Mercurial > repos > iuc > mothur_summary_shared
comparison macros.xml @ 2:88aa9d575274 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
author | iuc |
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date | Tue, 20 Mar 2018 22:12:56 -0400 |
parents | eb727b7b76b4 |
children | 74c8ebee088c |
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1:8e74259d96c3 | 2:88aa9d575274 |
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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 & Clayton theta similarity coefficient</option> | 69 <option value="thetayc">thetayc - Community Structure Similarity the Yue & 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$"/> | |
157 </xml> | |
158 <xml name="test-alignreport-format"> | |
159 <has_line_matching expression="^QueryName\tQueryLength\tTemplateName\tTemplateLength\tSearchMethod\tSearchScore\tAlignmentMethod\tQueryStart\tQueryEnd\tTemplateStart\tTemplateEnd\tPairwiseAlignmentLength\tGapsInQuery\tGapsInTemplate\tLongestInsert\tSimBtwnQuery&Template$"/> | |
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> |