Mercurial > repos > iuc > mothur_sens_spec
comparison sens.spec.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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-1:000000000000 | 0:78776d48bbad |
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1 <tool profile="16.07" id="mothur_sens_spec" name="Sens.spec" version="@WRAPPER_VERSION@.0"> | |
2 <description>Determine the quality of OTU assignment</description> | |
3 <macros> | |
4 <import>macros.xml</import> | |
5 </macros> | |
6 <expand macro="requirements"/> | |
7 <expand macro="stdio"/> | |
8 <expand macro="version_command"/> | |
9 <command><![CDATA[ | |
10 @SHELL_OPTIONS@ | |
11 | |
12 ## create symlinks to input datasets | |
13 ln -s "$otu" otu.dat && | |
14 ln -s "$dist" dist.dat && | |
15 | |
16 echo 'sens.spec( | |
17 list=otu.dat, | |
18 #if $dist.is_of_type("mothur.dist"): | |
19 column=dist.dat, | |
20 #else | |
21 phylip=dist.dat, | |
22 #end if | |
23 #if $label: | |
24 label=${ str($label).replace(",","-") }, | |
25 #end if | |
26 precision=$precision, | |
27 cutoff=$cutoff, | |
28 hard=$hard | |
29 )' | |
30 | sed 's/ //g' ## mothur trips over whitespace | |
31 | mothur | |
32 | tee mothur.out.log | |
33 ]]></command> | |
34 <inputs> | |
35 <param name="otu" type="data" format="mothur.list" label="list - OTU List"/> | |
36 <param name="dist" type="data" format="mothur.dist,phylip,tabular" label="phylip,column - Distance Matrix"/> | |
37 <param name="label" type="select" optional="true" label="label - Select OTU Labels to include" multiple="true" help="By default all are included if no selection is made."> | |
38 <options> | |
39 <filter type="data_meta" ref="otu" key="labels"/> | |
40 </options> | |
41 </param> | |
42 <param name="precision" type="integer" value="100" min="0" optional="true" label="precision - Precision for rounding distance values"/> | |
43 <param name="cutoff" type="float" value="-1" label="cutoff - Distance Cutoff threshold - ignored if not > 0" help="Ignore pairwise distances larger than this, a common value would be 0.10"/> | |
44 <param name="hard" type="boolean" checked="false" truevalue="true" falsevalue="false" label="hard - Use hard cutoff instead of rounding"/> | |
45 </inputs> | |
46 <outputs> | |
47 <expand macro="logfile-output"/> | |
48 <data name="sensspec" format="tabular" from_work_dir="otu*.sensspec" label="${tool.name} on ${on_string}: sensspec"/> | |
49 </outputs> | |
50 <tests> | |
51 <test> | |
52 <param name="otu" value="amazon.an.list" ftype="mothur.list"/> | |
53 <param name="dist" value="amazon.dist" ftype="mothur.dist"/> | |
54 <output name="sensspec" md5="5eb92a89c4e1fd78c10e5bbe55ee2a7a" ftype="tabular"/> | |
55 <expand macro="logfile-test"/> | |
56 </test> | |
57 <test> | |
58 <param name="otu" value="amazon.an.list" ftype="mothur.list"/> | |
59 <param name="dist" value="amazon.dist" ftype="mothur.dist"/> | |
60 <param name="cutoff" value="0.10"/> | |
61 <param name="label" value="0.03,0.05,0.22"/> | |
62 <output name="sensspec" md5="8e2f46ef59b1ac097a9de2e0ab669bb2" ftype="tabular"/> | |
63 <expand macro="logfile-test"/> | |
64 </test> | |
65 </tests> | |
66 <help> | |
67 <![CDATA[ | |
68 | |
69 @MOTHUR_OVERVIEW@ | |
70 | |
71 **Command Documentation** | |
72 | |
73 The sens.spec_ command takes a list_ and either a column_ or phylip_ distance matrix to determine the quality of OTU assignment. | |
74 | |
75 | |
76 .. _list: https://www.mothur.org/wiki/List_file | |
77 .. _column: https://www.mothur.org/wiki/Column-formatted_distance_matrix | |
78 .. _phylip: https://www.mothur.org/wiki/Phylip-formatted_distance_matrix | |
79 .. _sens.spec: https://www.mothur.org/wiki/Sens.spec | |
80 ]]> | |
81 </help> | |
82 <expand macro="citations"/> | |
83 </tool> |