Mercurial > repos > iuc > mothur_get_dists

comparison get.dists.xml @ 0:a38b4b058203 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author iuc
date Fri, 19 May 2017 05:47:05 -0400
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-1:000000000000 0:a38b4b058203
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="stdio"/>
8 <expand macro="version_command"/>
9 <command><![CDATA[
10 @SHELL_OPTIONS@
11
12 ## create symlinks to input datasets
13 ln -s "$accnos" accnos.dat &&
14 ln -s "$input.dist" input.dist.dat &&
15
16 echo 'get.dists(
17 accnos=accnos.dat,
18 #if $input.source == "phylip":
19 phylip=input.dist.dat
20 #else
21 column=input.dist.dat
22 #end if
23 )'
24 | sed 's/ //g' ## mothur trips over whitespace
25 | mothur
26 | tee mothur.out.log
27 ]]></command>
28 <inputs>
29 <conditional name="input">
30 <param name="source" type="select" label="Select input format">
31 <option value="column">Pairwise Column Distance Matrix</option>
32 <option value="phylip">Phylip Distance Matrix</option>
33 </param>
34 <when value="column">
35 <param name="dist" type="data" format="mothur.pair.dist" label="column - Distance Matrix"/>
36 </when>
37 <when value="phylip">
38 <param name="dist" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/>
39 </when>
40 </conditional>
41 <param name="accnos" type="data" format="mothur.accnos" label="accnos - sort" help="format must be mothur.accnos"/>
42 </inputs>
43 <outputs>
44 <expand macro="logfile-output"/>
45 <data name="pick_dist" format_source="dist" from_work_dir="input.dist*.pick.dat" label="${tool.name} on ${on_string}: pick.dist"/>
46 </outputs>
47 <tests>
48 <test>
49 <param name="source" value="phylip"/>
50 <param name="dist" value="98_sq_phylip_amazon.dist" ftype="mothur.square.dist"/>
51 <param name="accnos" value="amazon.bad.accnos" ftype="mothur.accnos"/>
52 <output name="pick_dist" md5="d853cca7b67723e889a563420f6ccc13" ftype="mothur.square.dist"/>
53 <expand macro="logfile-test"/>
54 </test>
55 </tests>
56 <help>
57 <![CDATA[
58
59 @MOTHUR_OVERVIEW@
60
61 **Command Documentation**
62
63 The get.dists_ command selects distances from a phylip or column file related to groups or sequences listed in an accnos file.
64
65 .. _get.dists: https://www.mothur.org/wiki/Get.dists
66
67 v.1.20.0: Updated to Mothur 1.33
68 ]]>
69 </help>
70 <expand macro="citations"/>
71 </tool>