Mercurial > repos > iuc > mothur_filter_shared

comparison filter.shared.xml @ 4:b82c30e359e0 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 13:55:29 -0400
parents d3f5d41208c1
children 9ce5cadfb1ef
comparison
equal deleted inserted replaced
3:d3f5d41208c1 4:b82c30e359e0
62 <param argument="mintotal" type="integer" value="0" min="0" max="100" label="mintotal - indicate the minimum abundance required for a given OTU" 62 <param argument="mintotal" type="integer" value="0" min="0" max="100" label="mintotal - indicate the minimum abundance required for a given OTU"
63 help="If abundance across all samples falls below the minimum, the OTU is removed"/> 63 help="If abundance across all samples falls below the minimum, the OTU is removed"/>
64 <param argument="makerare" type="boolean" truevalue="true" falsevalue="false" checked="true" 64 <param argument="makerare" type="boolean" truevalue="true" falsevalue="false" checked="true"
65 label="makerare - indicate you want the abundances of any removed OTUs to be saved and a new rare OTU created with its abundances equal to the sum of the OTUs removed" 65 label="makerare - indicate you want the abundances of any removed OTUs to be saved and a new rare OTU created with its abundances equal to the sum of the OTUs removed"
66 help="This will preserve the number of reads in your dataset"/> 66 help="This will preserve the number of reads in your dataset"/>
67 <expand macro="param-savelog"/>
67 </inputs> 68 </inputs>
68 <outputs> 69 <outputs>
69 <expand macro="logfile-output"/> 70 <expand macro="logfile-output"/>
70 <collection name="filter_shared" type="list" label="${tool.name} on ${on_string}: filter.shared"> 71 <collection name="filter_shared" type="list" label="${tool.name} on ${on_string}: filter.shared">
71 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.filter\.dat" format="mothur.shared"/> 72 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.filter\.dat" format="mothur.shared"/>
80 <expand macro="test-shared-format"/> 81 <expand macro="test-shared-format"/>
81 <has_text text="0.03"/> 82 <has_text text="0.03"/>
82 </assert_contents> 83 </assert_contents>
83 </element> 84 </element>
84 </output_collection> 85 </output_collection>
86 <param name="savelog" value="true"/>
85 <expand macro="logfile-test"/> 87 <expand macro="logfile-test"/>
86 </test> 88 </test>
87 <test><!-- test with label and group select --> 89 <test><!-- test with label and group select -->
88 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> 90 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
89 <param name="label" value="0.05,0.29,0.33"/> 91 <param name="label" value="0.05,0.29,0.33"/>
95 <expand macro="test-shared-format"/> 97 <expand macro="test-shared-format"/>
96 <has_text text="0.29"/> 98 <has_text text="0.29"/>
97 </assert_contents> 99 </assert_contents>
98 </element> 100 </element>
99 </output_collection> 101 </output_collection>
102 <param name="savelog" value="true"/>
100 <expand macro="logfile-test"/> 103 <expand macro="logfile-test"/>
101 </test> 104 </test>
102 </tests> 105 </tests>
103 <help><![CDATA[ 106 <help><![CDATA[
104 107