Mercurial > repos > iuc > mothur_classify_seqs

comparison classify.seqs.xml @ 0:0b58880da760 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
author iuc
date Fri, 24 Jun 2016 17:36:48 -0400
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children 7c45c65f957b
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-1:000000000000 0:0b58880da760
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="version_command"/>
8 <command detect_errors="aggressive"><![CDATA[
9 ## enable mothur to find blast
10 loc=`which mothur` && ln -s "\${loc%/mothur}"/* . &&
11
12 ## create symlinks to input datasets
13 ln -s "$fasta" fasta.dat &&
14 ln -s "$alignment.template" alignment.template.dat &&
15 ln -s "$tax.taxonomy" tax.taxonomy.dat &&
16 ln -s "$count" count.dat &&
17
18 echo 'classify.seqs(
19 fasta=fasta.dat,
20 reference=alignment.template.dat,
21 taxonomy=tax.taxonomy.dat,
22 method=$classify.method,
23 #if $classify.method == "wang":
24 ksize=$classify.ksize,
25 iters=$classify.iters,
26 cutoff=$classify.cutoff,
27 probs=$classify.probs,
28 #elif $classify.method == "knn":
29 numwanted=$classify.numwanted,
30 search=$classify.search.algorithm,
31 #if $classify.search.algorithm == "kmer":
32 ksize=$classify.search.ksize,
33 #elif $classify.search.algorithm == "blast":
34 match=$classify.search.match,
35 mismatch=$classify.search.mismatch,
36 gapopen=$classify.search.gapopen,
37 gapextend=$classify.search.gapextend,
38 #end if
39 #end if
40 #if $count:
41 count=count.dat,
42 #end if
43 relabund=$relabund,
44 processors='\${GALAXY_SLOTS:-8}'
45 )'
46 | sed 's/ //g' ## mothur trips over whitespace
47 | ./mothur
48 ]]></command>
49 <inputs>
50 <param name="fasta" type="data" format="fasta" label="fasta - Candiate Sequences"/>
51 <conditional name="alignment">
52 <param name="source" type="select" label="Select Reference Template from" help="">
53 <option value="hist">History</option>
54 <option value="ref">Cached Reference</option>
55 </param>
56 <when value="ref">
57 <param name="template" type="select" label="reference - Select an alignment database " help="">
58 <options from_data_table="mothur_aligndb">
59 </options>
60 </param>
61 </when>
62 <when value="hist">
63 <param name="template" type="data" format="fasta" label="reference - Reference to align with" help=""/>
64 </when>
65 </conditional>
66 <conditional name="tax">
67 <param name="source2" type="select" label="Select Taxonomy from" help="">
68 <option value="ref">Cached Reference</option>
69 <option value="hist">History</option>
70 </param>
71 <when value="ref">
72 <param name="taxonomy" type="select" format="mothur.seq.taxonomy" label="taxonomy - Taxonomy reference">
73 <options from_data_table="mothur_taxonomy"/>
74 </param>
75 </when>
76 <when value="hist">
77 <param name="taxonomy" type="data" format="mothur.seq.taxonomy" label="taxonomy - Taxonomy reference"/>
78 </when>
79 </conditional>
80 <conditional name="classify">
81 <param name="method" type="select" label="method - Select a classification method" help="">
82 <option value="wang" selected="true">Bayesian (default)</option>
83 <option value="knn">K-Nearest Neighbor (knn)</option>
84 </param>
85 <when value="wang">
86 <param name="ksize" type="integer" value="8" min="1" label="ksize - kmer length"/>
87 <param name="iters" type="integer" value="100" min="1" label="iters - iterations to do when calculating the bootstrap confidence score"/>
88 <param name="cutoff" type="integer" value="0" min="0" label="cutoff - specify a bootstrap confidence threshold for your taxonomy"/>
89 <param name="probs" type="boolean" falsevalue="false" truevalue="true" checked="true" label="probs - Show probabilities"/>
90 </when>
91 <when value="knn">
92 <param name="numwanted" type="integer" value="10" label="numwanted - the number of sequence matches you want with the knn method"/>
93 <conditional name="search">
94 <param name="algorithm" type="select" label="algorithm - " help="">
95 <option value="kmer" selected="true">Kmer (default)</option>
96 <option value="blast">BLAST</option>
97 <option value="suffix">Suffix Tree</option>
98 <option value="distance">Distance</option>
99 </param>
100 <when value="kmer">
101 <param name="ksize" type="integer" value="8" min="1" label="ksize - kmer length"/>
102 </when>
103 <when value="blast">
104 <param name="match" type="integer" value="1" label="match - Pairwise alignment reward for a match"/>
105 <param name="mismatch" type="integer" value="-1" label="mismatch - Pairwise alignment penalty for a mismatch"/>
106 <param name="gapopen" type="integer" value="-2" label="gapopen - Pairwise alignment penalty for opening a gap"/>
107 <param name="gapextend" type="integer" value="-1" label="gapextend - Pairwise alignment penalty for extending a gap"/>
108 </when>
109 <when value="suffix"/>
110 <when value="distance"/>
111 </conditional>
112 </when>
113 </conditional>
114 <param name="count" type="data" format="mothur.count_table" label="count 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"/>
116 </inputs>
117 <outputs>
118 <expand macro="logfile-output"/>
119 <data name="taxonomy_out" format="mothur.seq.taxonomy" from_work_dir="fasta*.taxonomy" label="${tool.name} on ${on_string}: taxonomy"/>
120 <data name="tax_summary" format="mothur.tax.summary" from_work_dir="fasta*.tax.summary" label="${tool.name} on ${on_string}: tax.summary"/>
121 <data name="tree_sum" format="tabular" from_work_dir="tax.taxonomy*.tree.sum" label="${tool.name} on ${on_string}: tree.sum"/>
122 </outputs>
123 <tests>
124 <test><!-- test with wang method -->
125 <param name="fasta" value="amazon.fasta" ftype="fasta"/>
126 <param name="source" value="hist"/>
127 <param name="template" value="abrecovery.fasta" ftype="fasta"/>
128 <param name="source2" value="hist"/>
129 <param name="taxonomy" value="abrecovery.pds.wang.taxonomy" ftype="mothur.seq.taxonomy"/>
130 <output name="tax_summary" md5="d6f02a20cdf415fb84e394d0dab2314f" ftype="mothur.tax.summary"/>
131 <output name="taxonomy_out" ftype="mothur.seq.taxonomy">
132 <assert_contents>
133 <has_text text="Bacteria"/>
134 <has_text text="U68589"/>
135 </assert_contents>
136 </output>
137 <output name="tree_sum" md5="a6ae5cc82edd181082dd23f348b621d9" ftype="tabular"/>
138 <expand macro="logfile-test"/>
139 </test>
140 <test><!-- test with knn method -->
141 <param name="fasta" value="amazon.fasta" ftype="fasta"/>
142 <param name="source" value="hist"/>
143 <param name="template" value="abrecovery.fasta" ftype="fasta"/>
144 <param name="source2" value="hist"/>
145 <param name="taxonomy" value="abrecovery.pds.wang.taxonomy" ftype="mothur.seq.taxonomy"/>
146 <param name="method" value="knn"/>
147 <output name="tax_summary" md5="4931072238dcf29344f4a1e3332f3415" ftype="mothur.tax.summary"/>
148 <output name="taxonomy_out" md5="1080c7676c1a1f4f429c7d8df6a62f47" ftype="mothur.seq.taxonomy"/>
149 <expand macro="logfile-test"/>
150 </test>
151 <test><!-- test with knn method and blast algorithm -->
152 <param name="fasta" value="abrecovery.fasta" ftype="fasta"/>
153 <param name="source" value="hist"/>
154 <param name="template" value="abrecovery.fasta" ftype="fasta"/>
155 <param name="source2" value="hist"/>
156 <param name="taxonomy" value="abrecovery.pds.wang.taxonomy" ftype="mothur.seq.taxonomy"/>
157 <param name="method" value="knn"/>
158 <param name="algorithm" value="blast"/>
159 <output name="tax_summary" md5="4d6e1fa3be9abe5f57b0660fe5ae5887" ftype="mothur.tax.summary"/>
160 <output name="taxonomy_out" md5="1296e2a2c8efd58f9c840760bed55042" ftype="mothur.seq.taxonomy"/>
161 <expand macro="logfile-test"/>
162 </test>
163 </tests>
164 <help>
165 <![CDATA[
166
167 @MOTHUR_OVERVIEW@
168
169 **Command Documenation**
170
171 The classify.seqs_ command assigns sequences to chosen taxonomy outline.
172
173 .. _classify.seqs: http://www.mothur.org/wiki/Classify.seqs
174
175
176 v1.22.0: Updated for Mothur 1.33. Added count parameter (1.28), added relabund parameter (1.33), bayesian term changed to wang.
177 ]]>
178 </help>
179 <expand macro="citations"/>
180 </tool>