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comparison macros.xml @ 1:122c47c8dad6 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
author iuc
date Thu, 18 May 2017 18:10:46 -0400
parents 6efb9d6ab2b1
children 0ec0e6261ee6
comparison
equal deleted inserted replaced
0:6efb9d6ab2b1 1:122c47c8dad6
5 </requirements> 5 </requirements>
6 </xml> 6 </xml>
7 <xml name="version_command"> 7 <xml name="version_command">
8 <version_command>mothur "#help()" | sed '7q;d' | cut -d" " -f2 </version_command> 8 <version_command>mothur "#help()" | sed '7q;d' | cut -d" " -f2 </version_command>
9 </xml> 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>
10 <token name="@WRAPPER_VERSION@">1.36.1</token> 16 <token name="@WRAPPER_VERSION@">1.36.1</token>
17 <token name="@SHELL_OPTIONS@">set -o pipefail;</token>
11 <token name="@MOTHUR_OVERVIEW@"> 18 <token name="@MOTHUR_OVERVIEW@">
12 <![CDATA[ 19 <![CDATA[
13 20
14 **Mothur Overview** 21 **Mothur Overview**
15 22
16 Mothur is a comprehensive suite of tools for microbial ecology community. It is initiated by Dr. Patrick Schloss and his software development team 23 Mothur is a comprehensive suite of tools for microbial ecology community. It is initiated by Dr. Patrick Schloss and his software development team
17 in the Department of Microbiology and Immunology at The University of Michigan. For more information, see Mothur-Wiki_. 24 in the Department of Microbiology and Immunology at The University of Michigan. For more information, see Mothur-Wiki_.
18 25
19 .. _Mothur-Wiki: http://www.mothur.org/wiki/Main_Page 26 .. _Mothur-Wiki: https://www.mothur.org/wiki/Main_Page
20 27
21 ]]> 28 ]]>
22 </token> 29 </token>
23 <xml name="labeloptions"> 30 <xml name="labeloptions">
24 <options> 31 <options>
25 <filter type="data_meta" ref="otu" key="labels"/> 32 <filter type="data_meta" ref="otu" key="labels"/>
26 </options> 33 </options>
27 </xml> 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 &amp; Clayton theta similarity coefficient</option>
78 <option value="whittaker">whittaker - Community Membership Similarity the Whittaker similarity coefficient</option>
79 <yield/>
80 </xml>
28 <xml name="logfile-output"> 81 <xml name="logfile-output">
29 <data name="logfile" format="txt" from_work_dir="mothur.*.logfile" label="${tool.name} on ${on_string}: logfile"/> 82 <data name="logfile" format="txt" from_work_dir="mothur.out.log" label="${tool.name} on ${on_string}: logfile"/>
30 </xml> 83 </xml>
31 <xml name="logfile-test"> 84 <xml name="logfile-test">
32 <output name="logfile" ftype="txt"> 85 <output name="logfile" ftype="txt">
33 <assert_contents> 86 <assert_contents>
34 <has_text text="mothur"/> 87 <has_text text="mothur"/>