Mercurial > repos > iuc > mothur_get_otulist
comparison macros.xml @ 0:2e6fb8f23d5e 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 05:52:08 -0400 |
parents | |
children | 7a922d81eca2 |
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-1:000000000000 | 0:2e6fb8f23d5e |
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1 <macros> | |
2 <xml name="requirements"> | |
3 <requirements> | |
4 <requirement type="package" version="1.36.1">mothur</requirement> | |
5 </requirements> | |
6 </xml> | |
7 <xml name="version_command"> | |
8 <version_command>mothur "#help()" | sed '7q;d' | cut -d" " -f2 </version_command> | |
9 </xml> | |
10 <xml name="stdio"> | |
11 <stdio> | |
12 <regex match="\[ERROR\]" source="stdout" level="fatal"/> | |
13 <exit_code range="1:" level="fatal"/> | |
14 </stdio> | |
15 </xml> | |
16 <token name="@WRAPPER_VERSION@">1.36.1</token> | |
17 <token name="@SHELL_OPTIONS@">set -o pipefail;</token> | |
18 <token name="@MOTHUR_OVERVIEW@"> | |
19 <![CDATA[ | |
20 | |
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"> | |
31 <options> | |
32 <filter type="data_meta" ref="otu" key="labels"/> | |
33 </options> | |
34 </xml> | |
35 <xml name="calc-common"> | |
36 <!-- you can set defaults in tool xml by repeating those options again after macro expand, overriding first --> | |
37 <option value="anderberg">anderberg - Community Membership Similarity the Anderberg similarity coefficient</option> | |
38 <option value="braycurtis">braycurtis - Community Structure Similarity the Bray-Curtis similarity coefficient</option> | |
39 <option value="canberra">canberra - Community Structure Similarity</option> | |
40 <option value="gower">gower - Community Structure Similarity</option> | |
41 <option value="hamming">hamming - Community Membership Similarity</option> | |
42 <option value="hellinger">hellinger - Community Structure Similarity</option> | |
43 <option value="jabund">jabund - Community Structure Similarity the abundance-based Jaccard similarity coefficient</option> | |
44 <option value="jclass">jclass - Community Membership Similarity the traditional Jaccard similarity coefficient based on the observed richness</option> | |
45 <option value="jest">jest - Community Membership Similarity the Jaccard similarity coefficient based on the Chao1 estimated richnesses</option> | |
46 <option value="jsd">jsd</option> | |
47 <option value="kulczynski">kulczynski - Community Membership Similarity the Kulczynski similarity coefficient</option> | |
48 <option value="kulczynskicody">kulczynskicody - Community Membership Similarity the Kulczynski-Cody similarity coefficient</option> | |
49 <option value="kstest">kstest - Community Membership Similarity Kolmogorov-Smirnov test</option> | |
50 <option value="lennon">lennon - Community Membership Similarity the Lennon similarity coefficient</option> | |
51 <option value="manhattan">manhattan - Community Structure Similarity</option> | |
52 <option value="memchi2">memchi2 - Community Membership Similarity</option> | |
53 <option value="memchord">memchord - Community Membership Similarity</option> | |
54 <option value="memeuclidean">memeuclidean - Community Membership Similarity</option> | |
55 <option value="mempearson">mempearson - Community Membership Similarity</option> | |
56 <option value="morisitahorn">morisitahorn - Community Structure Similarity the Morisita-Horn similarity coefficient</option> | |
57 <option value="ochiai">ochiai - Community Membership Similarity the Ochiai similarity coefficient</option> | |
58 <option value="odum">odum - Community Structure Similarity</option> | |
59 <option value="rjsd">rjsd</option> | |
60 <option value="sharedace">sharedace - Shared community richness the two sample shared ACE richness estimator</option> | |
61 <option value="sharednseqs">sharednseqs - Utility the number of sequences in two samples</option> | |
62 <option value="sharedobserved">sharedobserved - Utility the number of sequences in two samples</option> | |
63 <option value="sharedsobs">sharedsobs - Shared community richness the observed richness shared between two or more samples</option> | |
64 <option value="sharedchao">sharedchao - Shared community richness the two or more sample shared Chao1 richness estimator</option> | |
65 <option value="soergel">soergel - Community Structure Similarity</option> | |
66 <option value="sorabund">sorabund - Community Structure Similarity the abundance-based Sorenson similarity coefficient</option> | |
67 <option value="sorclass">sorclass - Community Membership Similarity the Sorenson similarity coefficient based on the observed richness</option> | |
68 <option value="sorest">sorest - Community Membership Similarity the Sorenson similarity coefficient based on the Chao1 estimated richnesses</option> | |
69 <option value="spearman">spearman - Community Structure Similarity</option> | |
70 <option value="speciesprofile">speciesprofile - Community Structure Similarity</option> | |
71 <option value="structchi2">structchi2 - Community Structure Similarity</option> | |
72 <option value="structchord">structchord - Community Structure Similarity</option> | |
73 <option value="structeuclidean">structeuclidean - Community Structure Similarity</option> | |
74 <option value="structkulczynski">structkulczynski - Community Structure Similarity</option> | |
75 <option value="structpearson">structpearson - Community Structure Similarity</option> | |
76 <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> | |
78 <option value="whittaker">whittaker - Community Membership Similarity the Whittaker similarity coefficient</option> | |
79 <yield/> | |
80 </xml> | |
81 <xml name="logfile-output"> | |
82 <data name="logfile" format="txt" from_work_dir="mothur.out.log" label="${tool.name} on ${on_string}: logfile"/> | |
83 </xml> | |
84 <xml name="logfile-test"> | |
85 <output name="logfile" ftype="txt"> | |
86 <assert_contents> | |
87 <has_text text="mothur"/> | |
88 <has_text text="@WRAPPER_VERSION@"/> | |
89 </assert_contents> | |
90 </output> | |
91 </xml> | |
92 <xml name="citations"> | |
93 <citations> | |
94 <citation type="doi">10.1128/AEM.01541-09</citation> | |
95 <yield/> | |
96 </citations> | |
97 </xml> | |
98 </macros> |