Mercurial > repos > iuc > mothur_classify_otu

comparison classify.otu.xml @ 3:ccbf829666b6 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 09:34:34 -0500
parents 225b9e8ba32d
children 5301655f34bb
comparison
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2:248a0277c324 3:ccbf829666b6
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 ## create symlinks to input datasets 12 ## create symlinks to input datasets
13 ln -s "$otu" otu.dat && 13 ln -s '$otu' otu.dat &&
14 ln -s "$tax.taxonomy" tax.taxonomy.dat && 14 ln -s '$tax.taxonomy' tax.taxonomy.dat &&
15 ln -s "$name" name.dat && 15 ln -s '$name' name.dat &&
16 ln -s "$count" count.dat && 16 ln -s '$count' count.dat &&
17 ln -s "$group" group.dat && 17 ln -s '$group' group.dat &&
18 #if $reftax.source2: 18
19 ln -s "$reftax.taxonomy" myreftax.taxonomy && 19 echo 'classify.otu(
20 ln -s "$sum" myreftax.tree.sum && 20 list=otu.dat,
21 #end if 21 taxonomy=tax.taxonomy.dat,
22 22 #if $name:
23 echo 'classify.otu( 23 name=name.dat,
24 list=otu.dat, 24 #end if
25 taxonomy=tax.taxonomy.dat, 25 #if $count:
26 #if $name: 26 count=count.dat,
27 name=name.dat, 27 #end if
28 #end if 28 #if $label:
29 #if $count: 29 label=${ str($label).replace(",","-") },
30 count=count.dat, 30 #end if
31 #end if 31 #if $group:
32 #if $reftax.source2: 32 group=group.dat,
33 reftaxonomy=myreftax.taxonomy, 33 #end if
34 #end if 34 basis=$basis,
35 #if $label: 35 probs=$probs,
36 label=${ str($label).replace(",","-") }, 36 persample=$persample,
37 #end if 37 cutoff=$cutoff,
38 #if $group: 38 relabund=$relabund,
39 group=group.dat, 39 output=$output,
40 #end if 40 printlevel=$printlevel
41 basis=$basis, 41 )'
42 probs=$probs, 42 | sed 's/ //g' ## mothur trips over whitespace
43 persample=$persample, 43 | mothur
44 cutoff=$cutoff 44 | tee mothur.out.log
45 )'
46 | sed 's/ //g' ## mothur trips over whitespace
47 | mothur
48 | tee mothur.out.log
49 ]]></command> 45 ]]></command>
50 <inputs> 46 <inputs>
51 <param name="otu" type="data" format="mothur.list" label="list - OTU List "/> 47 <param argument="list" name="otu" type="data" format="mothur.list" label="list - OTU List "/>
52 <param name="name" type="data" format="mothur.names" optional="true" label="name - taxonomy sequence names"/> 48 <param argument="name" type="data" format="mothur.names" optional="true" label="name - taxonomy sequence names"/>
53 <param name="count" type="data" format="mothur.count_table" optional="true" label="count - used to represent the number of duplicate sequences for a given representative sequence"/> 49 <param argument="count" type="data" format="mothur.count_table" optional="true" label="count - used to represent the number of duplicate sequences for a given representative sequence"/>
54 <conditional name="tax"> 50 <conditional name="tax">
55 <param name="source" type="select" label="Select Taxonomy from" help=""> 51 <param name="source" type="select" label="Select Taxonomy from" help="">
56 <option value="hist">History</option> 52 <option value="hist">History</option>
57 <option value="ref">Cached Reference</option> 53 <option value="ref">Cached Reference</option>
58 </param> 54 </param>
59 <when value="ref"> 55 <when value="ref">
60 <param name="taxonomy" type="select" format="mothur.seq.taxonomy" label="taxonomy - Taxonomy Reference"> 56 <param argument="taxonomy" type="select" format="mothur.seq.taxonomy" label="taxonomy - Taxonomy Reference">
61 <options from_data_table="mothur_taxonomy"/> 57 <options from_data_table="mothur_taxonomy"/>
62 </param> 58 </param>
63 </when> 59 </when>
64 <when value="hist"> 60 <when value="hist">
65 <param name="taxonomy" type="data" format="mothur.seq.taxonomy" label="taxonomy - Taxonomy Reference"/> 61 <param argument="taxonomy" type="data" format="mothur.seq.taxonomy" label="taxonomy - Taxonomy Reference"/>
66 </when> 62 </when>
67 </conditional> 63 </conditional>
68 <conditional name="reftax"> 64 <param argument="label" type="select" label="label - OTU Labels" multiple="true">
69 <param name="source2" type="select" label="Select Reference Taxonomy used in Classify.seqs from" help="Including the reference taxonomy file used when you classified your sequences keep the rankIDs in the summary file static.">
70 <option value="">Selection is Optional</option>
71 <option value="hist">History</option>
72 <option value="ref">Cached Reference</option>
73 </param>
74 <when value=""/>
75 <when value="ref">
76 <param name="taxonomy" type="select" format="mothur.seq.taxonomy" label="reftaxonomy - Taxonomy Reference used when sequences were classified">
77 <options from_data_table="mothur_taxonomy"/>
78 </param>
79 <param name="sum" type="data" format="tabular" label="tree.sum - summary file produced when sequences were classified" help="run classify.seqs to get this file"/>
80 </when>
81 <when value="hist">
82 <param name="taxonomy" type="data" format="mothur.seq.taxonomy" label="reftaxonomy - Taxonomy Reference used when sequences were classified"/>
83 <param name="sum" type="data" format="tabular" label="tree.sum - summary file produced when sequences were classified" help="run classify.seqs to get this file"/>
84 </when>
85 </conditional>
86 <param name="label" type="select" label="label - OTU Labels" multiple="true">
87 <expand macro="labeloptions"/> 65 <expand macro="labeloptions"/>
88 </param> 66 </param>
89 <param name="cutoff" type="integer" value="60" min="0" max="100" label="cutoff - Confindence percentage cutoff between 1 and 100"/> 67 <param argument="cutoff" type="integer" value="60" min="0" max="100" label="cutoff - Confindence percentage cutoff between 1 and 100"/>
90 <param name="probs" type="boolean" falsevalue="false" truevalue="true" checked="true" label="probs - Show probabilities"/> 68 <param argument="probs" type="boolean" falsevalue="false" truevalue="true" checked="true" label="probs - Show probabilities"/>
91 <param name="basis" type="select" label="basis - Summary file gives numbers of" help=""> 69 <param argument="basis" type="select" label="basis - Summary file gives numbers of" help="">
92 <option value="otu">OTU</option> 70 <option value="otu">OTU</option>
93 <option value="sequence">sequence</option> 71 <option value="sequence">sequence</option>
94 </param> 72 </param>
95 <param name="group" type="data" format="mothur.groups" optional="true" label="group - Groups for summary file"/> 73 <param argument="group" type="data" format="mothur.groups" optional="true" label="group - Groups for summary file"/>
96 <param name="persample" type="boolean" falsevalue="false" truevalue="true" checked="false" label="persample - allows you to find a consensus taxonomy for each group. default=f"/> 74 <param argument="persample" type="boolean" falsevalue="false" truevalue="true" checked="false"
75 label="persample - allows you to find a consensus taxonomy for each group"
76 help="default false"/>
77 <param argument="relabund" type="boolean" checked="false" truevalue="T" falsevalue="F" label="Relative abundance values?"
78 help="use relative abundances rather than raw abundances for the tax.summary file"/>
79 <expand macro="param-output"/>
80 <expand macro="param-printlevel"/>
97 </inputs> 81 </inputs>
98 <outputs> 82 <outputs>
99 <expand macro="logfile-output"/> 83 <expand macro="logfile-output"/>
100 <collection name="taxsummaries" type="list" label="${tool.name} on ${on_string}: tax.summary"> 84 <collection name="taxsummaries" type="list" label="${tool.name} on ${on_string}: tax.summary">
101 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.cons\.tax\.summary" format="mothur.tax.summary"/> 85 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.cons\.tax\.summary" format="mothur.tax.summary"/>
108 <test><!-- test with defaults --> 92 <test><!-- test with defaults -->
109 <param name="otu" value="amazon.an.list" ftype="mothur.list"/> 93 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
110 <param name="source" value="hist"/> 94 <param name="source" value="hist"/>
111 <param name="taxonomy" value="abrecovery.pds.wang.taxonomy" ftype="mothur.seq.taxonomy"/> 95 <param name="taxonomy" value="abrecovery.pds.wang.taxonomy" ftype="mothur.seq.taxonomy"/>
112 <output_collection name="taxonomies" count="36"> 96 <output_collection name="taxonomies" count="36">
113 <element name="0.18" md5="69a80ebaeb368d4944aa95ce120c6643" ftype="mothur.cons.taxonomy"/> 97 <element name="0.18" ftype="mothur.cons.taxonomy">
98 <assert_contents>
99 <expand macro="test-taxonomy-format"/>
100 <has_text text="Otu01"/>
101 </assert_contents>
102 </element>
114 </output_collection> 103 </output_collection>
115 <output_collection name="taxsummaries" count="36"> 104 <output_collection name="taxsummaries" count="36">
116 <element name="0.18" md5="bd5613b544a70c5c19f21a3d6602d926" ftype="mothur.tax.summary"/> 105 <element name="0.18" ftype="mothur.tax.summary">
117 </output_collection> 106 <assert_contents>
118 <expand macro="logfile-test"/> 107 <expand macro="test-taxsummary-format"/>
119 </test> 108 <has_text text="Root"/>
120 <test><!-- test with reftaxonomy and names file and label select --> 109 </assert_contents>
110 </element>
111 </output_collection>
112 <expand macro="logfile-test"/>
113 </test>
114 <test><!-- test with names file and label select -->
121 <param name="otu" value="amazon.an.list" ftype="mothur.list"/> 115 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
122 <param name="name" value="amazon1.names" ftype="mothur.names"/> 116 <param name="name" value="amazon1.names" ftype="mothur.names"/>
123 <param name="source" value="hist"/> 117 <param name="source" value="hist"/>
124 <param name="taxonomy" value="abrecovery.pds.wang.taxonomy" ftype="mothur.seq.taxonomy"/> 118 <param name="taxonomy" value="abrecovery.pds.wang.taxonomy" ftype="mothur.seq.taxonomy"/>
125 <param name="source2" value="hist"/>
126 <param name="reftaxonomy" value="abrecovery.pds.wang.taxonomy" ftype="mothur.seq.taxonomy"/>
127 <param name="sum" value="abrecovery.pds.wang.tree.sum"/> 119 <param name="sum" value="abrecovery.pds.wang.tree.sum"/>
128 <param name="label" value="unique,0.05,0.18"/> 120 <param name="label" value="unique,0.05,0.18"/>
129 <output_collection name="taxonomies" count="3"> 121 <output_collection name="taxonomies" count="3">
130 <element name="0.18" md5="69a80ebaeb368d4944aa95ce120c6643" ftype="mothur.cons.taxonomy"/> 122 <element name="0.18" ftype="mothur.cons.taxonomy">
123 <assert_contents>
124 <expand macro="test-taxonomy-format"/>
125 <has_text text="Otu01"/>
126 </assert_contents>
127 </element>
131 </output_collection> 128 </output_collection>
132 <output_collection name="taxsummaries" count="3"> 129 <output_collection name="taxsummaries" count="3">
133 <element name="0.18" md5="115769aa33dcfd121dd945a40ea11dcb" ftype="mothur.tax.summary"/> 130 <element name="0.18" ftype="mothur.tax.summary">
131 <assert_contents>
132 <expand macro="test-taxsummary-format"/>
133 <has_text text="Root"/>
134 </assert_contents>
135 </element>
134 </output_collection> 136 </output_collection>
135 <expand macro="logfile-test"/> 137 <expand macro="logfile-test"/>
136 </test> 138 </test>
137 <test><!-- test with count table --> 139 <test><!-- test with count table -->
138 <param name="otu" value="amazon.an.list" ftype="mothur.list"/> 140 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
139 <param name="count" value="amazon1.count_table" ftype="mothur.count_table"/> 141 <param name="count" value="amazon1.count_table" ftype="mothur.count_table"/>
140 <param name="source" value="hist"/> 142 <param name="source" value="hist"/>
141 <param name="label" value="unique,0.05,0.18"/> 143 <param name="label" value="unique,0.05,0.18"/>
142 <param name="taxonomy" value="abrecovery.pds.wang.taxonomy" ftype="mothur.seq.taxonomy"/> 144 <param name="taxonomy" value="abrecovery.pds.wang.taxonomy" ftype="mothur.seq.taxonomy"/>
143 <output_collection name="taxonomies" count="3"> 145 <output_collection name="taxonomies" count="3">
144 <element name="0.18" md5="69a80ebaeb368d4944aa95ce120c6643" ftype="mothur.cons.taxonomy"/> 146 <element name="0.18" ftype="mothur.cons.taxonomy">
147 <assert_contents>
148 <expand macro="test-taxonomy-format"/>
149 <has_text text="Otu01"/>
150 </assert_contents>
151 </element>
145 </output_collection> 152 </output_collection>
146 <output_collection name="taxsummaries" count="3"> 153 <output_collection name="taxsummaries" count="3">
147 <element name="0.18" md5="bd5613b544a70c5c19f21a3d6602d926" ftype="mothur.tax.summary"/> 154 <element name="0.18" ftype="mothur.tax.summary">
155 <assert_contents>
156 <expand macro="test-taxsummary-format"/>
157 <has_text text="Root"/>
158 </assert_contents>
159 </element>
148 </output_collection> 160 </output_collection>
149 <expand macro="logfile-test"/> 161 <expand macro="logfile-test"/>
150 </test> 162 </test>
151 <test><!-- test with group file --> 163 <test><!-- test with group file -->
152 <param name="otu" value="amazon.an.list" ftype="mothur.list"/> 164 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
153 <param name="group" value="amazon.groups" ftype="mothur.groups"/> 165 <param name="group" value="amazon.groups" ftype="mothur.groups"/>
154 <param name="source" value="hist"/> 166 <param name="source" value="hist"/>
155 <param name="label" value="unique,0.05,0.18"/> 167 <param name="label" value="unique,0.05,0.18"/>
156 <param name="taxonomy" value="abrecovery.pds.wang.taxonomy" ftype="mothur.seq.taxonomy"/> 168 <param name="taxonomy" value="abrecovery.pds.wang.taxonomy" ftype="mothur.seq.taxonomy"/>
157 <output_collection name="taxonomies" count="3"> 169 <output_collection name="taxonomies" count="3">
158 <element name="0.18" md5="69a80ebaeb368d4944aa95ce120c6643" ftype="mothur.cons.taxonomy"/> 170 <element name="0.18" ftype="mothur.cons.taxonomy">
171 <assert_contents>
172 <expand macro="test-taxonomy-format"/>
173 <has_text text="Otu01"/>
174 </assert_contents>
175 </element>
159 </output_collection> 176 </output_collection>
160 <output_collection name="taxsummaries" count="3"> 177 <output_collection name="taxsummaries" count="3">
161 <element name="0.18" md5="fe038e7670fbc5d68c1f5bb79d8ef4ac" ftype="mothur.tax.summary"/> 178 <element name="0.18" ftype="mothur.tax.summary">
179 <assert_contents>
180 <expand macro="test-taxsummary-format"/>
181 <has_text text="Root"/>
182 </assert_contents>
183 </element>
162 </output_collection> 184 </output_collection>
163 <expand macro="logfile-test"/> 185 <expand macro="logfile-test"/>
164 </test> 186 </test>
165 </tests> 187 </tests>
166 <help> 188 <help><![CDATA[
167 <![CDATA[
168 189
169 @MOTHUR_OVERVIEW@ 190 @MOTHUR_OVERVIEW@
170 191
171 **Command Documentation** 192 **Command Documentation**
172 193
175 The basis parameter allows you indicate what you want the summary file to represent, options are otu and sequence. Default is otu. For example consider the following basis=sequence could give Clostridiales 3 105 16 43 46, where 105 is the total number of sequences whose otu classified to Clostridiales. 16 is the number of sequences in the otus from groupA, 43 is the number of sequences in the otus from groupB, and 46 is the number of sequences in the otus from groupC. Now for basis=otu could give Clostridiales 3 7 6 1 2, where 7 is the number of otus that classified to Clostridiales. 6 is the number of otus containing sequences from groupA, 1 is the number of otus containing sequences from groupB, and 2 is the number of otus containing sequences from groupC. 196 The basis parameter allows you indicate what you want the summary file to represent, options are otu and sequence. Default is otu. For example consider the following basis=sequence could give Clostridiales 3 105 16 43 46, where 105 is the total number of sequences whose otu classified to Clostridiales. 16 is the number of sequences in the otus from groupA, 43 is the number of sequences in the otus from groupB, and 46 is the number of sequences in the otus from groupC. Now for basis=otu could give Clostridiales 3 7 6 1 2, where 7 is the number of otus that classified to Clostridiales. 6 is the number of otus containing sequences from groupA, 1 is the number of otus containing sequences from groupB, and 2 is the number of otus containing sequences from groupC.
176 197
177 .. _classify.otu: https://www.mothur.org/wiki/Classify.otu 198 .. _classify.otu: https://www.mothur.org/wiki/Classify.otu
178 199
179 v1.21.0: Updated to use Mothur 1.33. Added count parameter (1.28.0) and persample parameter (1.29.0) 200 v1.21.0: Updated to use Mothur 1.33. Added count parameter (1.28.0) and persample parameter (1.29.0)
180 ]]> 201
181 </help> 202 ]]></help>
182 <expand macro="citations"/> 203 <expand macro="citations"/>
183 </tool> 204 </tool>