Mercurial > repos > iuc > mothur_classify_seqs

comparison classify.seqs.xml @ 4:5780dd6cfec9 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
author iuc
date Wed, 14 Feb 2018 09:36:32 -0500
parents af9313bec520
children a4e9f02da98c
comparison
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3:af9313bec520 4:5780dd6cfec9
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <expand macro="stdio"/> 7 <expand macro="stdio"/>
8 <expand macro="version_command"/> 8 <expand macro="version_command"/>
9 <command><![CDATA[ 9 <command><![CDATA[
10 @SHELL_OPTIONS@ 10 @SHELL_OPTIONS@
11 11
12 ## enable mothur to find blast 12 ## enable mothur to find blast
13 loc=`which mothur` && ln -s "\${loc%/mothur}"/* . && 13 ln -s `dirname \$(which mothur)`/* . &&
14 14
15 ## create symlinks to input datasets 15 ## create symlinks to input datasets
16 ln -s "$fasta" fasta.dat && 16 ln -s '$fasta' fasta.dat &&
17 ln -s "$alignment.template" alignment.template.dat && 17 ln -s '$alignment.template' alignment.template.dat &&
18 ln -s "$tax.taxonomy" tax.taxonomy.dat && 18 ln -s '$tax.taxonomy' tax.taxonomy.dat &&
19 ln -s "$count" count.dat && 19 ln -s '$count' count.dat &&
20 ln -s "$name" name.dat && 20 ln -s '$name' name.dat &&
21 21
22 echo 'classify.seqs( 22 echo 'classify.seqs(
23 fasta=fasta.dat, 23 fasta=fasta.dat,
24 reference=alignment.template.dat, 24 reference=alignment.template.dat,
25 taxonomy=tax.taxonomy.dat, 25 taxonomy=tax.taxonomy.dat,
26 method=$classify.method, 26 method=$classify.method,
27 #if $classify.method == "wang": 27 #if $classify.method == "wang":
28 ksize=$classify.ksize, 28 ksize=$classify.ksize,
29 iters=$classify.iters, 29 iters=$classify.iters,
30 cutoff=$classify.cutoff, 30 cutoff=$classify.cutoff,
31 probs=$classify.probs, 31 probs=$classify.probs,
32 #elif $classify.method == "knn": 32 #elif $classify.method == "knn":
33 numwanted=$classify.numwanted, 33 numwanted=$classify.numwanted,
34 search=$classify.search.algorithm, 34 search=$classify.search.algorithm,
35 #if $classify.search.algorithm == "kmer": 35 #if $classify.search.algorithm == "kmer":
36 ksize=$classify.search.ksize, 36 ksize=$classify.search.ksize,
37 #elif $classify.search.algorithm == "blast": 37 #elif $classify.search.algorithm == "blast":
38 match=$classify.search.match, 38 match=$classify.search.match,
39 mismatch=$classify.search.mismatch, 39 mismatch=$classify.search.mismatch,
40 gapopen=$classify.search.gapopen, 40 gapopen=$classify.search.gapopen,
41 gapextend=$classify.search.gapextend, 41 gapextend=$classify.search.gapextend,
42 #end if 42 #end if
43 #end if 43 #end if
44 #if $count: 44 #if $count:
45 count=count.dat, 45 count=count.dat,
46 #end if 46 #end if
47 #if $name: 47 #if $name:
48 name=name.dat, 48 name=name.dat,
49 #end if 49 #end if
50 relabund=$relabund, 50 relabund=$relabund,
51 processors='\${GALAXY_SLOTS:-8}' 51 output=$output,
52 )' 52 printlevel=$printlevel,
53 | sed 's/ //g' ## mothur trips over whitespace 53 processors='\${GALAXY_SLOTS:-8}'
54 | ./mothur 54 )'
55 | tee mothur.out.log 55 | sed 's/ //g' ## mothur trips over whitespace
56 | ./mothur
57 | tee mothur.out.log
56 ]]></command> 58 ]]></command>
57 <inputs> 59 <inputs>
58 <param name="fasta" type="data" format="fasta" label="fasta - Candiate Sequences"/> 60 <param argument="fasta" type="data" format="fasta" label="fasta - Candiate Sequences"/>
59 <conditional name="alignment"> 61 <conditional name="alignment">
60 <param name="source" type="select" label="Select Reference Template from" help=""> 62 <param name="source" type="select" label="Select Reference Template from">
61 <option value="hist">History</option> 63 <option value="hist">History</option>
62 <option value="ref">Cached Reference</option> 64 <option value="ref">Cached Reference</option>
63 </param> 65 </param>
64 <when value="ref"> 66 <when value="ref">
65 <param name="template" type="select" label="reference - Select an alignment database " help=""> 67 <param argument="reference" name="template" type="select" label="reference - Select an alignment database " help="">
66 <options from_data_table="mothur_aligndb"> 68 <options from_data_table="mothur_aligndb">
67 </options> 69 </options>
68 </param> 70 </param>
69 </when> 71 </when>
70 <when value="hist"> 72 <when value="hist">
71 <param name="template" type="data" format="fasta" label="reference - Reference to align with" help=""/> 73 <param argument="reference" name="template" type="data" format="fasta" label="reference - Reference to align with" help=""/>
72 </when> 74 </when>
73 </conditional> 75 </conditional>
74 <conditional name="tax"> 76 <conditional name="tax">
75 <param name="source2" type="select" label="Select Taxonomy from" help=""> 77 <param name="source2" type="select" label="Select Taxonomy from">
76 <option value="ref">Cached Reference</option> 78 <option value="ref">Cached Reference</option>
77 <option value="hist">History</option> 79 <option value="hist">History</option>
78 </param> 80 </param>
79 <when value="ref"> 81 <when value="ref">
80 <param name="taxonomy" type="select" format="mothur.seq.taxonomy" label="taxonomy - Taxonomy reference"> 82 <param argument="taxonomy" type="select" format="mothur.seq.taxonomy" label="taxonomy - Taxonomy reference">
81 <options from_data_table="mothur_taxonomy"/> 83 <options from_data_table="mothur_taxonomy"/>
82 </param> 84 </param>
83 </when> 85 </when>
84 <when value="hist"> 86 <when value="hist">
85 <param name="taxonomy" type="data" format="mothur.seq.taxonomy" label="taxonomy - Taxonomy reference"/> 87 <param argument="taxonomy" type="data" format="mothur.seq.taxonomy" label="taxonomy - Taxonomy reference"/>
86 </when> 88 </when>
87 </conditional> 89 </conditional>
88 <conditional name="classify"> 90 <conditional name="classify">
89 <param name="method" type="select" label="method - Select a classification method" help=""> 91 <param argument="method" type="select" label="method - Select a classification method">
90 <option value="wang" selected="true">Wang (default)</option> 92 <option value="wang" selected="true">Wang (default)</option>
91 <option value="knn">K-Nearest Neighbor (knn)</option> 93 <option value="knn">K-Nearest Neighbor (knn)</option>
92 </param> 94 </param>
93 <when value="wang"> 95 <when value="wang">
94 <param name="ksize" type="integer" value="8" min="1" label="ksize - kmer length"/> 96 <param argument="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"/> 97 <param argument="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"/> 98 <param argument="cutoff" type="integer" value="80" 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"/> 99 <param argument="probs" type="boolean" falsevalue="false" truevalue="true" checked="true" label="probs - Show probabilities"/>
98 </when> 100 </when>
99 <when value="knn"> 101 <when value="knn">
100 <param name="numwanted" type="integer" value="10" label="numwanted - the number of sequence matches you want with the knn method"/> 102 <param argument="numwanted" type="integer" value="10" label="numwanted - the number of sequence matches you want with the knn method"/>
101 <conditional name="search"> 103 <conditional name="search">
102 <param name="algorithm" type="select" label="algorithm - " help=""> 104 <param argument="search" name="algorithm" type="select" label="algorithm - " help="">
103 <option value="kmer" selected="true">Kmer (default)</option> 105 <option value="kmer" selected="true">Kmer (default)</option>
104 <option value="blast">BLAST</option> 106 <option value="blast">BLAST</option>
105 <option value="suffix">Suffix Tree</option> 107 <option value="suffix">Suffix Tree</option>
106 <option value="distance">Distance</option> 108 <option value="distance">Distance</option>
107 </param> 109 </param>
108 <when value="kmer"> 110 <when value="kmer">
109 <param name="ksize" type="integer" value="8" min="1" label="ksize - kmer length"/> 111 <param argument="ksize" type="integer" value="8" min="1" label="ksize - kmer length"/>
110 </when> 112 </when>
111 <when value="blast"> 113 <when value="blast">
112 <param name="match" type="integer" value="1" label="match - Pairwise alignment reward for a match"/> 114 <param argument="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"/> 115 <param argument="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"/> 116 <param argument="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"/> 117 <param argument="gapextend" type="integer" value="-1" label="gapextend - Pairwise alignment penalty for extending a gap"/>
116 </when> 118 </when>
117 <when value="suffix"/> 119 <when value="suffix"/>
118 <when value="distance"/> 120 <when value="distance"/>
119 </conditional> 121 </conditional>
120 </when> 122 </when>
121 </conditional> 123 </conditional>
122 <param name="count" type="data" format="mothur.count_table" label="count file" optional="true"/> 124 <param argument="count" type="data" format="mothur.count_table" optional="true" label="count file"/>
123 <param name="name" type="data" format="mothur.names" label="names file" optional="true"/> 125 <param argument="name" type="data" format="mothur.names" optional="true" label="names file"/>
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"/> 126 <param argument="relabund" type="boolean" falsevalue="false" truevalue="true" checked="false"
127 label="relabund - allows you to indicate that you want the summary files to be relative abundances rather than raw abundances"/>
128 <expand macro="param-output"/>
129 <expand macro="param-printlevel"/>
125 </inputs> 130 </inputs>
126 <outputs> 131 <outputs>
127 <expand macro="logfile-output"/> 132 <expand macro="logfile-output"/>
128 <data name="taxonomy_out" format="mothur.seq.taxonomy" from_work_dir="fasta*.taxonomy" label="${tool.name} on ${on_string}: taxonomy"/> 133 <data name="taxonomy_out" format="mothur.seq.taxonomy" from_work_dir="fasta*.taxonomy" label="${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 ${on_string}: tax.summary"/> 134 <data name="tax_summary" format="mothur.tax.summary" from_work_dir="fasta*.tax.summary" label="${tool.name} on ${on_string}: tax.summary"/>
134 <param name="fasta" value="amazon.fasta" ftype="fasta"/> 139 <param name="fasta" value="amazon.fasta" ftype="fasta"/>
135 <param name="source" value="hist"/> 140 <param name="source" value="hist"/>
136 <param name="template" value="abrecovery.fasta" ftype="fasta"/> 141 <param name="template" value="abrecovery.fasta" ftype="fasta"/>
137 <param name="source2" value="hist"/> 142 <param name="source2" value="hist"/>
138 <param name="taxonomy" value="abrecovery.pds.wang.taxonomy" ftype="mothur.seq.taxonomy"/> 143 <param name="taxonomy" value="abrecovery.pds.wang.taxonomy" ftype="mothur.seq.taxonomy"/>
139 <output name="tax_summary" md5="d6f02a20cdf415fb84e394d0dab2314f" ftype="mothur.tax.summary"/> 144 <output name="tax_summary" ftype="mothur.tax.summary">
145 <assert_contents>
146 <expand macro="test-taxsummary-format"/>
147 <has_text text="Root"/>
148 <has_text text="Bacteria"/>
149 </assert_contents>
150 </output>
140 <output name="taxonomy_out" ftype="mothur.seq.taxonomy"> 151 <output name="taxonomy_out" ftype="mothur.seq.taxonomy">
141 <assert_contents> 152 <assert_contents>
142 <has_text text="Bacteria"/> 153 <has_text text="Bacteria"/>
143 <has_text text="U68589"/> 154 <has_text text="U68589"/>
144 </assert_contents> 155 </assert_contents>
145 </output> 156 </output>
146 <output name="tree_sum" md5="a6ae5cc82edd181082dd23f348b621d9" ftype="tabular"/> 157 <output name="tree_sum" md5="b44a392a719cf083e5a26d45904926c6" ftype="tabular">
158 <assert_contents>
159 <has_text text="@WRAPPER_VERSION@"/>
160 <has_text text="Root"/>
161 <has_text text="Bacteria"/>
162 </assert_contents>
163 </output>
147 <expand macro="logfile-test"/> 164 <expand macro="logfile-test"/>
148 </test> 165 </test>
149 <test><!-- test with knn method --> 166 <test><!-- test with knn method -->
150 <param name="fasta" value="amazon.fasta" ftype="fasta"/> 167 <param name="fasta" value="amazon.fasta" ftype="fasta"/>
151 <param name="source" value="hist"/> 168 <param name="source" value="hist"/>
152 <param name="template" value="abrecovery.fasta" ftype="fasta"/> 169 <param name="template" value="abrecovery.fasta" ftype="fasta"/>
153 <param name="source2" value="hist"/> 170 <param name="source2" value="hist"/>
154 <param name="taxonomy" value="abrecovery.pds.wang.taxonomy" ftype="mothur.seq.taxonomy"/> 171 <param name="taxonomy" value="abrecovery.pds.wang.taxonomy" ftype="mothur.seq.taxonomy"/>
155 <param name="method" value="knn"/> 172 <param name="method" value="knn"/>
156 <output name="tax_summary" md5="4931072238dcf29344f4a1e3332f3415" ftype="mothur.tax.summary"/> 173 <output name="tax_summary" ftype="mothur.tax.summary">
157 <output name="taxonomy_out" md5="1080c7676c1a1f4f429c7d8df6a62f47" ftype="mothur.seq.taxonomy"/> 174 <assert_contents>
175 <expand macro="test-taxsummary-format"/>
176 <has_text text="Root"/>
177 <has_text text="Bacteria"/>
178 </assert_contents>
179 </output>
180 <output name="taxonomy_out" ftype="mothur.seq.taxonomy">
181 <assert_contents>
182 <has_text text="Bacteria"/>
183 <has_text text="U68589"/>
184 </assert_contents>
185 </output>
158 <expand macro="logfile-test"/> 186 <expand macro="logfile-test"/>
159 </test> 187 </test>
160 <test><!-- test with knn method and blast algorithm --> 188 <test><!-- test with knn method and blast algorithm -->
161 <param name="fasta" value="abrecovery.fasta" ftype="fasta"/> 189 <param name="fasta" value="abrecovery.fasta" ftype="fasta"/>
162 <param name="source" value="hist"/> 190 <param name="source" value="hist"/>
163 <param name="template" value="abrecovery.fasta" ftype="fasta"/> 191 <param name="template" value="abrecovery.fasta" ftype="fasta"/>
164 <param name="source2" value="hist"/> 192 <param name="source2" value="hist"/>
165 <param name="taxonomy" value="abrecovery.pds.wang.taxonomy" ftype="mothur.seq.taxonomy"/> 193 <param name="taxonomy" value="abrecovery.pds.wang.taxonomy" ftype="mothur.seq.taxonomy"/>
166 <param name="method" value="knn"/> 194 <param name="method" value="knn"/>
167 <param name="algorithm" value="blast"/> 195 <param name="algorithm" value="blast"/>
168 <output name="tax_summary" md5="4d6e1fa3be9abe5f57b0660fe5ae5887" ftype="mothur.tax.summary"/> 196 <output name="tax_summary" ftype="mothur.tax.summary">
169 <output name="taxonomy_out" md5="1296e2a2c8efd58f9c840760bed55042" ftype="mothur.seq.taxonomy"/> 197 <assert_contents>
198 <expand macro="test-taxsummary-format"/>
199 <has_text text="Root"/>
200 <has_text text="Bacteria"/>
201 </assert_contents>
202 </output>
203 <output name="taxonomy_out" ftype="mothur.seq.taxonomy">
204 <assert_contents>
205 <has_text text="Bacteria"/>
206 <has_text text="AY457914"/>
207 </assert_contents>
208 </output>
170 <expand macro="logfile-test"/> 209 <expand macro="logfile-test"/>
171 </test> 210 </test>
172 </tests> 211 </tests>
173 <help> 212 <help><![CDATA[
174 <![CDATA[
175 213
176 @MOTHUR_OVERVIEW@ 214 @MOTHUR_OVERVIEW@
177 215
178 **Command Documentation** 216 **Command Documentation**
179 217
181 219
182 .. _classify.seqs: https://www.mothur.org/wiki/Classify.seqs 220 .. _classify.seqs: https://www.mothur.org/wiki/Classify.seqs
183 221
184 222
185 v1.22.0: Updated for Mothur 1.33. Added count parameter (1.28), added relabund parameter (1.33), bayesian term changed to wang. 223 v1.22.0: Updated for Mothur 1.33. Added count parameter (1.28), added relabund parameter (1.33), bayesian term changed to wang.
186 ]]> 224
187 </help> 225 ]]></help>
188 <expand macro="citations"/> 226 <expand macro="citations"/>
189 </tool> 227 </tool>