Mercurial > repos > iuc > mothur_make_biom

comparison make.biom.xml @ 3:a3f5c90f1f65 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
author iuc
date Tue, 20 Mar 2018 22:18:35 -0400
parents 5dc4d49a238a
children 0b5397a74165
comparison
equal deleted inserted replaced
2:5dc4d49a238a 3:a3f5c90f1f65
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <expand macro="stdio"/> 7 <expand macro="stdio"/>
8 <expand macro="version_command"/> 8 <expand macro="version_command"/>
9 <command><![CDATA[ 9 <command><![CDATA[
10 @SHELL_OPTIONS@ 10 @SHELL_OPTIONS@
11 11
12 ## create symlinks to input datasets 12 ## create symlinks to input datasets
13 ln -s "$otu" otu.dat && 13 ln -s '$otu' otu.dat &&
14 ln -s "$constaxonomy" constaxonomy.dat && 14 ln -s '$constaxonomy' constaxonomy.dat &&
15 ln -s "$metadata" metadata.dat && 15 ln -s '$metadata' metadata.dat &&
16 #if $picrustc.use == "yes": 16 #if $picrustc.use == "yes":
17 ln -s "$picrustc.picrust" picrustc.picrust.dat && 17 ln -s '$picrustc.picrust' picrustc.picrust.dat &&
18 ln -s "$picrustc.reftax" picrustc.reftax.dat && 18 ln -s '$picrustc.reftax' picrustc.reftax.dat &&
19 #end if 19 #end if
20 20
21 echo 'make.biom( 21 echo 'make.biom(
22 shared=otu.dat, 22 shared=otu.dat,
23 #if $constaxonomy: 23 #if $constaxonomy:
24 constaxonomy=constaxonomy.dat, 24 constaxonomy=constaxonomy.dat,
25 #end if 25 #end if
26 #if $label: 26 #if $label:
27 label=${ str($label).replace(",","-") }, 27 label=${ str($label).replace(",","-") },
28 #end if 28 #end if
29 #if $groups: 29 #if $groups:
30 groups=${ str($groups).replace(",","-") }, 30 groups=${ str($groups).replace(",","-") },
31 #end if 31 #end if
32 #if $metadata: 32 #if $metadata:
33 metadata=metadata.dat, 33 metadata=metadata.dat,
34 #end if 34 #end if
35 #if $picrustc.use == "yes": 35 #if $picrustc.use == "yes":
36 picrust=picrustc.picrust.dat, 36 picrust=picrustc.picrust.dat,
37 reftaxonomy=picrustc.reftax.dat, 37 reftaxonomy=picrustc.reftax.dat,
38 #end if 38 #end if
39 matrixtype=$matrixtype 39 matrixtype=$matrixtype
40 )' 40 )'
41 | sed 's/ //g' ## mothur trips over whitespace 41 | sed 's/ //g' ## mothur trips over whitespace
42 | mothur 42 | mothur
43 | tee mothur.out.log 43 | tee mothur.out.log
44 ]]></command> 44 ]]></command>
45 <inputs> 45 <inputs>
46 <param name="otu" type="data" format="mothur.shared" label="shared - OTU Shared file"/> 46 <param name="otu" type="data" format="mothur.shared" label="shared - OTU Shared file"/>
47 <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"/> 47 <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"/>
48 <param name="metadata" type="data" format="tabular" label="metadata" optional="true" help="You can add sample data support here"/> 48 <param name="metadata" type="data" format="tabular,txt" label="metadata" optional="true" help="You can add sample data support here"/>
49 <conditional name="picrustc"> 49 <conditional name="picrustc">
50 <param name="use" type="select" label="use picrust program"> 50 <param name="use" type="select" label="use picrust program">
51 <option value="no" selected="true">no</option> 51 <option value="no" selected="true">no</option>
52 <option value="yes">yes</option> 52 <option value="yes">yes</option>
53 </param> 53 </param>
67 </options> 67 </options>
68 </param> 68 </param>
69 <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"> 69 <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">
70 <expand macro="labeloptions"/> 70 <expand macro="labeloptions"/>
71 </param> 71 </param>
72 <expand macro="param-savelog"/>
72 </inputs> 73 </inputs>
73 <outputs> 74 <outputs>
74 <expand macro="logfile-output"/> 75 <expand macro="logfile-output"/>
75 <collection name="biomfiles" type="list" label="${tool.name} on ${on_string}: calculators"> 76 <collection name="biomfiles" type="list" label="${tool.name} on ${on_string}: biom files">
76 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.biom" format="biom1"/> 77 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.biom" format="biom1"/>
77 </collection> 78 </collection>
78 </outputs> 79 </outputs>
79 <tests> 80 <tests>
80 <test><!-- test with defaults --> 81 <test><!-- test with defaults -->
87 <has_text text="forest"/> 88 <has_text text="forest"/>
88 <has_text text="pasture"/> 89 <has_text text="pasture"/>
89 </assert_contents> 90 </assert_contents>
90 </element> 91 </element>
91 </output_collection> 92 </output_collection>
93 <param name="savelog" value="true"/>
92 <expand macro="logfile-test"/> 94 <expand macro="logfile-test"/>
93 </test> 95 </test>
94 <test><!-- test with subset of labels and groups--> 96 <test><!-- test with subset of labels and groups-->
95 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> 97 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
96 <param name="label" value="0.36,0.38,0.41"/> 98 <param name="label" value="0.36,0.38,0.41"/>
103 <has_text text="forest"/> 105 <has_text text="forest"/>
104 <not_has_text text="pasture"/> 106 <not_has_text text="pasture"/>
105 </assert_contents> 107 </assert_contents>
106 </element> 108 </element>
107 </output_collection> 109 </output_collection>
110 <param name="savelog" value="true"/>
108 <expand macro="logfile-test"/> 111 <expand macro="logfile-test"/>
109 </test> 112 </test>
110 <test><!-- test with constaxonomy and metadata --> 113 <test><!-- test with constaxonomy and metadata -->
111 <param name="otu" value="final.tx.1.subsample.1.pick.shared" ftype="mothur.shared"/> 114 <param name="otu" value="final.tx.1.subsample.1.pick.shared" ftype="mothur.shared"/>
112 <param name="constaxonomy" value="final.tx.1.cons.taxonomy" ftype="mothur.cons.taxonomy"/> 115 <param name="constaxonomy" value="final.tx.1.cons.taxonomy" ftype="mothur.cons.taxonomy"/>
118 <has_text text="generated_by"/> 121 <has_text text="generated_by"/>
119 <has_text text="galaxy rocks"/> 122 <has_text text="galaxy rocks"/>
120 </assert_contents> 123 </assert_contents>
121 </element> 124 </element>
122 </output_collection> 125 </output_collection>
126 <param name="savelog" value="true"/>
123 <expand macro="logfile-test"/> 127 <expand macro="logfile-test"/>
124 </test> 128 </test>
125 <!-- TODO: test with picrust option (need file with greengenes OTU IDs) --> 129 <!-- TODO: test with picrust option (need file with greengenes OTU IDs) -->
126 </tests> 130 </tests>
127 <help> 131 <help><![CDATA[
128 <![CDATA[
129 132
130 @MOTHUR_OVERVIEW@ 133 @MOTHUR_OVERVIEW@
131 134
132 **Command Documentation** 135 **Command Documentation**
133 136
136 139
137 140
138 .. _shared: https://www.mothur.org/wiki/Shared_file 141 .. _shared: https://www.mothur.org/wiki/Shared_file
139 .. _biom: http://biom-format.org/documentation/biom_format.html 142 .. _biom: http://biom-format.org/documentation/biom_format.html
140 .. _make.biom: https://www.mothur.org/wiki/Make.biom 143 .. _make.biom: https://www.mothur.org/wiki/Make.biom
141 ]]> 144
142 </help> 145 ]]></help>
143 <expand macro="citations"/> 146 <expand macro="citations"/>
144 </tool> 147 </tool>