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comparison clearcut.xml @ 1:eedf2aef456a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
author iuc
date Thu, 18 May 2017 18:50:03 -0400
parents 0c5468e0d272
children 6fb0ea14dac3
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0:0c5468e0d272 1:eedf2aef456a
2 <description>Generate a tree using relaxed neighbor joining</description> 2 <description>Generate a tree using relaxed neighbor joining</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <expand macro="stdio"/>
7 <expand macro="version_command"/> 8 <expand macro="version_command"/>
8 <command detect_errors="aggressive"><![CDATA[ 9 <command><![CDATA[
10 @SHELL_OPTIONS@
11
9 ## create symlinks to input datasets 12 ## create symlinks to input datasets
10 ln -s "$input.infile" input.infile.dat && 13 ln -s "$input.infile" input.infile.dat &&
11 14
12 echo 'clearcut( 15 echo 'clearcut(
13 #if $input.source == "dna": 16 #if $input.source == "dna":
32 expdist=$expdist, 35 expdist=$expdist,
33 neighbor=$neighbor 36 neighbor=$neighbor
34 )' 37 )'
35 | sed 's/ //g' ## mothur trips over whitespace 38 | sed 's/ //g' ## mothur trips over whitespace
36 | mothur 39 | mothur
40 | tee mothur.out.log
37 ]]></command> 41 ]]></command>
38 <inputs> 42 <inputs>
39 <conditional name="input"> 43 <conditional name="input">
40 <param name="source" type="select" label="Distance Matrix"> 44 <param name="source" type="select" label="Distance Matrix">
41 <option value="dna">DNA Alignment Fasta</option> 45 <option value="dna">DNA Alignment Fasta</option>
47 </when> 51 </when>
48 <when value="aa"> 52 <when value="aa">
49 <param name="infile" type="data" format="mothur.align" label="fasta - Alignment Fasta"/> 53 <param name="infile" type="data" format="mothur.align" label="fasta - Alignment Fasta"/>
50 </when> 54 </when>
51 <when value="phylip"> 55 <when value="phylip">
52 <param name="infile" type="data" format="mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/> 56 <param name="infile" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/>
53 </when> 57 </when>
54 </conditional> 58 </conditional>
55 <param name="seed" type="integer" value="" min="0" optional="true" label="seed - Set the PRNG seed to a specific value"/> 59 <param name="seed" type="integer" value="" min="0" optional="true" label="seed - Set the PRNG seed to a specific value"/>
56 <param name="ntrees" type="integer" value="1" label="ntrees - the number of output trees you want clearcut to generate (default 1)"/> 60 <param name="ntrees" type="integer" value="1" label="ntrees - the number of output trees you want clearcut to generate (default 1)"/>
57 <param name="norandom" type="boolean" checked="false" truevalue="true" falsevalue="false" label="norandom - Attempt joins deterministically"/> 61 <param name="norandom" type="boolean" checked="false" truevalue="true" falsevalue="false" label="norandom - Attempt joins deterministically"/>
105 <help> 109 <help>
106 <![CDATA[ 110 <![CDATA[
107 111
108 @MOTHUR_OVERVIEW@ 112 @MOTHUR_OVERVIEW@
109 113
110 **Command Documenation** 114 **Command Documentation**
111 115
112 The clearcut_ command runs clearcut 116 The clearcut_ command runs clearcut
113 117
114 The clearcut command allows mothur users to run the clearcut_program_ from within mothur. The clearcut program written by Initiative for Bioinformatics and Evolutionary Studies (IBEST) at the University of Idaho. For more information about clearcut please refer to http://bioinformatics.hungry.com/clearcut/ 118 The clearcut command allows mothur users to run the clearcut_program_ from within mothur. The clearcut program written by Initiative for Bioinformatics and Evolutionary Studies (IBEST) at the University of Idaho. For more information about clearcut please refer to http://bioinformatics.hungry.com/clearcut/
115 119
116 Clearcut is a stand-alone reference implementation of relaxed neighbor joining (RNJ). 120 Clearcut is a stand-alone reference implementation of relaxed neighbor joining (RNJ).
117 121
118 Clearcut is capable of taking either a distance matrix or a multiple sequence alignment (MSA) as input. If necessary, Clearcut will compute corrected distances based on a configurable distance correction model (Jukes-Cantor or Kimura). Clearcut outputs a phylogenetic tree in Newick format and an optional corrected distance matrix. 122 Clearcut is capable of taking either a distance matrix or a multiple sequence alignment (MSA) as input. If necessary, Clearcut will compute corrected distances based on a configurable distance correction model (Jukes-Cantor or Kimura). Clearcut outputs a phylogenetic tree in Newick format and an optional corrected distance matrix.
119 123
120 .. _clearcut_program: http://bioinformatics.hungry.com/clearcut/ 124 .. _clearcut_program: http://bioinformatics.hungry.com/clearcut/
121 .. _clearcut: http://www.mothur.org/wiki/Clearcut 125 .. _clearcut: https://www.mothur.org/wiki/Clearcut
122 126
123 v.1.20.0: Trivial upgrade to Mothur 1.33 127 v.1.20.0: Trivial upgrade to Mothur 1.33
124 ]]> 128 ]]>
125 </help> 129 </help>
126 <expand macro="citations"/> 130 <expand macro="citations"/>