Mercurial > repos > iuc > mothur_sens_spec
diff macros.xml @ 0:78776d48bbad draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author | iuc |
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date | Fri, 19 May 2017 05:38:07 -0400 |
parents | |
children | edde8e7c2946 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Fri May 19 05:38:07 2017 -0400 @@ -0,0 +1,98 @@ +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="1.36.1">mothur</requirement> + </requirements> + </xml> + <xml name="version_command"> + <version_command>mothur "#help()" | sed '7q;d' | cut -d" " -f2 </version_command> + </xml> + <xml name="stdio"> + <stdio> + <regex match="\[ERROR\]" source="stdout" level="fatal"/> + <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> + <xml name="labeloptions"> + <options> + <filter type="data_meta" ref="otu" key="labels"/> + </options> + </xml> + <xml name="calc-common"> + <!-- you can set defaults in tool xml by repeating those options again after macro expand, overriding first --> + <option value="anderberg">anderberg - Community Membership Similarity the Anderberg similarity coefficient</option> + <option value="braycurtis">braycurtis - Community Structure Similarity the Bray-Curtis similarity coefficient</option> + <option value="canberra">canberra - Community Structure Similarity</option> + <option value="gower">gower - Community Structure Similarity</option> + <option value="hamming">hamming - Community Membership Similarity</option> + <option value="hellinger">hellinger - Community Structure Similarity</option> + <option value="jabund">jabund - Community Structure Similarity the abundance-based Jaccard similarity coefficient</option> + <option value="jclass">jclass - Community Membership Similarity the traditional Jaccard similarity coefficient based on the observed richness</option> + <option value="jest">jest - Community Membership Similarity the Jaccard similarity coefficient based on the Chao1 estimated richnesses</option> + <option value="jsd">jsd</option> + <option value="kulczynski">kulczynski - Community Membership Similarity the Kulczynski similarity coefficient</option> + <option value="kulczynskicody">kulczynskicody - Community Membership Similarity the Kulczynski-Cody similarity coefficient</option> + <option value="kstest">kstest - Community Membership Similarity Kolmogorov-Smirnov test</option> + <option value="lennon">lennon - Community Membership Similarity the Lennon similarity coefficient</option> + <option value="manhattan">manhattan - Community Structure Similarity</option> + <option value="memchi2">memchi2 - Community Membership Similarity</option> + <option value="memchord">memchord - Community Membership Similarity</option> + <option value="memeuclidean">memeuclidean - Community Membership Similarity</option> + <option value="mempearson">mempearson - Community Membership Similarity</option> + <option value="morisitahorn">morisitahorn - Community Structure Similarity the Morisita-Horn similarity coefficient</option> + <option value="ochiai">ochiai - Community Membership Similarity the Ochiai similarity coefficient</option> + <option value="odum">odum - Community Structure Similarity</option> + <option value="rjsd">rjsd</option> + <option value="sharedace">sharedace - Shared community richness the two sample shared ACE richness estimator</option> + <option value="sharednseqs">sharednseqs - Utility the number of sequences in two samples</option> + <option value="sharedobserved">sharedobserved - Utility the number of sequences in two samples</option> + <option value="sharedsobs">sharedsobs - Shared community richness the observed richness shared between two or more samples</option> + <option value="sharedchao">sharedchao - Shared community richness the two or more sample shared Chao1 richness estimator</option> + <option value="soergel">soergel - Community Structure Similarity</option> + <option value="sorabund">sorabund - Community Structure Similarity the abundance-based Sorenson similarity coefficient</option> + <option value="sorclass">sorclass - Community Membership Similarity the Sorenson similarity coefficient based on the observed richness</option> + <option value="sorest">sorest - Community Membership Similarity the Sorenson similarity coefficient based on the Chao1 estimated richnesses</option> + <option value="spearman">spearman - Community Structure Similarity</option> + <option value="speciesprofile">speciesprofile - Community Structure Similarity</option> + <option value="structchi2">structchi2 - Community Structure Similarity</option> + <option value="structchord">structchord - Community Structure Similarity</option> + <option value="structeuclidean">structeuclidean - Community Structure Similarity</option> + <option value="structkulczynski">structkulczynski - Community Structure Similarity</option> + <option value="structpearson">structpearson - Community Structure Similarity</option> + <option value="thetan">thetan - Community Structure Similarity the Smith theta similarity coefficient</option> + <option value="thetayc">thetayc - Community Structure Similarity the Yue & Clayton theta similarity coefficient</option> + <option value="whittaker">whittaker - Community Membership Similarity the Whittaker similarity coefficient</option> + <yield/> + </xml> + <xml name="logfile-output"> + <data name="logfile" format="txt" from_work_dir="mothur.out.log" label="${tool.name} on ${on_string}: logfile"/> + </xml> + <xml name="logfile-test"> + <output name="logfile" ftype="txt"> + <assert_contents> + <has_text text="mothur"/> + <has_text text="@WRAPPER_VERSION@"/> + </assert_contents> + </output> + </xml> + <xml name="citations"> + <citations> + <citation type="doi">10.1128/AEM.01541-09</citation> + <yield/> + </citations> + </xml> +</macros>