Mercurial > repos > iuc > mothur_pairwise_seqs

comparison pairwise.seqs.xml @ 1:4f382764768a 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 18:26:27 -0400
parents 4e1ecccf9ab0
children cc74f42d74a2
comparison
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0:4e1ecccf9ab0 1:4f382764768a
2 <description>calculate uncorrected pairwise distances between sequences</description> 2 <description>calculate uncorrected pairwise distances between sequences</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 "$fasta" fasta.dat && 13 ln -s "$fasta" fasta.dat &&
11 14
12 echo 'pairwise.seqs( 15 echo 'pairwise.seqs(
13 fasta=fasta.dat, 16 fasta=fasta.dat,
30 #end if 33 #end if
31 processors='\${GALAXY_SLOTS:-8}' 34 processors='\${GALAXY_SLOTS:-8}'
32 )' 35 )'
33 | sed 's/ //g' ## mothur trips over whitespace 36 | sed 's/ //g' ## mothur trips over whitespace
34 | mothur 37 | mothur
38 | tee mothur.out.log
35 ]]></command> 39 ]]></command>
36 <inputs> 40 <inputs>
37 <param name="fasta" type="data" format="fasta" label="fasta - Fasta"/> 41 <param name="fasta" type="data" format="fasta" label="fasta - Fasta"/>
38 <param name="align" type="select" label="align - Select a pairwise alignment method" help=""> 42 <param name="align" type="select" label="align - Select a pairwise alignment method" help="">
39 <option value="needleman" selected="true">needleman (default)</option> 43 <option value="needleman" selected="true">needleman (default)</option>
48 </param> 52 </param>
49 <param name="countends" type="boolean" checked="true" truevalue="" falsevalue="countends=false," label="countends - Countends" help="Penalize terminal gaps"/> 53 <param name="countends" type="boolean" checked="true" truevalue="" falsevalue="countends=false," label="countends - Countends" help="Penalize terminal gaps"/>
50 <param name="cutoff" type="float" value="0.0" min="0" label="cutoff - Distance Cutoff threshold - ignored if not > 0" help="Do not save any distances larger than this, a common value would be 0.10"/> 54 <param name="cutoff" type="float" value="0.0" min="0" label="cutoff - Distance Cutoff threshold - ignored if not > 0" help="Do not save any distances larger than this, a common value would be 0.10"/>
51 <conditional name="scoring"> 55 <conditional name="scoring">
52 <param name="setby" type="select" label="Scoring match, mismatch, gapopen, and gapextend" help=""> 56 <param name="setby" type="select" label="Scoring match, mismatch, gapopen, and gapextend" help="">
53 <option value="default" selecte="true">Use default settings</option> 57 <option value="default" selected="true">Use default settings</option>
54 <option value="user">Manually set scoring values</option> 58 <option value="user">Manually set scoring values</option>
55 </param> 59 </param>
56 <when value="default"/> 60 <when value="default"/>
57 <when value="user"> 61 <when value="user">
58 <param name="match" type="integer" value="1" label="match - Pairwise alignment reward for a match"/> 62 <param name="match" type="integer" value="1" label="match - Pairwise alignment reward for a match"/>
107 <help> 111 <help>
108 <![CDATA[ 112 <![CDATA[
109 113
110 @MOTHUR_OVERVIEW@ 114 @MOTHUR_OVERVIEW@
111 115
112 .. _Mothur: http://www.mothur.org/wiki/Main_Page 116 .. _Mothur: https://www.mothur.org/wiki/Main_Page
113 117
114 **Command Documenation** 118 **Command Documentation**
115 119
116 The pairwise.seqs_ command will calculate uncorrected pairwise distances between sequencesi as a column-formatted_distance_matrix_ or phylip-formatted_distance_matrix_. 120 The pairwise.seqs_ command will calculate uncorrected pairwise distances between sequencesi as a column-formatted_distance_matrix_ or phylip-formatted_distance_matrix_.
117 121
118 .. _column-formatted_distance_matrix: http://www.mothur.org/wiki/Column-formatted_distance_matrix 122 .. _column-formatted_distance_matrix: https://www.mothur.org/wiki/Column-formatted_distance_matrix
119 .. _phylip-formatted_distance_matrix: http://www.mothur.org/wiki/Phylip-formatted_distance_matrix 123 .. _phylip-formatted_distance_matrix: https://www.mothur.org/wiki/Phylip-formatted_distance_matrix
120 .. _pairwise.seqs: http://www.mothur.org/wiki/Pairwise.seqs 124 .. _pairwise.seqs: https://www.mothur.org/wiki/Pairwise.seqs
121 125
122 ]]> 126 ]]>
123 </help> 127 </help>
124 <expand macro="citations"/> 128 <expand macro="citations"/>
125 </tool> 129 </tool>