Mercurial > repos > iuc > mothur_classify_seqs

comparison classify.seqs.xml @ 0:2a0d8b8c3ade draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author iuc
date Fri, 19 May 2017 05:13:36 -0400
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children cc9c7b550c29
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-1:000000000000 0:2a0d8b8c3ade
1 <tool profile="16.07" id="mothur_classify_seqs" name="Classify.seqs" version="@WRAPPER_VERSION@.0">
2 <description>Assign sequences to taxonomy</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <expand macro="stdio"/>
8 <expand macro="version_command"/>
9 <command><![CDATA[
10 @SHELL_OPTIONS@
11
12 ## enable mothur to find blast
13 loc=`which mothur` && ln -s "\${loc%/mothur}"/* . &&
14
15 ## create symlinks to input datasets
16 ln -s "$fasta" fasta.dat &&
17 ln -s "$alignment.template" alignment.template.dat &&
18 ln -s "$tax.taxonomy" tax.taxonomy.dat &&
19 ln -s "$count" count.dat &&
20 ln -s "$name" name.dat &&
21
22 echo 'classify.seqs(
23 fasta=fasta.dat,
24 reference=alignment.template.dat,
25 taxonomy=tax.taxonomy.dat,
26 method=$classify.method,
27 #if $classify.method == "wang":
28 ksize=$classify.ksize,
29 iters=$classify.iters,
30 cutoff=$classify.cutoff,
31 probs=$classify.probs,
32 #elif $classify.method == "knn":
33 numwanted=$classify.numwanted,
34 search=$classify.search.algorithm,
35 #if $classify.search.algorithm == "kmer":
36 ksize=$classify.search.ksize,
37 #elif $classify.search.algorithm == "blast":
38 match=$classify.search.match,
39 mismatch=$classify.search.mismatch,
40 gapopen=$classify.search.gapopen,
41 gapextend=$classify.search.gapextend,
42 #end if
43 #end if
44 #if $count:
45 count=count.dat,
46 #end if
47 #if $name:
48 name=name.dat,
49 #end if
50 relabund=$relabund,
51 processors='\${GALAXY_SLOTS:-8}'
52 )'
53 | sed 's/ //g' ## mothur trips over whitespace
54 | ./mothur
55 | tee mothur.out.log
56 ]]></command>
57 <inputs>
58 <param name="fasta" type="data" format="fasta" label="fasta - Candiate Sequences"/>
59 <conditional name="alignment">
60 <param name="source" type="select" label="Select Reference Template from" help="">
61 <option value="hist">History</option>
62 <option value="ref">Cached Reference</option>
63 </param>
64 <when value="ref">
65 <param name="template" type="select" label="reference - Select an alignment database " help="">
66 <options from_data_table="mothur_aligndb">
67 </options>
68 </param>
69 </when>
70 <when value="hist">
71 <param name="template" type="data" format="fasta" label="reference - Reference to align with" help=""/>
72 </when>
73 </conditional>
74 <conditional name="tax">
75 <param name="source2" type="select" label="Select Taxonomy from" help="">
76 <option value="ref">Cached Reference</option>
77 <option value="hist">History</option>
78 </param>
79 <when value="ref">
80 <param name="taxonomy" type="select" format="mothur.seq.taxonomy" label="taxonomy - Taxonomy reference">
81 <options from_data_table="mothur_taxonomy"/>
82 </param>
83 </when>
84 <when value="hist">
85 <param name="taxonomy" type="data" format="mothur.seq.taxonomy" label="taxonomy - Taxonomy reference"/>
86 </when>
87 </conditional>
88 <conditional name="classify">
89 <param name="method" type="select" label="method - Select a classification method" help="">
90 <option value="wang" selected="true">Bayesian (default)</option>
91 <option value="knn">K-Nearest Neighbor (knn)</option>
92 </param>
93 <when value="wang">
94 <param name="ksize" type="integer" value="8" min="1" label="ksize - kmer length"/>
95 <param name="iters" type="integer" value="100" min="1" label="iters - iterations to do when calculating the bootstrap confidence score"/>
96 <param name="cutoff" type="integer" value="0" min="0" label="cutoff - specify a bootstrap confidence threshold for your taxonomy"/>
97 <param name="probs" type="boolean" falsevalue="false" truevalue="true" checked="true" label="probs - Show probabilities"/>
98 </when>
99 <when value="knn">
100 <param name="numwanted" type="integer" value="10" label="numwanted - the number of sequence matches you want with the knn method"/>
101 <conditional name="search">
102 <param name="algorithm" type="select" label="algorithm - " help="">
103 <option value="kmer" selected="true">Kmer (default)</option>
104 <option value="blast">BLAST</option>
105 <option value="suffix">Suffix Tree</option>
106 <option value="distance">Distance</option>
107 </param>
108 <when value="kmer">
109 <param name="ksize" type="integer" value="8" min="1" label="ksize - kmer length"/>
110 </when>
111 <when value="blast">
112 <param name="match" type="integer" value="1" label="match - Pairwise alignment reward for a match"/>
113 <param name="mismatch" type="integer" value="-1" label="mismatch - Pairwise alignment penalty for a mismatch"/>
114 <param name="gapopen" type="integer" value="-2" label="gapopen - Pairwise alignment penalty for opening a gap"/>
115 <param name="gapextend" type="integer" value="-1" label="gapextend - Pairwise alignment penalty for extending a gap"/>
116 </when>
117 <when value="suffix"/>
118 <when value="distance"/>
119 </conditional>
120 </when>
121 </conditional>
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"/>
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"/>
125 </inputs>
126 <outputs>
127 <expand macro="logfile-output"/>
128 <data name="taxonomy_out" format="mothur.seq.taxonomy" from_work_dir="fasta*.taxonomy" label="${tool.name} on ${on_string}: taxonomy"/>
129 <data name="tax_summary" format="mothur.tax.summary" from_work_dir="fasta*.tax.summary" label="${tool.name} on ${on_string}: tax.summary"/>
130 <data name="tree_sum" format="tabular" from_work_dir="tax.taxonomy*.tree.sum" label="${tool.name} on ${on_string}: tree.sum"/>
131 </outputs>
132 <tests>
133 <test><!-- test with wang method -->
134 <param name="fasta" value="amazon.fasta" ftype="fasta"/>
135 <param name="source" value="hist"/>
136 <param name="template" value="abrecovery.fasta" ftype="fasta"/>
137 <param name="source2" value="hist"/>
138 <param name="taxonomy" value="abrecovery.pds.wang.taxonomy" ftype="mothur.seq.taxonomy"/>
139 <output name="tax_summary" md5="d6f02a20cdf415fb84e394d0dab2314f" ftype="mothur.tax.summary"/>
140 <output name="taxonomy_out" ftype="mothur.seq.taxonomy">
141 <assert_contents>
142 <has_text text="Bacteria"/>
143 <has_text text="U68589"/>
144 </assert_contents>
145 </output>
146 <output name="tree_sum" md5="a6ae5cc82edd181082dd23f348b621d9" ftype="tabular"/>
147 <expand macro="logfile-test"/>
148 </test>
149 <test><!-- test with knn method -->
150 <param name="fasta" value="amazon.fasta" ftype="fasta"/>
151 <param name="source" value="hist"/>
152 <param name="template" value="abrecovery.fasta" ftype="fasta"/>
153 <param name="source2" value="hist"/>
154 <param name="taxonomy" value="abrecovery.pds.wang.taxonomy" ftype="mothur.seq.taxonomy"/>
155 <param name="method" value="knn"/>
156 <output name="tax_summary" md5="4931072238dcf29344f4a1e3332f3415" ftype="mothur.tax.summary"/>
157 <output name="taxonomy_out" md5="1080c7676c1a1f4f429c7d8df6a62f47" ftype="mothur.seq.taxonomy"/>
158 <expand macro="logfile-test"/>
159 </test>
160 <test><!-- test with knn method and blast algorithm -->
161 <param name="fasta" value="abrecovery.fasta" ftype="fasta"/>
162 <param name="source" value="hist"/>
163 <param name="template" value="abrecovery.fasta" ftype="fasta"/>
164 <param name="source2" value="hist"/>
165 <param name="taxonomy" value="abrecovery.pds.wang.taxonomy" ftype="mothur.seq.taxonomy"/>
166 <param name="method" value="knn"/>
167 <param name="algorithm" value="blast"/>
168 <output name="tax_summary" md5="4d6e1fa3be9abe5f57b0660fe5ae5887" ftype="mothur.tax.summary"/>
169 <output name="taxonomy_out" md5="1296e2a2c8efd58f9c840760bed55042" ftype="mothur.seq.taxonomy"/>
170 <expand macro="logfile-test"/>
171 </test>
172 </tests>
173 <help>
174 <![CDATA[
175
176 @MOTHUR_OVERVIEW@
177
178 **Command Documentation**
179
180 The classify.seqs_ command assigns sequences to chosen taxonomy outline.
181
182 .. _classify.seqs: https://www.mothur.org/wiki/Classify.seqs
183
184
185 v1.22.0: Updated for Mothur 1.33. Added count parameter (1.28), added relabund parameter (1.33), bayesian term changed to wang.
186 ]]>
187 </help>
188 <expand macro="citations"/>
189 </tool>