Mercurial > repos > iuc > mothur_dist_seqs

comparison dist.seqs.xml @ 1:699ed9de9edf 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 18:09:02 -0400
parents 2b4254acee00
children 2211f97b6d1b
comparison
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0:2b4254acee00 1:699ed9de9edf
2 <description>calculate uncorrected pairwise distances between aligned sequences</description> 2 <description>calculate uncorrected pairwise distances between aligned 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 'dist.seqs( 15 echo 'dist.seqs(
13 fasta=fasta.dat, 16 fasta=fasta.dat,
23 #end if 26 #end if
24 processors='\${GALAXY_SLOTS:-8}' 27 processors='\${GALAXY_SLOTS:-8}'
25 )' 28 )'
26 | sed 's/ //g' ## mothur trips over whitespace 29 | sed 's/ //g' ## mothur trips over whitespace
27 | mothur 30 | mothur
31 | tee mothur.out.log
28 ]]></command> 32 ]]></command>
29 <inputs> 33 <inputs>
30 <param name="fasta" type="data" format="mothur.align" label="fasta - Alignment Fasta"/> 34 <param name="fasta" type="data" format="mothur.align,fasta" label="fasta - Alignment Fasta"/>
31 <param name="calc" type="select" label="calc - Calc Method - Gap Penality"> 35 <param name="calc" type="select" label="calc - Calc Method - Gap Penality">
32 <option value="" selected="true">use default</option> 36 <option value="" selected="true">use default</option>
33 <option value="onegap">onegap - counts a string of gaps as a single gap</option> 37 <option value="onegap">onegap - counts a string of gaps as a single gap</option>
34 <option value="nogaps">nogaps - ignores gaps</option> 38 <option value="nogaps">nogaps - ignores gaps</option>
35 <option value="eachgap ">eachgap - penalize each gap</option> 39 <option value="eachgap ">eachgap - penalize each gap</option>
70 <help> 74 <help>
71 <![CDATA[ 75 <![CDATA[
72 76
73 @MOTHUR_OVERVIEW@ 77 @MOTHUR_OVERVIEW@
74 78
75 **Command Documenation** 79 **Command Documentation**
76 80
77 The dist.seqs_ command will calculate uncorrected pairwise distances between aligned sequences. The command will generate a column-formatted_distance_matrix_ that is compatible with the column option in the read.dist command. The command is also able to generate a phylip-formatted_distance_matrix_. There are several options for how to handle gap comparisons and terminal gaps. 81 The dist.seqs_ command will calculate uncorrected pairwise distances between aligned sequences. The command will generate a column-formatted_distance_matrix_ that is compatible with the column option in the read.dist command. The command is also able to generate a phylip-formatted_distance_matrix_. There are several options for how to handle gap comparisons and terminal gaps.
78 82
79 .. _column-formatted_distance_matrix: http://www.mothur.org/wiki/Column-formatted_distance_matrix 83 .. _column-formatted_distance_matrix: https://www.mothur.org/wiki/Column-formatted_distance_matrix
80 .. _phylip-formatted_distance_matrix: http://www.mothur.org/wiki/Phylip-formatted_distance_matrix 84 .. _phylip-formatted_distance_matrix: https://www.mothur.org/wiki/Phylip-formatted_distance_matrix
81 .. _dist.seqs: http://www.mothur.org/wiki/Dist.seqs 85 .. _dist.seqs: https://www.mothur.org/wiki/Dist.seqs
82 86
83 v.1.20.0: Updated to Mothur 1.33 87 v.1.20.0: Updated to Mothur 1.33
84 88
85 ]]> 89 ]]>
86 </help> 90 </help>