Mercurial > repos > iuc > mothur_remove_dists

comparison remove.dists.xml @ 1:27ab74145f55 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 18:18:47 -0400
parents 1c601f47dd3d
children 9067f78ae9bd
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0:1c601f47dd3d 1:27ab74145f55
2 <description>Removes distances from a phylip or column file</description> 2 <description>Removes distances from a phylip or column file</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 "$accnos" accnos.dat && 13 ln -s "$accnos" accnos.dat &&
11 ln -s "$input.dist" input_dist.dat && 14 ln -s "$input.dist" input_dist.dat &&
12 15
13 echo 'remove.dists( 16 echo 'remove.dists(
18 column=input_dist.dat 21 column=input_dist.dat
19 #end if 22 #end if
20 )' 23 )'
21 | sed 's/ //g' ## mothur trips over whitespace 24 | sed 's/ //g' ## mothur trips over whitespace
22 | mothur 25 | mothur
26 | tee mothur.out.log
23 ]]></command> 27 ]]></command>
24 <inputs> 28 <inputs>
25 <conditional name="input"> 29 <conditional name="input">
26 <param name="source" type="select" label="Select input format"> 30 <param name="source" type="select" label="Select input format">
27 <option value="column">Pairwise Column Distance Matrix</option> 31 <option value="column">Pairwise Column Distance Matrix</option>
29 </param> 33 </param>
30 <when value="column"> 34 <when value="column">
31 <param name="dist" type="data" format="mothur.pair.dist" label="column - Distance Matrix"/> 35 <param name="dist" type="data" format="mothur.pair.dist" label="column - Distance Matrix"/>
32 </when> 36 </when>
33 <when value="phylip"> 37 <when value="phylip">
34 <param name="dist" type="data" format="mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/> 38 <param name="dist" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/>
35 </when> 39 </when>
36 </conditional> 40 </conditional>
37 <param name="accnos" type="data" format="mothur.accnos" label="accnos - sort" help="format must be mothur.accnos"/> 41 <param name="accnos" type="data" format="mothur.accnos" label="accnos - sort" help="format must be mothur.accnos"/>
38 </inputs> 42 </inputs>
39 <outputs> 43 <outputs>
52 <help> 56 <help>
53 <![CDATA[ 57 <![CDATA[
54 58
55 @MOTHUR_OVERVIEW@ 59 @MOTHUR_OVERVIEW@
56 60
57 **Command Documenation** 61 **Command Documentation**
58 62
59 The remove.dists_ removes distances from a phylip or column file related to groups or sequences listed in an accnos file. 63 The remove.dists_ removes distances from a phylip or column file related to groups or sequences listed in an accnos file.
60 64
61 .. _remove.dists: http://www.mothur.org/wiki/Remove.dists 65 .. _remove.dists: https://www.mothur.org/wiki/Remove.dists
62 66
63 ]]> 67 ]]>
64 </help> 68 </help>
65 <expand macro="citations"/> 69 <expand macro="citations"/>
66 </tool> 70 </tool>