Mercurial > repos > iuc > mothur_get_dists

comparison get.dists.xml @ 2:bc5112d1d317 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
author iuc
date Tue, 20 Mar 2018 21:57:53 -0400
parents a38b4b058203
children
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1:749e94120241 2:bc5112d1d317
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <expand macro="stdio"/> 7 <expand macro="stdio"/>
8 <expand macro="version_command"/> 8 <expand macro="version_command"/>
9 <command><![CDATA[ 9 <command><![CDATA[
10 @SHELL_OPTIONS@ 10 @SHELL_OPTIONS@
11 11
12 ## create symlinks to input datasets 12 ## create symlinks to input datasets
13 ln -s "$accnos" accnos.dat && 13 ln -s '$accnos' accnos.dat &&
14 ln -s "$input.dist" input.dist.dat && 14 ln -s '$input.dist' input.dist.dat &&
15 15
16 echo 'get.dists( 16 echo 'get.dists(
17 accnos=accnos.dat, 17 accnos=accnos.dat,
18 #if $input.source == "phylip": 18 #if $input.source == "phylip":
19 phylip=input.dist.dat 19 phylip=input.dist.dat
20 #else 20 #else
21 column=input.dist.dat 21 column=input.dist.dat
22 #end if 22 #end if
23 )' 23 )'
24 | sed 's/ //g' ## mothur trips over whitespace 24 | sed 's/ //g' ## mothur trips over whitespace
25 | mothur 25 | mothur
26 | tee mothur.out.log 26 | tee mothur.out.log
27 ]]></command> 27 ]]></command>
28 <inputs> 28 <inputs>
29 <conditional name="input"> 29 <conditional name="input">
30 <param name="source" type="select" label="Select input format"> 30 <param name="source" type="select" label="Select input format">
31 <option value="column">Pairwise Column Distance Matrix</option> 31 <option value="column">Pairwise Column Distance Matrix</option>
37 <when value="phylip"> 37 <when value="phylip">
38 <param name="dist" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/> 38 <param name="dist" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/>
39 </when> 39 </when>
40 </conditional> 40 </conditional>
41 <param name="accnos" type="data" format="mothur.accnos" label="accnos - sort" help="format must be mothur.accnos"/> 41 <param name="accnos" type="data" format="mothur.accnos" label="accnos - sort" help="format must be mothur.accnos"/>
42 <expand macro="param-savelog"/>
42 </inputs> 43 </inputs>
43 <outputs> 44 <outputs>
44 <expand macro="logfile-output"/> 45 <expand macro="logfile-output"/>
45 <data name="pick_dist" format_source="dist" from_work_dir="input.dist*.pick.dat" label="${tool.name} on ${on_string}: pick.dist"/> 46 <data name="pick_dist" format_source="dist" from_work_dir="input.dist*.pick.dat" label="${tool.name} on ${on_string}: pick.dist"/>
46 </outputs> 47 </outputs>
48 <test> 49 <test>
49 <param name="source" value="phylip"/> 50 <param name="source" value="phylip"/>
50 <param name="dist" value="98_sq_phylip_amazon.dist" ftype="mothur.square.dist"/> 51 <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 <param name="accnos" value="amazon.bad.accnos" ftype="mothur.accnos"/>
52 <output name="pick_dist" md5="d853cca7b67723e889a563420f6ccc13" ftype="mothur.square.dist"/> 53 <output name="pick_dist" md5="d853cca7b67723e889a563420f6ccc13" ftype="mothur.square.dist"/>
54 <param name="savelog" value="true"/>
53 <expand macro="logfile-test"/> 55 <expand macro="logfile-test"/>
54 </test> 56 </test>
55 </tests> 57 </tests>
56 <help> 58 <help><![CDATA[
57 <![CDATA[
58 59
59 @MOTHUR_OVERVIEW@ 60 @MOTHUR_OVERVIEW@
60 61
61 **Command Documentation** 62 **Command Documentation**
62 63
63 The get.dists_ command selects distances from a phylip or column file related to groups or sequences listed in an accnos file. 64 The get.dists_ command selects distances from a phylip or column file related to groups or sequences listed in an accnos file.
64 65
65 .. _get.dists: https://www.mothur.org/wiki/Get.dists 66 .. _get.dists: https://www.mothur.org/wiki/Get.dists
66 67
67 v.1.20.0: Updated to Mothur 1.33 68 v.1.20.0: Updated to Mothur 1.33
68 ]]> 69
69 </help> 70 ]]></help>
70 <expand macro="citations"/> 71 <expand macro="citations"/>
71 </tool> 72 </tool>