ln -s "$alignment.template" alignment.template.dat &&
31 #end if 34 #end if
32 ignorechimeras=$ignorechimeras, 35 ignorechimeras=$ignorechimeras,
33 #if $count: 36 #if $count:
34 count=count.dat, 37 count=count.dat,
35 #end if 38 #end if
39 #if $fasta_in.is_of_type('mothur.align')
40 aligned=T,
41 #else
42 aligned=F,
43 #end if
36 processors='\${GALAXY_SLOTS:-8}' 44 processors='\${GALAXY_SLOTS:-8}'
37 )' 45 )'
38 | sed 's/ //g' ## mothur trips over whitespace 46 | sed 's/ //g' ## mothur trips over whitespace
39 | mothur 47 | mothur
48 | tee mothur.out.log
40 ]]></command> 49 ]]></command>
41 <inputs> 50 <inputs>
42 <param name="fasta_in" type="data" format="mothur.align" label="fasta - Candidate Sequences" help="sequences must be aligned"/> 51 <param name="fasta_in" type="data" format="mothur.align,fasta" label="fasta - Candidate Sequences" help="sequences must be aligned"/>
43 <conditional name="alignment"> 52 <conditional name="alignment">
44 <param name="source" type="select" label="Select Reference Template from" help=""> 53 <param name="source" type="select" label="Select Reference Template from" help="">
45 <option value="ref">Cached Reference</option> 54 <option value="ref">Cached Reference</option>
46 <option value="history">Your History</option> 55 <option value="history">Your History</option>
47 </param> 56 </param>
49 <param name="template" type="select" label="reference - Select an alignment database" help=""> 58 <param name="template" type="select" label="reference - Select an alignment database" help="">
50 <options from_data_table="mothur_aligndb"/> 59 <options from_data_table="mothur_aligndb"/>
51 </param> 60 </param>
52 </when> 61 </when>
53 <when value="history"> 62 <when value="history">
54 <param name="template" type="data" format="mothur.align" label="reference - Reference to align with" help=""/> 63 <param name="template" type="data" format="mothur.align,fasta" label="reference - Reference to align with" help=""/>
55 </when> 64 </when>
56 </conditional> 65 </conditional>
57 <param name="name_in" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/> 66 <param name="name_in" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/>
58 <conditional name="qual"> 67 <conditional name="qual">
59 <param name="use" type="select" label="Include a quality file and an alignment report as inputs" help=""> 68 <param name="use" type="select" label="Include a quality file and an alignment report as inputs" help="">
64 <param name="qfile_in" type="data" format="qual" label="qfile - Fasta Quality"/> 73 <param name="qfile_in" type="data" format="qual" label="qfile - Fasta Quality"/>
65 <param name="alignreport_in" type="data" format="mothur.align.report" label="alignreport - Align Report"/> 74 <param name="alignreport_in" type="data" format="mothur.align.report" label="alignreport - Align Report"/>
66 </when> 75 </when>
67 <when value="no"/> 76 <when value="no"/>
68 </conditional> 77 </conditional>
69 <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"/> 78 <param name="count" type="data" format="mothur.count_table" optional="true" label="count table"/>
70 <param name="threshold" type="float" value="" min="0" max="1" optional="true" label="threshold - error rate at which to report (default 1.)"/> 79 <param name="threshold" type="float" value="" min="0" max="1" optional="true" label="threshold - error rate at which to report (default 1.)"/>
71 <param name="ignorechimeras" type="boolean" truevalue="true" falsevalue="false" checked="true" label="ignorechimeras - "/> 80 <param name="ignorechimeras" type="boolean" truevalue="true" falsevalue="false" checked="true" label="ignorechimeras - "/>
72 <param name="output_sel" type="select" multiple="true" display="checkboxes" label="Outputs as history datasets">
73 <option value="summary">error.summary</option>
74 <option value="seq">error.seq</option>
75 <option value="seq_forward">error.seq.forward</option>
76 <option value="seq_reverse">error.seq.reverse</option>
77 <option value="chimera">error.chimera</option>
78 <option value="count">error.count</option>
79 <option value="matrix">error.matrix</option>
80 <option value="quality">error.quality</option>
81 <option value="qual_forward">error.qual.forward</option>
82 <option value="qual_reverse">error.qual.reverse</option>
83 <option value="ref_query">error.ref-query</option>
84 </param>
85 </inputs> 81 </inputs>
86 <outputs> 82 <outputs>
87 <expand macro="logfile-output"/> 83 <expand macro="logfile-output"/>
88 <data name="summary_out" format="tabular" from_work_dir="fasta_in*.error.summary" label="${tool.name} on ${on_string}: error.summary"> 84 <data name="summary_out" format="tabular" from_work_dir="fasta_in*.error.summary" label="${tool.name} on ${on_string}: error.summary">
89 <filter>'summary' in output_sel</filter> 85 <filter>'summary' in output_sel</filter>
160 <help> 156 <help>
161 <![CDATA[ 157 <![CDATA[
162 158
163 @MOTHUR_OVERVIEW@ 159 @MOTHUR_OVERVIEW@
164 160
165 **Command Documenation** 161 **Command Documentation**
166 162
167 The seq.error_ command evaluates error rate for sequences by comparing to the fasta-formatted template_alignment_. 163 The seq.error_ command evaluates error rate for sequences by comparing to the fasta-formatted template_alignment_.
168 This is demonstrated in http://www.mothur.org/wiki/Schloss_SOP#Error_analysis 164 This is demonstrated in https://www.mothur.org/wiki/Schloss_SOP#Error_analysis
169 165
170 .. _template_alignment: http://www.mothur.org/wiki/Alignment_database 166 .. _template_alignment: https://www.mothur.org/wiki/Alignment_database
171 .. _seq.error: http://www.mothur.org/wiki/Seq.error 167 .. _seq.error: https://www.mothur.org/wiki/Seq.error
172 168
173 ]]> 169 ]]>
174 </help> 170 </help>
175 <expand macro="citations"/> 171 <expand macro="citations"/>
176 </tool> 172 </tool>