Mercurial > repos > iuc > mothur_make_biom

comparison make.biom.xml @ 6:063d478e1c94 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 38a2bbee32eaaceeb22d7549b13dbc0c613ee173
author iuc
date Tue, 20 Mar 2018 14:06:55 -0400
parents 9da0a5f7df8c
children
comparison
equal deleted inserted replaced
5:fac40662959e 6:063d478e1c94
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 ${on_string}: biom files"> 76 <collection name="biomfiles" type="list" label="${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"/>
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><![CDATA[ 131 <help><![CDATA[