Mercurial > repos > iuc > mothur_biom_info

comparison biom.info.xml @ 0:c664838f087c draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
author iuc
date Tue, 20 Mar 2018 21:53:45 -0400
parents
children 458d9a13d2f5
comparison
equal deleted inserted replaced
-1:000000000000 0:c664838f087c
1 <tool profile="16.07" id="mothur_biom_info" name="Biom.info" version="@WRAPPER_VERSION@.0">
2 <description>create shared and taxonomy files from biom</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 ln -s '$biom' input.biom &&
13
14 echo 'biom.info(
15 biom=input.biom,
16 #if str($label) != '':
17 label=$label,
18 #end if
19 basis=$basis,
20 output=$output,
21 relabund=$relabund,
22 printlevel=$printlevel
23 )'
24 | sed 's/ //g' ## mothur trips over whitespace
25 | mothur
26 | tee mothur.out.log
27 ]]></command>
28 <inputs>
29 <param argument="biom" type="data" format="biom1" label="Biom input dataset"/>
30 <!-- TODO: read label options from biom file -->
31 <param argument="label" type="text" value="userLabel" label="label - OTU Labels"
32 help="Enter a distance label to be used in the shared file created from your biom file (e.g. 0.03)"/>
33 <param argument="basis" type="select" label="Summary type"
34 help="indicate what you want the summary file to represent, options are otu and sequence. Default is otu.
35 For example consider the following basis=sequence could give Clostridiales 3 105, where 105 is the total
36 number of sequences whose otu classified to Clostridiales. Now for basis=otu could give Clostridiales 3 7,
37 where 7 is the number of otus that classified to Clostridiales. ">
38 <option value="otu" selected="true">OTU</option>
39 <option value="sequence">Sequence</option>
40 </param>
41 <param argument="relabund" type="boolean" truevalue="T" falsevalue="F" label="Relative abundance values"
42 help="use relative abundances rather than raw abundances for the tax.summary file"/>
43 <expand macro="param-output"/>
44 <expand macro="param-printlevel"/>
45 <expand macro="param-savelog"/>
46 </inputs>
47 <outputs>
48 <expand macro="logfile-output"/>
49 <data name="shared" format="mothur.shared" from_work_dir="input*.shared" label="${tool.name} on ${on_string}: shared"/>
50 <data name="taxonomy" format="mothur.cons.taxonomy" from_work_dir="input*.cons.taxonomy" label="${tool.name} on ${on_string}: cons.taxonomy"/>
51 <data name="tax.summary" format="mothur.tax.summary" from_work_dir="input*.tax.summary" label="${tool.name} on ${on_string}: tax.summary"/>
52 </outputs>
53 <tests>
54 <test><!-- test with biom without metadata -->
55 <param name="biom" value="samplebiom.biom1"/>
56 <output name="shared" ftype="mothur.shared">
57 <assert_contents>
58 <expand macro="test-shared-format"/>
59 </assert_contents>
60 </output>
61 <param name="savelog" value="true"/>
62 <expand macro="logfile-test"/>
63 </test>
64 <test><!-- test with biom file with metadata -->
65 <param name="biom" value="example.biom"/>
66 <output name="shared" ftype="mothur.shared">
67 <assert_contents>
68 <expand macro="test-shared-format"/>
69 </assert_contents>
70 </output>
71 <output name="taxonomy" ftype="mothur.cons.taxonomy">
72 <assert_contents>
73 <expand macro="test-taxonomy-format"/>
74 <has_text text="GG_OTU_1"/>
75 </assert_contents>
76 </output>
77 <output name="tax.summary" ftype="mothur.tax.summary">
78 <assert_contents>
79 <expand macro="test-taxsummary-format"/>
80 </assert_contents>
81 </output>
82 <param name="savelog" value="true"/>
83 <expand macro="logfile-test"/>
84 </test>
85 <test><!-- test with some more parameters -->
86 <param name="biom" value="example.biom"/>
87 <param name="label" value="0.03"/>
88 <param name="output" value="detail"/>
89 <param name="basis" value="sequence"/>
90 <param name="printlevel" value="4"/>
91 <output name="shared" ftype="mothur.shared">
92 <assert_contents>
93 <expand macro="test-shared-format"/>
94 </assert_contents>
95 </output>
96 <output name="taxonomy" ftype="mothur.cons.taxonomy">
97 <assert_contents>
98 <expand macro="test-taxonomy-format"/>
99 <has_text text="GG_OTU_1"/>
100 </assert_contents>
101 </output>
102 <output name="tax.summary" ftype="mothur.tax.summary">
103 <assert_contents>
104 <expand macro="test-taxsummary-format"/>
105 <has_text text="Euryarchaeota"/>
106 </assert_contents>
107 </output>
108 <param name="savelog" value="true"/>
109 <expand macro="logfile-test"/>
110 </test>
111 </tests>
112 <help><![CDATA[
113
114 @MOTHUR_OVERVIEW@
115
116 **Command Documentation**
117
118 The biom.info command reads a biom file creates a shared file. If your biom file contains metadata mothur will also
119 create taxonomy or constaxonomy along with tax.summary files.
120
121 ]]></help>
122 <expand macro="citations"/>
123 </tool>