Mercurial > repos > iuc > mothur_classify_otu
diff macros.xml @ 2:1ae93cdb2383 draft
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 |
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--- a/macros.xml Tue Sep 05 16:51:43 2017 -0400 +++ b/macros.xml Tue Mar 20 22:17:34 2018 -0400 @@ -1,11 +1,13 @@ <macros> + <token name="@WRAPPER_VERSION@">1.39.5</token> <xml name="requirements"> <requirements> - <requirement type="package" version="1.36.1">mothur</requirement> + <requirement type="package" version="@WRAPPER_VERSION@">mothur</requirement> + <yield/> </requirements> </xml> <xml name="version_command"> - <version_command>mothur "#help()" | sed '7q;d' | cut -d" " -f2 </version_command> + <version_command><![CDATA[ mothur "#help()" | sed '7q;d' | cut -d" " -f2 ]]></version_command> </xml> <xml name="stdio"> <stdio> @@ -13,20 +15,10 @@ <exit_code range="1:" level="fatal"/> </stdio> </xml> - <token name="@WRAPPER_VERSION@">1.36.1</token> <token name="@SHELL_OPTIONS@">set -o pipefail;</token> - <token name="@MOTHUR_OVERVIEW@"> -<![CDATA[ - -**Mothur Overview** -Mothur is a comprehensive suite of tools for microbial ecology community. It is initiated by Dr. Patrick Schloss and his software development team -in the Department of Microbiology and Immunology at The University of Michigan. For more information, see Mothur-Wiki_. -.. _Mothur-Wiki: https://www.mothur.org/wiki/Main_Page - -]]> - </token> + <!-- Input parameters --> <xml name="labeloptions"> <options> <filter type="data_meta" ref="otu" key="labels"/> @@ -78,9 +70,70 @@ <option value="whittaker">whittaker - Community Membership Similarity the Whittaker similarity coefficient</option> <yield/> </xml> + + <!-- CLUSTERING --> + <xml name="param-clustermethods"> + <param argument="method" type="select" label="Clustering Method"> + <option value="opti" selected="true">Opticlust method</option> + <option value="furthest">Furthest neighbor</option> + <option value="nearest">Nearest neighbor</option> + <option value="average">Average neighbor</option> + <yield/> + </param> + </xml> + <xml name="option-vsearch-clustermethods"> + <option value="agc">Abundance-based greedy clustering (agc)(VSEARCH)</option> + <option value="dgc">Distance-based greedy clustering (dgc)(VSEARCH)</option> + </xml> + <xml name="params-opticlust"> + <param argument="metric" type="select" label="metric - select the metric in the opticluster method" + help="Options are Matthews correlation coefficient (mcc), sensitivity (sens), specificity (spec), true positives + true negatives (tptn), + false positives + false negatives (fpfn), true positives (tp), true negative (tn), false positive (fp), false negative (fn), f1score (f1score), + accuracy (accuracy), positive predictive value (ppv), negative predictive value (npv), false discovery rate (fdr). Default=mcc."> + <option value="mcc" selected="true">Matthews correlation coefficient (mcc)</option> + <option value="sens">Sensitivity</option> + <option value="spec">specificity</option> + <option value="tptn">true positives + true negatives</option> + <option value="fpfn">false positives + false negatives</option> + <option value="tp">true positives</option> + <option value="tn">true negative</option> + <option value="fp">false positive</option> + <option value="fn">false negative</option> + <option value="f1score">f1score</option> + <option value="accuracy">accuracy</option> + <option value="ppv">positive predictive value</option> + <option value="npv">negative predictive value</option> + <option value="fdr">false discovery rate</option> + </param> + <param argument="initialize" type="select" label="Initial randomization" + help="singleton: each sequence is randomly assigned to its own OTU; oneotu: all sequences are assigned to one otu"> + <option value="singleton" selected="true">Singleton</option> + <option value="oneotu">Oneotu</option> + </param> + <param argument="delta" type="float" value="0.0001" label="set the stable value for the metric in the opticluster method" + 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."/> + <param argument="iters" type="integer" value="100" label="Maximum number of iterations"/> + </xml> + <xml name="param-output"> + <param argument="output" type="select" label="Tax summary output type" + help="The detail format outputs the totals at each level, where as the simple format outputs the highest level"> + <option value="simple" selected="true">simple</option> + <option value="detail">detail</option> + </param> + </xml> + <xml name="param-printlevel"> + <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" /> + </xml> + <xml name="param-savelog"> + <param name="savelog" type="boolean" checked="false" label="Output logfile?"/> + </xml> <xml name="logfile-output"> - <data name="logfile" format="txt" from_work_dir="mothur.out.log" label="${tool.name} on ${on_string}: logfile"/> + <data name="logfile" format="txt" from_work_dir="mothur.out.log" label="${tool.name} on ${on_string}: logfile"> + <filter>savelog</filter> + </data> </xml> + + <!-- Output file tests --> <xml name="logfile-test"> <output name="logfile" ftype="txt"> <assert_contents> @@ -89,6 +142,101 @@ </assert_contents> </output> </xml> + + <xml name="test-accnos-format"> + <!-- one or two columns --> + <has_line_matching expression="^[\w\d\-]+(\t[^\t]+)?$"/> + </xml> + <xml name="test-align-format"> + <has_line_matching expression="^>.+$"/> + <has_line_matching expression="^[ACTG\-\.]+$"/> + </xml> + <xml name="test-aligncheck-format"> + <has_n_columns n="9"/> + <has_line_matching expression="^name\tpound\tdash\tplus\tequal\tloop\ttilde\ttotal\tnumseqs$"/> + </xml> + <xml name="test-alignreport-format"> + <has_line_matching expression="^QueryName\tQueryLength\tTemplateName\tTemplateLength\tSearchMethod\tSearchScore\tAlignmentMethod\tQueryStart\tQueryEnd\tTemplateStart\tTemplateEnd\tPairwiseAlignmentLength\tGapsInQuery\tGapsInTemplate\tLongestInsert\tSimBtwnQuery&Template$"/> + </xml> + <xml name="test-axes-format"> + <has_line_matching expression="^group(\taxis\d+)+$"/> + </xml> + <xml name="test-chimera-format"> + <has_line_matching expression="Score\tQuery\tParentA\tParentB\tIdQM\tIdQA\tIdQB\tIdAB\tIdQT\tLY\tLN\tLA\tRY\tRN\tRA\tDiv\tYN"/> + </xml> + <xml name="test-column-format"> + <has_n_columns n="3"/> + <has_line_matching expression="^[\w\d\-]+\t[\w\d\-]+\t[\d\.]+$"/> + </xml> + <xml name="test-contigsreport-format"> + <has_n_columns n="7"/> + <has_line_matching expression="^Name\tLength\tOverlap_Length\tOverlap_Start\tOverlap_End\tMisMatches\tNum_Ns$"/> + </xml> + <xml name="test-count-format"> + <has_line_matching expression="^Representative_Sequence\ttotal(\t\w+)*$"/> + <has_line_matching expression="^\w+(\t\d+)+(\s)*$"/> + </xml> + <xml name="test-dist-format"> + <has_line_matching expression="^[ \t]*\d+$"/> + <has_line_matching expression="^[\w\d\-]+(\t[\d\.]+)+\s?$"/> + </xml> + <xml name="test-fasta-format"> + <has_line_matching expression="^>.+$"/> + <has_line_matching expression="^[ACTGN-]+$"/> + </xml> + <xml name="test-fastq-format"> + <has_line_matching expression="^@.+$"/> + <has_line_matching expression="^[ACTGN]+$"/> + <has_line_matching expression="^\+$"/> + </xml> + <xml name="test-group-format"> + <has_line_matching expression="^Representative_Sequence\ttotal(\t[\w\d\-]+)+$"/> + <has_line_matching expression="^[\w\d\-]+(\t\d+)+$"/> + </xml> + <xml name="test-list-format"> + <has_line_matching expression="^label\tnumOtus(\tOtu\d+)+$"/> + <has_line_matching expression="^(unique|0\.\d+)\t\d+(\t[\w\d\-,]+)+$"/> + </xml> + <xml name="test-names-format"> + <has_line_matching expression="^[a-zA-Z0-9]+\t[a-zA-Z0-9]+$"/> + </xml> + <xml name="test-qfile-format"> + <has_line_matching expression="^(\d+ )+$"/> + <has_line_matching expression="^>.+$"/> + </xml> + <xml name="test-rabund-format"> + <has_line_matching expression="^(unique|0\.\d+)(\t\d+\.?\d*)+$"/> + </xml> + <xml name="test-sabund-format"> + <has_line_matching expression="^(unique|0\.\d+)(\t\d+)+$"/> + </xml> + <xml name="test-sensspec-format"> + <has_n_columns n="14"/> + <has_line_matching expression="^label\tcutoff\ttp\ttn\tfp\tfn\tsensitivity\tspecificity\tppv\tnpv\tfdr\taccuracy\t\w+\tf1score$"/> + </xml> + <xml name="test-shared-format"> + <has_line_matching expression="^label\tGroup\tnumOtus(\t(Otu|rareOTUs|.*OTU.*)\d+)+$"/> + </xml> + <xml name="test-taxonomy-format"> + <has_n_columns n="3"/> + <has_line_matching expression="^OTU\tSize\tTaxonomy$"/> + </xml> + <xml name="test-taxsummary-format"> + <has_line_matching expression="^((taxlevel\trankID\ttaxon\tdaughterlevels\ttotal(\t[\w\d\-]+)*)|(taxonomy\ttotal(\t[\w\d]+)*))$"/> + </xml> + <!-- backmatter --> + <token name="@MOTHUR_OVERVIEW@"> +<![CDATA[ + +**Mothur Overview** + +Mothur is a comprehensive suite of tools for microbial ecology community. It is initiated by Dr. Patrick Schloss and his software development team +in the Department of Microbiology and Immunology at The University of Michigan. For more information, see Mothur-Wiki_. + +.. _Mothur-Wiki: https://www.mothur.org/wiki/Main_Page + +]]> + </token> <xml name="citations"> <citations> <citation type="doi">10.1128/AEM.01541-09</citation>