Mercurial > repos > iuc > mothur_get_dists

comparison get.dists.xml @ 0:c5b0a5fca6d8 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
author iuc
date Fri, 24 Jun 2016 16:31:17 -0400
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children 9f28030ac5c5
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-1:000000000000 0:c5b0a5fca6d8
1 <tool profile="16.07" id="mothur_get_dists" name="Get.dists" version="@WRAPPER_VERSION@.0">
2 <description>selects distances from a phylip or column file</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <expand macro="version_command"/>
8 <command detect_errors="aggressive"><![CDATA[
9 ## create symlinks to input datasets
10 ln -s "$accnos" accnos.dat &&
11 ln -s "$input.dist" input.dist.dat &&
12
13 echo 'get.dists(
14 accnos=accnos.dat,
15 #if $input.source == "phylip":
16 phylip=input.dist.dat
17 #else
18 column=input.dist.dat
19 #end if
20 )'
21 | sed 's/ //g' ## mothur trips over whitespace
22 | mothur
23 ]]></command>
24 <inputs>
25 <conditional name="input">
26 <param name="source" type="select" label="Select input format">
27 <option value="column">Pairwise Column Distance Matrix</option>
28 <option value="phylip">Phylip Distance Matrix</option>
29 </param>
30 <when value="column">
31 <param name="dist" type="data" format="mothur.pair.dist" label="column - Distance Matrix"/>
32 </when>
33 <when value="phylip">
34 <param name="dist" type="data" format="mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/>
35 </when>
36 </conditional>
37 <param name="accnos" type="data" format="mothur.accnos" label="accnos - sort" help="format must be mothur.accnos"/>
38 </inputs>
39 <outputs>
40 <expand macro="logfile-output"/>
41 <data name="pick_dist" format_source="dist" from_work_dir="input.dist*.pick.dat" label="${tool.name} on ${on_string}: pick.dist"/>
42 </outputs>
43 <tests>
44 <test>
45 <param name="source" value="phylip"/>
46 <param name="dist" value="98_sq_phylip_amazon.dist" ftype="mothur.square.dist"/>
47 <param name="accnos" value="amazon.bad.accnos" ftype="mothur.accnos"/>
48 <output name="pick_dist" md5="d853cca7b67723e889a563420f6ccc13" ftype="mothur.square.dist"/>
49 <expand macro="logfile-test"/>
50 </test>
51 </tests>
52 <help>
53 <![CDATA[
54
55 @MOTHUR_OVERVIEW@
56
57 **Command Documenation**
58
59 The get.dists_ command selects distances from a phylip or column file related to groups or sequences listed in an accnos file.
60
61 .. _get.dists: http://www.mothur.org/wiki/Get.dists
62
63 v.1.20.0: Updated to Mothur 1.33
64 ]]>
65 </help>
66 <expand macro="citations"/>
67 </tool>