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comparison make.biom.xml @ 0:48e4f4dcf0ee draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
author iuc
date Fri, 24 Jun 2016 16:37:04 -0400
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children 0eae3db4c7a5
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-1:000000000000 0:48e4f4dcf0ee
1 <tool profile="16.07" id="mothur_make_biom" name="Make.biom" version="@WRAPPER_VERSION@.0">
2 <description>Make biom files from a shared file</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <expand macro="version_command"/>
8 <command detect_errors="aggressive"><![CDATA[
9 ## create symlinks to input datasets
10 ln -s "$otu" otu.dat &&
11 ln -s "$constaxonomy" constaxonomy.dat &&
12 ln -s "$metadata" metadata.dat &&
13 #if $picrustc.use == "yes":
14 ln -s "$picrustc.picrust" picrustc.picrust.dat &&
15 ln -s "$picrustc.reftax" picrustc.reftax.dat &&
16 #end if
17
18 echo 'make.biom(
19 shared=otu.dat,
20 #if $constaxonomy:
21 constaxonomy=constaxonomy.dat,
22 #end if
23 #if $label:
24 label=${ str($label).replace(",","-") },
25 #end if
26 #if $groups:
27 groups=${ str($groups).replace(",","-") },
28 #end if
29 #if $metadata:
30 metadata=metadata.dat,
31 #end if
32 #if $picrustc.use == "yes":
33 picrust=picrustc.picrust.dat,
34 reftaxonomy=picrustc.reftax.dat,
35 #end if
36 matrixtype=$matrixtype
37 )'
38 | sed 's/ //g' ## mothur trips over whitespace
39 | mothur
40 ]]></command>
41 <inputs>
42 <param name="otu" type="data" format="mothur.shared" label="shared - OTU Shared file"/>
43 <param name="constaxonomy" type="data" format="mothur.cons.taxonomy" optional="true" label="contaxonomy - consensus taxonomy" help="The contaxonomy file is the taxonomy file outputted by classify.otu"/>
44 <param name="metadata" type="data" format="metadata" label="metadata" optional="true" help="You can add sample data support here"/>
45 <conditional name="picrustc">
46 <param name="use" type="select" label="use picrust program">
47 <option value="no" selected="true">no</option>
48 <option value="yes">yes</option>
49 </param>
50 <when value="yes">
51 <param name="picrust" type="data" format="tabular" label="picrust" help="The picrust program requires green genes OTU IDs. The picrust parameter allows you to provide the OTU ID mapping table associated with your reference taxonomy"/>
52 <param name="reftax" type="data" format="mothur.ref.taxonomy" label="reftaxonomy" help="The referencetax parameter is used with the picrust parameter. Picrust requires the greengenes OTU IDs to be in the biom file, and the referencetax parameter allows you to provide your reference taxonomy file you used when classifying your sequences"/>
53 </when>
54 <when value="no"/>
55 </conditional>
56 <param name="matrixtype" type="select" label="matrixtype - sparse or dense">
57 <option value="sparse">sparse</option>
58 <option value="dense">dense</option>
59 </param>
60 <param name="groups" type="select" multiple="true" label="groups - Groups to include" help="By default all are included if no selection is made">
61 <options>
62 <filter type="data_meta" ref="otu" key="groups"/>
63 </options>
64 </param>
65 <param name="label" type="select" optional="true" multiple="true" label="label - Select OTU Labels to include" help="By default all are included if no selection is made">
66 <expand macro="labeloptions"/>
67 </param>
68 </inputs>
69 <outputs>
70 <expand macro="logfile-output"/>
71 <collection name="biomfiles" type="list" label="${tool.name} on ${on_string}: calculators">
72 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.biom" format="biom1"/>
73 </collection>
74 </outputs>
75 <tests>
76 <test><!-- test with defaults -->
77 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
78 <output_collection name="biomfiles" count="36">
79 <element name="0.36" ftype="biom1">
80 <assert_contents>
81 <has_text text="Biological Observation Matrix"/>
82 <has_text text="generated_by"/>
83 <has_text text="forest"/>
84 <has_text text="pasture"/>
85 </assert_contents>
86 </element>
87 </output_collection>
88 <expand macro="logfile-test"/>
89 </test>
90 <test><!-- test with subset of labels and groups-->
91 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
92 <param name="label" value="0.36,0.38,0.41"/>
93 <param name="groups" value="forest"/>
94 <output_collection name="biomfiles" count="3">
95 <element name="0.36">
96 <assert_contents>
97 <has_text text="Biological Observation Matrix"/>
98 <has_text text="generated_by"/>
99 <has_text text="forest"/>
100 <not_has_text text="pasture"/>
101 </assert_contents>
102 </element>
103 </output_collection>
104 <expand macro="logfile-test"/>
105 </test>
106 <test><!-- test with constaxonomy and metadata -->
107 <param name="otu" value="final.tx.1.subsample.1.pick.shared" ftype="mothur.shared"/>
108 <param name="constaxonomy" value="final.tx.1.cons.taxonomy" ftype="mothur.cons.taxonomy"/>
109 <param name="metadata" value="metadata"/>
110 <output_collection name="biomfiles" count="1">
111 <element name="1" ftype="biom1">
112 <assert_contents>
113 <has_text text="Biological Observation Matrix"/>
114 <has_text text="generated_by"/>
115 <has_text text="galaxy rocks"/>
116 </assert_contents>
117 </element>
118 </output_collection>
119 <expand macro="logfile-test"/>
120 </test>
121 <!-- TODO: test with picrust option (need file with greengenes OTU IDs) -->
122 </tests>
123 <help>
124 <![CDATA[
125
126 @MOTHUR_OVERVIEW@
127
128 **Command Documenation**
129
130 The make.biom command converts a shared_ shared file to biom_ files.
131 The output can be filtered by groups and labels.
132
133
134 .. _shared: http://www.mothur.org/wiki/Shared_file
135 .. _biom: http://biom-format.org/documentation/biom_format.html
136 .. _make.biom: http://www.mothur.org/wiki/Make.biom
137 ]]>
138 </help>
139 <expand macro="citations"/>
140 </tool>