Mercurial > repos > iuc > mothur_classify_otu

comparison macros.xml @ 2:1ae93cdb2383 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
author iuc
date Tue, 20 Mar 2018 22:17:34 -0400
parents ddb2e4c51634
children 29882f4a1ef3
comparison
equal deleted inserted replaced
1:e664787de3ab 2:1ae93cdb2383
1 <macros> 1 <macros>
2 <token name="@WRAPPER_VERSION@">1.39.5</token>
2 <xml name="requirements"> 3 <xml name="requirements">
3 <requirements> 4 <requirements>
4 <requirement type="package" version="1.36.1">mothur</requirement> 5 <requirement type="package" version="@WRAPPER_VERSION@">mothur</requirement>
6 <yield/>
5 </requirements> 7 </requirements>
6 </xml> 8 </xml>
7 <xml name="version_command"> 9 <xml name="version_command">
8 <version_command>mothur "#help()" | sed '7q;d' | cut -d" " -f2 </version_command> 10 <version_command><![CDATA[ mothur "#help()" | sed '7q;d' | cut -d" " -f2 ]]></version_command>
9 </xml> 11 </xml>
10 <xml name="stdio"> 12 <xml name="stdio">
11 <stdio> 13 <stdio>
12 <regex match="\[ERROR\]" source="stdout" level="fatal"/> 14 <regex match="\[ERROR\]" source="stdout" level="fatal"/>
13 <exit_code range="1:" level="fatal"/> 15 <exit_code range="1:" level="fatal"/>
14 </stdio> 16 </stdio>
15 </xml> 17 </xml>
16 <token name="@WRAPPER_VERSION@">1.36.1</token>
17 <token name="@SHELL_OPTIONS@">set -o pipefail;</token> 18 <token name="@SHELL_OPTIONS@">set -o pipefail;</token>
18 <token name="@MOTHUR_OVERVIEW@"> 19
19 <![CDATA[ 20
20 21 <!-- Input parameters -->
21 **Mothur Overview**
22
23 Mothur is a comprehensive suite of tools for microbial ecology community. It is initiated by Dr. Patrick Schloss and his software development team
24 in the Department of Microbiology and Immunology at The University of Michigan. For more information, see Mothur-Wiki_.
25
26 .. _Mothur-Wiki: https://www.mothur.org/wiki/Main_Page
27
28 ]]>
29 </token>
30 <xml name="labeloptions"> 22 <xml name="labeloptions">
31 <options> 23 <options>
32 <filter type="data_meta" ref="otu" key="labels"/> 24 <filter type="data_meta" ref="otu" key="labels"/>
33 </options> 25 </options>
34 </xml> 26 </xml>
76 <option value="thetan">thetan - Community Structure Similarity the Smith theta similarity coefficient</option> 68 <option value="thetan">thetan - Community Structure Similarity the Smith theta similarity coefficient</option>
77 <option value="thetayc">thetayc - Community Structure Similarity the Yue &amp; Clayton theta similarity coefficient</option> 69 <option value="thetayc">thetayc - Community Structure Similarity the Yue &amp; Clayton theta similarity coefficient</option>
78 <option value="whittaker">whittaker - Community Membership Similarity the Whittaker similarity coefficient</option> 70 <option value="whittaker">whittaker - Community Membership Similarity the Whittaker similarity coefficient</option>
79 <yield/> 71 <yield/>
80 </xml> 72 </xml>
73
74 <!-- CLUSTERING -->
75 <xml name="param-clustermethods">
76 <param argument="method" type="select" label="Clustering Method">
77 <option value="opti" selected="true">Opticlust method</option>
78 <option value="furthest">Furthest neighbor</option>
79 <option value="nearest">Nearest neighbor</option>
80 <option value="average">Average neighbor</option>
81 <yield/>
82 </param>
83 </xml>
84 <xml name="option-vsearch-clustermethods">
85 <option value="agc">Abundance-based greedy clustering (agc)(VSEARCH)</option>
86 <option value="dgc">Distance-based greedy clustering (dgc)(VSEARCH)</option>
87 </xml>
88 <xml name="params-opticlust">
89 <param argument="metric" type="select" label="metric - select the metric in the opticluster method"
90 help="Options are Matthews correlation coefficient (mcc), sensitivity (sens), specificity (spec), true positives + true negatives (tptn),
91 false positives + false negatives (fpfn), true positives (tp), true negative (tn), false positive (fp), false negative (fn), f1score (f1score),
92 accuracy (accuracy), positive predictive value (ppv), negative predictive value (npv), false discovery rate (fdr). Default=mcc.">
93 <option value="mcc" selected="true">Matthews correlation coefficient (mcc)</option>
94 <option value="sens">Sensitivity</option>
95 <option value="spec">specificity</option>
96 <option value="tptn">true positives + true negatives</option>
97 <option value="fpfn">false positives + false negatives</option>
98 <option value="tp">true positives</option>
99 <option value="tn">true negative</option>
100 <option value="fp">false positive</option>
101 <option value="fn">false negative</option>
102 <option value="f1score">f1score</option>
103 <option value="accuracy">accuracy</option>
104 <option value="ppv">positive predictive value</option>
105 <option value="npv">negative predictive value</option>
106 <option value="fdr">false discovery rate</option>
107 </param>
108 <param argument="initialize" type="select" label="Initial randomization"
109 help="singleton: each sequence is randomly assigned to its own OTU; oneotu: all sequences are assigned to one otu">
110 <option value="singleton" selected="true">Singleton</option>
111 <option value="oneotu">Oneotu</option>
112 </param>
113 <param argument="delta" type="float" value="0.0001" label="set the stable value for the metric in the opticluster method"
114 help="The delta parameter allows to set the stable value for the metric in the opticluster method. To reach a full convergence, set delta=0."/>
115 <param argument="iters" type="integer" value="100" label="Maximum number of iterations"/>
116 </xml>
117 <xml name="param-output">
118 <param argument="output" type="select" label="Tax summary output type"
119 help="The detail format outputs the totals at each level, where as the simple format outputs the highest level">
120 <option value="simple" selected="true">simple</option>
121 <option value="detail">detail</option>
122 </param>
123 </xml>
124 <xml name="param-printlevel">
125 <param argument="printlevel" type="integer" value="-1" min="-1" label="Print level" help="specify taxlevel of your *tax.summary file to print to. Options are 1 to the maz level in the file. The default is -1, meaning max level" />
126 </xml>
127 <xml name="param-savelog">
128 <param name="savelog" type="boolean" checked="false" label="Output logfile?"/>
129 </xml>
81 <xml name="logfile-output"> 130 <xml name="logfile-output">
82 <data name="logfile" format="txt" from_work_dir="mothur.out.log" label="${tool.name} on ${on_string}: logfile"/> 131 <data name="logfile" format="txt" from_work_dir="mothur.out.log" label="${tool.name} on ${on_string}: logfile">
83 </xml> 132 <filter>savelog</filter>
133 </data>
134 </xml>
135
136 <!-- Output file tests -->
84 <xml name="logfile-test"> 137 <xml name="logfile-test">
85 <output name="logfile" ftype="txt"> 138 <output name="logfile" ftype="txt">
86 <assert_contents> 139 <assert_contents>
87 <has_text text="mothur"/> 140 <has_text text="mothur"/>
88 <has_text text="@WRAPPER_VERSION@"/> 141 <has_text text="@WRAPPER_VERSION@"/>
89 </assert_contents> 142 </assert_contents>
90 </output> 143 </output>
91 </xml> 144 </xml>
145
146 <xml name="test-accnos-format">
147 <!-- one or two columns -->
148 <has_line_matching expression="^[\w\d\-]+(\t[^\t]+)?$"/>
149 </xml>
150 <xml name="test-align-format">
151 <has_line_matching expression="^>.+$"/>
152 <has_line_matching expression="^[ACTG\-\.]+$"/>
153 </xml>
154 <xml name="test-aligncheck-format">
155 <has_n_columns n="9"/>
156 <has_line_matching expression="^name\tpound\tdash\tplus\tequal\tloop\ttilde\ttotal\tnumseqs$"/>
157 </xml>
158 <xml name="test-alignreport-format">
159 <has_line_matching expression="^QueryName\tQueryLength\tTemplateName\tTemplateLength\tSearchMethod\tSearchScore\tAlignmentMethod\tQueryStart\tQueryEnd\tTemplateStart\tTemplateEnd\tPairwiseAlignmentLength\tGapsInQuery\tGapsInTemplate\tLongestInsert\tSimBtwnQuery&amp;Template$"/>
160 </xml>
161 <xml name="test-axes-format">
162 <has_line_matching expression="^group(\taxis\d+)+$"/>
163 </xml>
164 <xml name="test-chimera-format">
165 <has_line_matching expression="Score\tQuery\tParentA\tParentB\tIdQM\tIdQA\tIdQB\tIdAB\tIdQT\tLY\tLN\tLA\tRY\tRN\tRA\tDiv\tYN"/>
166 </xml>
167 <xml name="test-column-format">
168 <has_n_columns n="3"/>
169 <has_line_matching expression="^[\w\d\-]+\t[\w\d\-]+\t[\d\.]+$"/>
170 </xml>
171 <xml name="test-contigsreport-format">
172 <has_n_columns n="7"/>
173 <has_line_matching expression="^Name\tLength\tOverlap_Length\tOverlap_Start\tOverlap_End\tMisMatches\tNum_Ns$"/>
174 </xml>
175 <xml name="test-count-format">
176 <has_line_matching expression="^Representative_Sequence\ttotal(\t\w+)*$"/>
177 <has_line_matching expression="^\w+(\t\d+)+(\s)*$"/>
178 </xml>
179 <xml name="test-dist-format">
180 <has_line_matching expression="^[ \t]*\d+$"/>
181 <has_line_matching expression="^[\w\d\-]+(\t[\d\.]+)+\s?$"/>
182 </xml>
183 <xml name="test-fasta-format">
184 <has_line_matching expression="^>.+$"/>
185 <has_line_matching expression="^[ACTGN-]+$"/>
186 </xml>
187 <xml name="test-fastq-format">
188 <has_line_matching expression="^@.+$"/>
189 <has_line_matching expression="^[ACTGN]+$"/>
190 <has_line_matching expression="^\+$"/>
191 </xml>
192 <xml name="test-group-format">
193 <has_line_matching expression="^Representative_Sequence\ttotal(\t[\w\d\-]+)+$"/>
194 <has_line_matching expression="^[\w\d\-]+(\t\d+)+$"/>
195 </xml>
196 <xml name="test-list-format">
197 <has_line_matching expression="^label\tnumOtus(\tOtu\d+)+$"/>
198 <has_line_matching expression="^(unique|0\.\d+)\t\d+(\t[\w\d\-,]+)+$"/>
199 </xml>
200 <xml name="test-names-format">
201 <has_line_matching expression="^[a-zA-Z0-9]+\t[a-zA-Z0-9]+$"/>
202 </xml>
203 <xml name="test-qfile-format">
204 <has_line_matching expression="^(\d+ )+$"/>
205 <has_line_matching expression="^>.+$"/>
206 </xml>
207 <xml name="test-rabund-format">
208 <has_line_matching expression="^(unique|0\.\d+)(\t\d+\.?\d*)+$"/>
209 </xml>
210 <xml name="test-sabund-format">
211 <has_line_matching expression="^(unique|0\.\d+)(\t\d+)+$"/>
212 </xml>
213 <xml name="test-sensspec-format">
214 <has_n_columns n="14"/>
215 <has_line_matching expression="^label\tcutoff\ttp\ttn\tfp\tfn\tsensitivity\tspecificity\tppv\tnpv\tfdr\taccuracy\t\w+\tf1score$"/>
216 </xml>
217 <xml name="test-shared-format">
218 <has_line_matching expression="^label\tGroup\tnumOtus(\t(Otu|rareOTUs|.*OTU.*)\d+)+$"/>
219 </xml>
220 <xml name="test-taxonomy-format">
221 <has_n_columns n="3"/>
222 <has_line_matching expression="^OTU\tSize\tTaxonomy$"/>
223 </xml>
224 <xml name="test-taxsummary-format">
225 <has_line_matching expression="^((taxlevel\trankID\ttaxon\tdaughterlevels\ttotal(\t[\w\d\-]+)*)|(taxonomy\ttotal(\t[\w\d]+)*))$"/>
226 </xml>
227 <!-- backmatter -->
228 <token name="@MOTHUR_OVERVIEW@">
229 <![CDATA[
230
231 **Mothur Overview**
232
233 Mothur is a comprehensive suite of tools for microbial ecology community. It is initiated by Dr. Patrick Schloss and his software development team
234 in the Department of Microbiology and Immunology at The University of Michigan. For more information, see Mothur-Wiki_.
235
236 .. _Mothur-Wiki: https://www.mothur.org/wiki/Main_Page
237
238 ]]>
239 </token>
92 <xml name="citations"> 240 <xml name="citations">
93 <citations> 241 <citations>
94 <citation type="doi">10.1128/AEM.01541-09</citation> 242 <citation type="doi">10.1128/AEM.01541-09</citation>
95 <yield/> 243 <yield/>
96 </citations> 244 </citations>