Mercurial > repos > iuc > mothur_screen_seqs

annotate macros.xml @ 0:125a6ae65887 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author iuc
date Fri, 19 May 2017 05:48:41 -0400
parents
children 6202ff80199f
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0
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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1 <macros>
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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2 <xml name="requirements">
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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3 <requirements>
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4 <requirement type="package" version="1.36.1">mothur</requirement>
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5 </requirements>
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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6 </xml>
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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7 <xml name="version_command">
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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8 <version_command>mothur "#help()" | sed '7q;d' | cut -d" " -f2 </version_command>
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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9 </xml>
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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10 <xml name="stdio">
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11 <stdio>
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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12 <regex match="\[ERROR\]" source="stdout" level="fatal"/>
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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13 <exit_code range="1:" level="fatal"/>
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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14 </stdio>
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15 </xml>
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16 <token name="@WRAPPER_VERSION@">1.36.1</token>
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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17 <token name="@SHELL_OPTIONS@">set -o pipefail;</token>
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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18 <token name="@MOTHUR_OVERVIEW@">
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19 <![CDATA[
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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21 **Mothur Overview**
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22
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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23 Mothur is a comprehensive suite of tools for microbial ecology community. It is initiated by Dr. Patrick Schloss and his software development team
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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24 in the Department of Microbiology and Immunology at The University of Michigan. For more information, see Mothur-Wiki_.
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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26 .. _Mothur-Wiki: https://www.mothur.org/wiki/Main_Page
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27
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28 ]]>
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29 </token>
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30 <xml name="labeloptions">
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31 <options>
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32 <filter type="data_meta" ref="otu" key="labels"/>
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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33 </options>
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34 </xml>
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35 <xml name="calc-common">
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36 <!-- you can set defaults in tool xml by repeating those options again after macro expand, overriding first -->
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37 <option value="anderberg">anderberg - Community Membership Similarity the Anderberg similarity coefficient</option>
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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38 <option value="braycurtis">braycurtis - Community Structure Similarity the Bray-Curtis similarity coefficient</option>
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39 <option value="canberra">canberra - Community Structure Similarity</option>
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40 <option value="gower">gower - Community Structure Similarity</option>
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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41 <option value="hamming">hamming - Community Membership Similarity</option>
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42 <option value="hellinger">hellinger - Community Structure Similarity</option>
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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43 <option value="jabund">jabund - Community Structure Similarity the abundance-based Jaccard similarity coefficient</option>
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44 <option value="jclass">jclass - Community Membership Similarity the traditional Jaccard similarity coefficient based on the observed richness</option>
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45 <option value="jest">jest - Community Membership Similarity the Jaccard similarity coefficient based on the Chao1 estimated richnesses</option>
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46 <option value="jsd">jsd</option>
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47 <option value="kulczynski">kulczynski - Community Membership Similarity the Kulczynski similarity coefficient</option>
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48 <option value="kulczynskicody">kulczynskicody - Community Membership Similarity the Kulczynski-Cody similarity coefficient</option>
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49 <option value="kstest">kstest - Community Membership Similarity Kolmogorov-Smirnov test</option>
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50 <option value="lennon">lennon - Community Membership Similarity the Lennon similarity coefficient</option>
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51 <option value="manhattan">manhattan - Community Structure Similarity</option>
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52 <option value="memchi2">memchi2 - Community Membership Similarity</option>
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53 <option value="memchord">memchord - Community Membership Similarity</option>
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54 <option value="memeuclidean">memeuclidean - Community Membership Similarity</option>
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55 <option value="mempearson">mempearson - Community Membership Similarity</option>
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56 <option value="morisitahorn">morisitahorn - Community Structure Similarity the Morisita-Horn similarity coefficient</option>
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57 <option value="ochiai">ochiai - Community Membership Similarity the Ochiai similarity coefficient</option>
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58 <option value="odum">odum - Community Structure Similarity</option>
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59 <option value="rjsd">rjsd</option>
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60 <option value="sharedace">sharedace - Shared community richness the two sample shared ACE richness estimator</option>
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61 <option value="sharednseqs">sharednseqs - Utility the number of sequences in two samples</option>
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62 <option value="sharedobserved">sharedobserved - Utility the number of sequences in two samples</option>
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63 <option value="sharedsobs">sharedsobs - Shared community richness the observed richness shared between two or more samples</option>
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64 <option value="sharedchao">sharedchao - Shared community richness the two or more sample shared Chao1 richness estimator</option>
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65 <option value="soergel">soergel - Community Structure Similarity</option>
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66 <option value="sorabund">sorabund - Community Structure Similarity the abundance-based Sorenson similarity coefficient</option>
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67 <option value="sorclass">sorclass - Community Membership Similarity the Sorenson similarity coefficient based on the observed richness</option>
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68 <option value="sorest">sorest - Community Membership Similarity the Sorenson similarity coefficient based on the Chao1 estimated richnesses</option>
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69 <option value="spearman">spearman - Community Structure Similarity</option>
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70 <option value="speciesprofile">speciesprofile - Community Structure Similarity</option>
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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71 <option value="structchi2">structchi2 - Community Structure Similarity</option>
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72 <option value="structchord">structchord - Community Structure Similarity</option>
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73 <option value="structeuclidean">structeuclidean - Community Structure Similarity</option>
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74 <option value="structkulczynski">structkulczynski - Community Structure Similarity</option>
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75 <option value="structpearson">structpearson - Community Structure Similarity</option>
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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76 <option value="thetan">thetan - Community Structure Similarity the Smith theta similarity coefficient</option>
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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77 <option value="thetayc">thetayc - Community Structure Similarity the Yue &amp; Clayton theta similarity coefficient</option>
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78 <option value="whittaker">whittaker - Community Membership Similarity the Whittaker similarity coefficient</option>
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79 <yield/>
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80 </xml>
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81 <xml name="logfile-output">
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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82 <data name="logfile" format="txt" from_work_dir="mothur.out.log" label="${tool.name} on ${on_string}: logfile"/>
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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83 </xml>
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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84 <xml name="logfile-test">
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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85 <output name="logfile" ftype="txt">
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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86 <assert_contents>
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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87 <has_text text="mothur"/>
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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88 <has_text text="@WRAPPER_VERSION@"/>
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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89 </assert_contents>
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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90 </output>
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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91 </xml>
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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92 <xml name="citations">
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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93 <citations>
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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94 <citation type="doi">10.1128/AEM.01541-09</citation>
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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95 <yield/>
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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96 </citations>
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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97 </xml>
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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98 </macros>