Mercurial > repos > iuc > mothur_deunique_seqs

annotate macros.xml @ 10:3767f899f13c draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 7599ef16dc8b83ee49236ed5bb229260c969b0ab
author iuc
date Mon, 17 Jun 2024 13:11:24 +0000
parents 5faf0506611f
children
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4b2dabf45996 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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1 <macros>
2
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2 <token name="@WRAPPER_VERSION@">1.39.5</token>
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3767f899f13c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 7599ef16dc8b83ee49236ed5bb229260c969b0ab
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3 <xml name="biotools">
3767f899f13c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 7599ef16dc8b83ee49236ed5bb229260c969b0ab
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4 <xrefs>
3767f899f13c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 7599ef16dc8b83ee49236ed5bb229260c969b0ab
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5 <xref type="bio.tools">mothur</xref>
3767f899f13c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 7599ef16dc8b83ee49236ed5bb229260c969b0ab
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6 </xrefs>
3767f899f13c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 7599ef16dc8b83ee49236ed5bb229260c969b0ab
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7 </xml>
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4b2dabf45996 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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8 <xml name="requirements">
4b2dabf45996 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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9 <requirements>
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3291237294fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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10 <requirement type="package" version="@WRAPPER_VERSION@">mothur</requirement>
3291237294fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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11 <yield/>
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4b2dabf45996 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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12 </requirements>
4b2dabf45996 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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13 </xml>
4b2dabf45996 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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14 <xml name="version_command">
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3291237294fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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15 <version_command><![CDATA[ mothur "#help()" | sed '7q;d' | cut -d" " -f2 ]]></version_command>
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4b2dabf45996 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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16 </xml>
4b2dabf45996 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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17 <xml name="stdio">
4b2dabf45996 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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18 <stdio>
4b2dabf45996 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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19 <regex match="\[ERROR\]" source="stdout" level="fatal"/>
4b2dabf45996 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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20 <exit_code range="1:" level="fatal"/>
4b2dabf45996 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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21 </stdio>
4b2dabf45996 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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22 </xml>
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5faf0506611f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ff56a4c9218ddea84ff5cd72fd98c62db212465d"
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23 <token name="@SHELL_OPTIONS@">set -o pipefail; export TERM=vt100; </token>
0
4b2dabf45996 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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24
4b2dabf45996 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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25
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26 <!-- Input parameters -->
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4b2dabf45996 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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27 <xml name="labeloptions">
4b2dabf45996 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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28 <options>
4b2dabf45996 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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29 <filter type="data_meta" ref="otu" key="labels"/>
4b2dabf45996 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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30 </options>
4b2dabf45996 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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31 </xml>
4b2dabf45996 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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32 <xml name="calc-common">
4b2dabf45996 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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33 <!-- you can set defaults in tool xml by repeating those options again after macro expand, overriding first -->
4b2dabf45996 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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34 <option value="anderberg">anderberg - Community Membership Similarity the Anderberg similarity coefficient</option>
4b2dabf45996 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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35 <option value="braycurtis">braycurtis - Community Structure Similarity the Bray-Curtis similarity coefficient</option>
4b2dabf45996 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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36 <option value="canberra">canberra - Community Structure Similarity</option>
4b2dabf45996 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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37 <option value="gower">gower - Community Structure Similarity</option>
4b2dabf45996 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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38 <option value="hamming">hamming - Community Membership Similarity</option>
4b2dabf45996 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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39 <option value="hellinger">hellinger - Community Structure Similarity</option>
4b2dabf45996 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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40 <option value="jabund">jabund - Community Structure Similarity the abundance-based Jaccard similarity coefficient</option>
4b2dabf45996 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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41 <option value="jclass">jclass - Community Membership Similarity the traditional Jaccard similarity coefficient based on the observed richness</option>
4b2dabf45996 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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42 <option value="jest">jest - Community Membership Similarity the Jaccard similarity coefficient based on the Chao1 estimated richnesses</option>
4b2dabf45996 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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43 <option value="jsd">jsd</option>
4b2dabf45996 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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44 <option value="kulczynski">kulczynski - Community Membership Similarity the Kulczynski similarity coefficient</option>
4b2dabf45996 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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45 <option value="kulczynskicody">kulczynskicody - Community Membership Similarity the Kulczynski-Cody similarity coefficient</option>
4b2dabf45996 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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46 <option value="kstest">kstest - Community Membership Similarity Kolmogorov-Smirnov test</option>
4b2dabf45996 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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47 <option value="lennon">lennon - Community Membership Similarity the Lennon similarity coefficient</option>
4b2dabf45996 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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48 <option value="manhattan">manhattan - Community Structure Similarity</option>
4b2dabf45996 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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49 <option value="memchi2">memchi2 - Community Membership Similarity</option>
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50 <option value="memchord">memchord - Community Membership Similarity</option>
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51 <option value="memeuclidean">memeuclidean - Community Membership Similarity</option>
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52 <option value="mempearson">mempearson - Community Membership Similarity</option>
4b2dabf45996 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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53 <option value="morisitahorn">morisitahorn - Community Structure Similarity the Morisita-Horn similarity coefficient</option>
4b2dabf45996 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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54 <option value="ochiai">ochiai - Community Membership Similarity the Ochiai similarity coefficient</option>
4b2dabf45996 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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55 <option value="odum">odum - Community Structure Similarity</option>
4b2dabf45996 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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56 <option value="rjsd">rjsd</option>
4b2dabf45996 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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57 <option value="sharedace">sharedace - Shared community richness the two sample shared ACE richness estimator</option>
4b2dabf45996 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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58 <option value="sharednseqs">sharednseqs - Utility the number of sequences in two samples</option>
4b2dabf45996 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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59 <option value="sharedobserved">sharedobserved - Utility the number of sequences in two samples</option>
4b2dabf45996 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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60 <option value="sharedsobs">sharedsobs - Shared community richness the observed richness shared between two or more samples</option>
4b2dabf45996 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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61 <option value="sharedchao">sharedchao - Shared community richness the two or more sample shared Chao1 richness estimator</option>
4b2dabf45996 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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62 <option value="soergel">soergel - Community Structure Similarity</option>
4b2dabf45996 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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63 <option value="sorabund">sorabund - Community Structure Similarity the abundance-based Sorenson similarity coefficient</option>
4b2dabf45996 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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64 <option value="sorclass">sorclass - Community Membership Similarity the Sorenson similarity coefficient based on the observed richness</option>
4b2dabf45996 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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65 <option value="sorest">sorest - Community Membership Similarity the Sorenson similarity coefficient based on the Chao1 estimated richnesses</option>
4b2dabf45996 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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66 <option value="spearman">spearman - Community Structure Similarity</option>
4b2dabf45996 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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67 <option value="speciesprofile">speciesprofile - Community Structure Similarity</option>
4b2dabf45996 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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68 <option value="structchi2">structchi2 - Community Structure Similarity</option>
4b2dabf45996 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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69 <option value="structchord">structchord - Community Structure Similarity</option>
4b2dabf45996 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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70 <option value="structeuclidean">structeuclidean - Community Structure Similarity</option>
4b2dabf45996 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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71 <option value="structkulczynski">structkulczynski - Community Structure Similarity</option>
4b2dabf45996 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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72 <option value="structpearson">structpearson - Community Structure Similarity</option>
4b2dabf45996 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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73 <option value="thetan">thetan - Community Structure Similarity the Smith theta similarity coefficient</option>
4b2dabf45996 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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74 <option value="thetayc">thetayc - Community Structure Similarity the Yue &amp; Clayton theta similarity coefficient</option>
4b2dabf45996 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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75 <option value="whittaker">whittaker - Community Membership Similarity the Whittaker similarity coefficient</option>
4b2dabf45996 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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76 <yield/>
4b2dabf45996 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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77 </xml>
2
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78
3291237294fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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79 <!-- CLUSTERING -->
3291237294fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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80 <xml name="param-clustermethods">
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81 <param argument="method" type="select" label="Clustering Method">
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82 <option value="opti" selected="true">Opticlust method</option>
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83 <option value="furthest">Furthest neighbor</option>
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84 <option value="nearest">Nearest neighbor</option>
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85 <option value="average">Average neighbor</option>
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86 <yield/>
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87 </param>
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88 </xml>
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89 <xml name="option-vsearch-clustermethods">
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90 <option value="agc">Abundance-based greedy clustering (agc)(VSEARCH)</option>
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91 <option value="dgc">Distance-based greedy clustering (dgc)(VSEARCH)</option>
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92 </xml>
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93 <xml name="params-opticlust">
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94 <param argument="metric" type="select" label="metric - select the metric in the opticluster method"
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95 help="Options are Matthews correlation coefficient (mcc), sensitivity (sens), specificity (spec), true positives + true negatives (tptn),
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96 false positives + false negatives (fpfn), true positives (tp), true negative (tn), false positive (fp), false negative (fn), f1score (f1score),
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97 accuracy (accuracy), positive predictive value (ppv), negative predictive value (npv), false discovery rate (fdr). Default=mcc.">
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98 <option value="mcc" selected="true">Matthews correlation coefficient (mcc)</option>
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99 <option value="sens">Sensitivity</option>
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100 <option value="spec">specificity</option>
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101 <option value="tptn">true positives + true negatives</option>
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102 <option value="fpfn">false positives + false negatives</option>
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103 <option value="tp">true positives</option>
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104 <option value="tn">true negative</option>
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105 <option value="fp">false positive</option>
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106 <option value="fn">false negative</option>
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107 <option value="f1score">f1score</option>
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108 <option value="accuracy">accuracy</option>
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109 <option value="ppv">positive predictive value</option>
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110 <option value="npv">negative predictive value</option>
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111 <option value="fdr">false discovery rate</option>
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112 </param>
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113 <param argument="initialize" type="select" label="Initial randomization"
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114 help="singleton: each sequence is randomly assigned to its own OTU; oneotu: all sequences are assigned to one otu">
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115 <option value="singleton" selected="true">Singleton</option>
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116 <option value="oneotu">Oneotu</option>
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117 </param>
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118 <param argument="delta" type="float" value="0.0001" label="set the stable value for the metric in the opticluster method"
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119 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."/>
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120 <param argument="iters" type="integer" value="100" label="Maximum number of iterations"/>
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121 </xml>
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122 <xml name="param-output">
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123 <param argument="output" type="select" label="Tax summary output type"
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124 help="The detail format outputs the totals at each level, where as the simple format outputs the highest level">
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125 <option value="simple" selected="true">simple</option>
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126 <option value="detail">detail</option>
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127 </param>
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128 </xml>
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129 <xml name="param-printlevel">
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130 <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" />
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131 </xml>
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132 <xml name="param-savelog">
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133 <param name="savelog" type="boolean" checked="false" label="Output logfile?"/>
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134 </xml>
0
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135 <xml name="logfile-output">
2
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136 <data name="logfile" format="txt" from_work_dir="mothur.out.log" label="${tool.name} on ${on_string}: logfile">
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137 <filter>savelog</filter>
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138 </data>
0
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139 </xml>
2
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140
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141 <!-- Output file tests -->
0
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142 <xml name="logfile-test">
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143 <output name="logfile" ftype="txt">
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144 <assert_contents>
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145 <has_text text="mothur"/>
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146 <has_text text="@WRAPPER_VERSION@"/>
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147 </assert_contents>
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148 </output>
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149 </xml>
2
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150
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151 <xml name="test-accnos-format">
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152 <!-- one or two columns -->
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153 <has_line_matching expression="^[\w\d\-]+(\t[^\t]+)?$"/>
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154 </xml>
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155 <xml name="test-align-format">
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156 <has_line_matching expression="^>.+$"/>
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157 <has_line_matching expression="^[ACTG\-\.]+$"/>
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158 </xml>
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159 <xml name="test-aligncheck-format">
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160 <has_n_columns n="9"/>
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161 <has_line_matching expression="^name\tpound\tdash\tplus\tequal\tloop\ttilde\ttotal\tnumseqs$"/>
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162 </xml>
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163 <xml name="test-alignreport-format">
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164 <has_line_matching expression="^QueryName\tQueryLength\tTemplateName\tTemplateLength\tSearchMethod\tSearchScore\tAlignmentMethod\tQueryStart\tQueryEnd\tTemplateStart\tTemplateEnd\tPairwiseAlignmentLength\tGapsInQuery\tGapsInTemplate\tLongestInsert\tSimBtwnQuery&amp;Template$"/>
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165 </xml>
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166 <xml name="test-axes-format">
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167 <has_line_matching expression="^group(\taxis\d+)+$"/>
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168 </xml>
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169 <xml name="test-chimera-format">
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170 <has_line_matching expression="Score\tQuery\tParentA\tParentB\tIdQM\tIdQA\tIdQB\tIdAB\tIdQT\tLY\tLN\tLA\tRY\tRN\tRA\tDiv\tYN"/>
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171 </xml>
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172 <xml name="test-column-format">
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173 <has_n_columns n="3"/>
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174 <has_line_matching expression="^[\w\d\-]+\t[\w\d\-]+\t[\d\.]+$"/>
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175 </xml>
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176 <xml name="test-contigsreport-format">
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177 <has_n_columns n="7"/>
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178 <has_line_matching expression="^Name\tLength\tOverlap_Length\tOverlap_Start\tOverlap_End\tMisMatches\tNum_Ns$"/>
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179 </xml>
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180 <xml name="test-count-format">
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181 <has_line_matching expression="^Representative_Sequence\ttotal(\t\w+)*$"/>
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182 <has_line_matching expression="^\w+(\t\d+)+(\s)*$"/>
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183 </xml>
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184 <xml name="test-dist-format">
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185 <has_line_matching expression="^[ \t]*\d+$"/>
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186 <has_line_matching expression="^[\w\d\-]+(\t[\d\.]+)+\s?$"/>
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187 </xml>
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188 <xml name="test-fasta-format">
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189 <has_line_matching expression="^>.+$"/>
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190 <has_line_matching expression="^[ACTGN-]+$"/>
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191 </xml>
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192 <xml name="test-fastq-format">
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193 <has_line_matching expression="^@.+$"/>
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194 <has_line_matching expression="^[ACTGN]+$"/>
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195 <has_line_matching expression="^\+$"/>
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196 </xml>
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197 <xml name="test-group-format">
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198 <has_line_matching expression="^Representative_Sequence\ttotal(\t[\w\d\-]+)+$"/>
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199 <has_line_matching expression="^[\w\d\-]+(\t\d+)+$"/>
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200 </xml>
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201 <xml name="test-list-format">
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202 <has_line_matching expression="^label\tnumOtus(\tOtu\d+)+$"/>
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203 <has_line_matching expression="^(unique|0\.\d+)\t\d+(\t[\w\d\-,]+)+$"/>
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204 </xml>
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205 <xml name="test-names-format">
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206 <has_line_matching expression="^[a-zA-Z0-9]+\t[a-zA-Z0-9]+$"/>
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207 </xml>
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208 <xml name="test-qfile-format">
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209 <has_line_matching expression="^(\d+ )+$"/>
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210 <has_line_matching expression="^>.+$"/>
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211 </xml>
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212 <xml name="test-rabund-format">
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213 <has_line_matching expression="^(unique|0\.\d+)(\t\d+\.?\d*)+$"/>
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214 </xml>
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215 <xml name="test-sabund-format">
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216 <has_line_matching expression="^(unique|0\.\d+)(\t\d+)+$"/>
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217 </xml>
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218 <xml name="test-sensspec-format">
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219 <has_n_columns n="14"/>
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220 <has_line_matching expression="^label\tcutoff\ttp\ttn\tfp\tfn\tsensitivity\tspecificity\tppv\tnpv\tfdr\taccuracy\t\w+\tf1score$"/>
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221 </xml>
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222 <xml name="test-shared-format">
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223 <has_line_matching expression="^label\tGroup\tnumOtus(\t(Otu|rareOTUs|.*OTU.*)\d+)+$"/>
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224 </xml>
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225 <xml name="test-taxonomy-format">
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226 <has_n_columns n="3"/>
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227 <has_line_matching expression="^OTU\tSize\tTaxonomy$"/>
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228 </xml>
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229 <xml name="test-taxsummary-format">
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230 <has_line_matching expression="^((taxlevel\trankID\ttaxon\tdaughterlevels\ttotal(\t[\w\d\-]+)*)|(taxonomy\ttotal(\t[\w\d]+)*))$"/>
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231 </xml>
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232 <!-- backmatter -->
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233 <token name="@MOTHUR_OVERVIEW@">
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234 <![CDATA[
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235
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236 **Mothur Overview**
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237
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238 Mothur is a comprehensive suite of tools for microbial ecology community. It is initiated by Dr. Patrick Schloss and his software development team
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239 in the Department of Microbiology and Immunology at The University of Michigan. For more information, see Mothur-Wiki_.
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240
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241 .. _Mothur-Wiki: https://www.mothur.org/wiki/Main_Page
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242
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243 ]]>
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244 </token>
0
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245 <xml name="citations">
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246 <citations>
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247 <citation type="doi">10.1128/AEM.01541-09</citation>
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248 <yield/>
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249 </citations>
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250 </xml>
5
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251 <xml name="citations-ecology">
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252 <citation type="bibtex">
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253 @book{mccune2002analysis,
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254 title={Analysis of ecological communities},
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255 author={McCune, Bruce and Grace, James B and Urban, Dean L},
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256 volume={28},
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257 year={2002},
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258 publisher={MjM software design Gleneden Beach, OR}
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259 }
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260 </citation>
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261 <citation type="bibtex">
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262 @misc{legendre1998numerical,
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263 title={Numerical Ecology, Volume 24, (Developments in Environmental Modelling)},
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264 author={Legendre, Pierre and Legendre, Louis},
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265 year={1998},
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266 publisher={Elsevier Science Amsterdam, The Netherlands}
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267 }
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268 </citation>
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269 </xml>
0
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270 </macros>