Mercurial > repos > iuc > mothur_remove_dists

comparison remove.dists.xml @ 2:0df1987fb914 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 22:20:36 -0400
parents 741303a463c8
children
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1:0ec8be51451b 2:0df1987fb914
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 'remove.dists( 16 echo 'remove.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>
32 <option value="phylip">Phylip Distance Matrix</option> 32 <option value="phylip">Phylip Distance Matrix</option>
33 </param> 33 </param>
34 <when value="column"> 34 <when value="column">
35 <param name="dist" type="data" format="mothur.pair.dist" label="column - Distance Matrix"/> 35 <param name="dist" argument="column" type="data" format="mothur.pair.dist" label="column - Distance Matrix"/>
36 </when> 36 </when>
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" argument="phylip" 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 argument="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 ${on_string}: pick.dist"/>
46 </outputs> 47 </outputs>
47 <tests> 48 <tests>
48 <test> 49 <test>
49 <param name="source" value="phylip"/> 50 <param name="source" value="phylip"/>
50 <param name="dist" value="98_sq_phylip_amazon.dist" ftype="mothur.square.dist"/> 51 <param name="dist" value="98_sq_phylip_amazon.dist" ftype="mothur.square.dist"/>
51 <param name="accnos" value="amazon.bad.accnos" ftype="mothur.accnos"/> 52 <param name="accnos" value="amazon.bad.accnos" ftype="mothur.accnos"/>
52 <output name="pick_dist" md5="ec444ddb897d21864a245e8645fcda33" ftype="mothur.square.dist"/> 53 <output name="pick_dist" ftype="mothur.square.dist">
54 <assert_contents>
55 <expand macro="test-dist-format"/>
56 <has_text text="U68589"/>
57 <has_line_matching expression="^90$"/>
58 </assert_contents>
59 </output>
60 <param name="savelog" value="true"/>
53 <expand macro="logfile-test"/> 61 <expand macro="logfile-test"/>
54 </test> 62 </test>
55 </tests> 63 </tests>
56 <help> 64 <help><![CDATA[
57 <![CDATA[
58 65
59 @MOTHUR_OVERVIEW@ 66 @MOTHUR_OVERVIEW@
60 67
61 **Command Documentation** 68 **Command Documentation**
62 69
63 The remove.dists_ removes distances from a phylip or column file related to groups or sequences listed in an accnos file. 70 The remove.dists_ removes distances from a phylip or column file related to groups or sequences listed in an accnos file.
64 71
65 .. _remove.dists: https://www.mothur.org/wiki/Remove.dists 72 .. _remove.dists: https://www.mothur.org/wiki/Remove.dists
66 73
67 ]]> 74 ]]></help>
68 </help>
69 <expand macro="citations"/> 75 <expand macro="citations"/>
70 </tool> 76 </tool>