Mercurial > repos > iuc > mothur_classify_seqs

comparison classify.seqs.xml @ 1:7c45c65f957b 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 18:10:02 -0400
parents 0b58880da760
children af9313bec520
comparison
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0:0b58880da760 1:7c45c65f957b
2 <description>Assign sequences to taxonomy</description> 2 <description>Assign sequences to taxonomy</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 ## enable mothur to find blast 12 ## enable mothur to find blast
10 loc=`which mothur` && ln -s "\${loc%/mothur}"/* . && 13 loc=`which mothur` && ln -s "\${loc%/mothur}"/* . &&
11 14
12 ## create symlinks to input datasets 15 ## create symlinks to input datasets
13 ln -s "$fasta" fasta.dat && 16 ln -s "$fasta" fasta.dat &&
14 ln -s "$alignment.template" alignment.template.dat && 17 ln -s "$alignment.template" alignment.template.dat &&
15 ln -s "$tax.taxonomy" tax.taxonomy.dat && 18 ln -s "$tax.taxonomy" tax.taxonomy.dat &&
16 ln -s "$count" count.dat && 19 ln -s "$count" count.dat &&
20 ln -s "$name" name.dat &&
17 21
18 echo 'classify.seqs( 22 echo 'classify.seqs(
19 fasta=fasta.dat, 23 fasta=fasta.dat,
20 reference=alignment.template.dat, 24 reference=alignment.template.dat,
21 taxonomy=tax.taxonomy.dat, 25 taxonomy=tax.taxonomy.dat,
38 #end if 42 #end if
39 #end if 43 #end if
40 #if $count: 44 #if $count:
41 count=count.dat, 45 count=count.dat,
42 #end if 46 #end if
47 #if $name:
48 name=name.dat,
49 #end if
43 relabund=$relabund, 50 relabund=$relabund,
44 processors='\${GALAXY_SLOTS:-8}' 51 processors='\${GALAXY_SLOTS:-8}'
45 )' 52 )'
46 | sed 's/ //g' ## mothur trips over whitespace 53 | sed 's/ //g' ## mothur trips over whitespace
47 | ./mothur 54 | ./mothur
55 | tee mothur.out.log
48 ]]></command> 56 ]]></command>
49 <inputs> 57 <inputs>
50 <param name="fasta" type="data" format="fasta" label="fasta - Candiate Sequences"/> 58 <param name="fasta" type="data" format="fasta" label="fasta - Candiate Sequences"/>
51 <conditional name="alignment"> 59 <conditional name="alignment">
52 <param name="source" type="select" label="Select Reference Template from" help=""> 60 <param name="source" type="select" label="Select Reference Template from" help="">
110 <when value="distance"/> 118 <when value="distance"/>
111 </conditional> 119 </conditional>
112 </when> 120 </when>
113 </conditional> 121 </conditional>
114 <param name="count" type="data" format="mothur.count_table" label="count file" optional="true"/> 122 <param name="count" type="data" format="mothur.count_table" label="count file" optional="true"/>
123 <param name="name" type="data" format="mothur.names" label="names file" optional="true"/>
115 <param name="relabund" type="boolean" falsevalue="false" truevalue="true" checked="false" label="relabund - allows you to indicate that you want the summary files to be relative abundances rather than raw abundances. default=f"/> 124 <param name="relabund" type="boolean" falsevalue="false" truevalue="true" checked="false" label="relabund - allows you to indicate that you want the summary files to be relative abundances rather than raw abundances. default=f"/>
116 </inputs> 125 </inputs>
117 <outputs> 126 <outputs>
118 <expand macro="logfile-output"/> 127 <expand macro="logfile-output"/>
119 <data name="taxonomy_out" format="mothur.seq.taxonomy" from_work_dir="fasta*.taxonomy" label="${tool.name} on ${on_string}: taxonomy"/> 128 <data name="taxonomy_out" format="mothur.seq.taxonomy" from_work_dir="fasta*.taxonomy" label="${tool.name} on ${on_string}: taxonomy"/>
164 <help> 173 <help>
165 <![CDATA[ 174 <![CDATA[
166 175
167 @MOTHUR_OVERVIEW@ 176 @MOTHUR_OVERVIEW@
168 177
169 **Command Documenation** 178 **Command Documentation**
170 179
171 The classify.seqs_ command assigns sequences to chosen taxonomy outline. 180 The classify.seqs_ command assigns sequences to chosen taxonomy outline.
172 181
173 .. _classify.seqs: http://www.mothur.org/wiki/Classify.seqs 182 .. _classify.seqs: https://www.mothur.org/wiki/Classify.seqs
174 183
175 184
176 v1.22.0: Updated for Mothur 1.33. Added count parameter (1.28), added relabund parameter (1.33), bayesian term changed to wang. 185 v1.22.0: Updated for Mothur 1.33. Added count parameter (1.28), added relabund parameter (1.33), bayesian term changed to wang.
177 ]]> 186 ]]>
178 </help> 187 </help>