Mercurial > repos > iuc > mothur_clearcut

comparison clearcut.xml @ 6:f872e70bdeef 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 13:48:35 -0400
parents 0cbf1a5ba59c
children d780522d97bb
comparison
equal deleted inserted replaced
5:7bfd6a0ceeb0 6:f872e70bdeef
62 <param argument="shuffle" type="boolean" checked="false" truevalue="true" falsevalue="false" label="shuffle - Randomly shuffle the distance matrix"/> 62 <param argument="shuffle" type="boolean" checked="false" truevalue="true" falsevalue="false" label="shuffle - Randomly shuffle the distance matrix"/>
63 <param argument="neighbor" type="boolean" checked="true" truevalue="true" falsevalue="false" label="neighbor - Use traditional Neighbor-Joining algorithm"/> 63 <param argument="neighbor" type="boolean" checked="true" truevalue="true" falsevalue="false" label="neighbor - Use traditional Neighbor-Joining algorithm"/>
64 <param argument="expblen" type="boolean" checked="false" truevalue="ON" falsevalue="OFF" label="expblen - Use exponential notation for branch lengths"/> 64 <param argument="expblen" type="boolean" checked="false" truevalue="ON" falsevalue="OFF" label="expblen - Use exponential notation for branch lengths"/>
65 <param argument="expdist" type="boolean" checked="false" truevalue="ON" falsevalue="OFF" label="expdist - Use exponential notation for distance"/> 65 <param argument="expdist" type="boolean" checked="false" truevalue="ON" falsevalue="OFF" label="expdist - Use exponential notation for distance"/>
66 <param argument="matrixout" type="boolean" checked="false" truevalue="true" falsevalue="false" label="matrixout - Generate a Distance Matrix"/> 66 <param argument="matrixout" type="boolean" checked="false" truevalue="true" falsevalue="false" label="matrixout - Generate a Distance Matrix"/>
67 <expand macro="param-savelog"/>
67 </inputs> 68 </inputs>
68 <outputs> 69 <outputs>
69 <expand macro="logfile-output"/> 70 <expand macro="logfile-output"/>
70 <data name="tree" format="mothur.tre" from_work_dir="input.infile.tre" label="${tool.name} on ${on_string}: tree"/> 71 <data name="tree" format="mothur.tre" from_work_dir="input.infile.tre" label="${tool.name} on ${on_string}: tree"/>
71 <data name="matrix" format="mothur.lower.dist" from_work_dir="matrixout.dist" label="${tool.name} on ${on_string}: Phylip Distance Matrix"> 72 <data name="matrix" format="mothur.lower.dist" from_work_dir="matrixout.dist" label="${tool.name} on ${on_string}: Phylip Distance Matrix">
75 <tests> 76 <tests>
76 <test><!-- test with phylip and default params--> 77 <test><!-- test with phylip and default params-->
77 <param name="source" value="phylip"/> 78 <param name="source" value="phylip"/>
78 <param name="infile" value="env.dist"/> 79 <param name="infile" value="env.dist"/>
79 <output name="tree" md5="9c78d54267a985c8ae37dcfbddf6f8d0"/> 80 <output name="tree" md5="9c78d54267a985c8ae37dcfbddf6f8d0"/>
81 <param name="savelog" value="true"/>
80 <expand macro="logfile-test"/> 82 <expand macro="logfile-test"/>
81 </test> 83 </test>
82 <test><!-- test with phylip and params set--> 84 <test><!-- test with phylip and params set-->
83 <param name="source" value="phylip"/> 85 <param name="source" value="phylip"/>
84 <param name="infile" value="env.dist"/> 86 <param name="infile" value="env.dist"/>
93 <assert_contents> 95 <assert_contents>
94 <has_text text="group"/> 96 <has_text text="group"/>
95 </assert_contents> 97 </assert_contents>
96 </output> 98 </output>
97 <output name="matrix" md5="ebc0c296d46cbe4b8d50780b9f5f8314" ftype="mothur.lower.dist"/> 99 <output name="matrix" md5="ebc0c296d46cbe4b8d50780b9f5f8314" ftype="mothur.lower.dist"/>
100 <param name="savelog" value="true"/>
98 <expand macro="logfile-test"/> 101 <expand macro="logfile-test"/>
99 </test> 102 </test>
100 <test><!-- test with fasta (dna) and matrixout--> 103 <test><!-- test with fasta (dna) and matrixout-->
101 <param name="source" value="dna"/> 104 <param name="source" value="dna"/>
102 <param name="infile" value="amazon.align_head"/> 105 <param name="infile" value="amazon.align_head"/>
103 <param name="matrixout" value="true"/> 106 <param name="matrixout" value="true"/>
104 <output name="tree" md5="54ca5ad8aea6598f8ed03e0616b1b568"/> 107 <output name="tree" md5="54ca5ad8aea6598f8ed03e0616b1b568"/>
105 <output name="matrix" md5="1c9d7acbd2f1eaba31714cb659c521e8" ftype="mothur.lower.dist"/> 108 <output name="matrix" md5="1c9d7acbd2f1eaba31714cb659c521e8" ftype="mothur.lower.dist"/>
109 <param name="savelog" value="true"/>
106 <expand macro="logfile-test"/> 110 <expand macro="logfile-test"/>
107 </test> 111 </test>
108 </tests> 112 </tests>
109 <help><![CDATA[ 113 <help><![CDATA[
110 114