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comparison pairwise.seqs.xml @ 0:4e1ecccf9ab0 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 16:43:30 -0400
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-1:000000000000 0:4e1ecccf9ab0
1 <tool profile="16.07" id="mothur_pairwise_seqs" name="Pairwise.seqs" version="@WRAPPER_VERSION@.0">
2 <description>calculate uncorrected pairwise distances between sequences</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 "$fasta" fasta.dat &&
11
12 echo 'pairwise.seqs(
13 fasta=fasta.dat,
14 align=$align,
15 #if $calc:
16 calc=$calc,
17 #end if
18 $countends
19 #if float($cutoff) > 0.0:
20 cutoff=$cutoff,
21 #end if
22 #if $scoring.setby == "user":
23 match=$scoring.match,
24 mismatch=$scoring.mismatch,
25 gapopen=$scoring.gapopen,
26 gapextend=$scoring.gapextend,
27 #end if
28 #if $output:
29 output=$output,
30 #end if
31 processors='\${GALAXY_SLOTS:-8}'
32 )'
33 | sed 's/ //g' ## mothur trips over whitespace
34 | mothur
35 ]]></command>
36 <inputs>
37 <param name="fasta" type="data" format="fasta" label="fasta - Fasta"/>
38 <param name="align" type="select" label="align - Select a pairwise alignment method" help="">
39 <option value="needleman" selected="true">needleman (default)</option>
40 <option value="gotoh">gotoh</option>
41 <option value="blast">blast</option>
42 </param>
43 <param name="calc" type="select" label="calc - Calc Method - Gap Penality" help="">
44 <option value="" selected="true">use default</option>
45 <option value="onegap">onegap - counts a string of gaps as a single gap</option>
46 <option value="nogaps">nogaps - ignores gaps</option>
47 <option value="eachgap">eachgap - penalize each gap</option>
48 </param>
49 <param name="countends" type="boolean" checked="true" truevalue="" falsevalue="countends=false," label="countends - Countends" help="Penalize terminal gaps"/>
50 <param name="cutoff" type="float" value="0.0" min="0" label="cutoff - Distance Cutoff threshold - ignored if not > 0" help="Do not save any distances larger than this, a common value would be 0.10"/>
51 <conditional name="scoring">
52 <param name="setby" type="select" label="Scoring match, mismatch, gapopen, and gapextend" help="">
53 <option value="default" selecte="true">Use default settings</option>
54 <option value="user">Manually set scoring values</option>
55 </param>
56 <when value="default"/>
57 <when value="user">
58 <param name="match" type="integer" value="1" label="match - Pairwise alignment reward for a match"/>
59 <param name="mismatch" type="integer" value="-1" label="mismatch - Pairwise alignment penalty for a mismatch"/>
60 <param name="gapopen" type="integer" value="-2" label="gapopen - Pairwise alignment penalty for opening a gap"/>
61 <param name="gapextend" type="integer" value="-1" label="gapextend - Pairwise alignment penalty for extending a gap"/>
62 </when>
63 </conditional>
64 <param name="output" type="select" label="output - Distance Matrix Output Format" help="">
65 <option value="" selected="true">Column-Formatted Matrix (Default)</option>
66 <option value="lt">Phylip formatted Lower Triangle Matrix</option>
67 <option value="square">Phylip formatted Square Matrix</option>
68 </param>
69 </inputs>
70 <outputs>
71 <expand macro="logfile-output"/>
72 <data name="out_dist" format="mothur.pair.dist" from_work_dir="fasta*.dist" label="${tool.name} on ${on_string}: dist">
73 <change_format>
74 <when input="output" value="lt" format="mothur.lower.dist"/>
75 <when input="output" value="square" format="mothur.square.dist"/>
76 </change_format>
77 </data>
78 </outputs>
79 <tests>
80 <test>
81 <param name="fasta" value="amazon.unique.fasta"/>
82 <param name="align" value="needleman"/>
83 <param name="calc" value=""/>
84 <param name="countends" value=""/>
85 <param name="cutoff" value="0.0"/>
86 <param name="setby" value="default"/>
87 <param name="output" value=""/>
88 <expand macro="logfile-test"/>
89 <output name="out_dist" md5="bb2fefcda217604cd0e985f676168379"/>
90 </test>
91 <test>
92 <param name="fasta" value="amazon.unique.fasta"/>
93 <param name="align" value="gotoh"/>
94 <param name="calc" value="onegap"/>
95 <param name="countends" value="countends=false,"/>
96 <param name="cutoff" value="0.01"/>
97 <param name="setby" value="user"/>
98 <param name="match" value="2"/>
99 <param name="mismatch" value="-1"/>
100 <param name="gapopen" value="-2"/>
101 <param name="gapextend" value="-1"/>
102 <param name="output" value="lt"/>
103 <expand macro="logfile-test"/>
104 <output name="out_dist" md5="945c494bee1700c7f9a4ce5d87355190"/>
105 </test>
106 </tests>
107 <help>
108 <![CDATA[
109
110 @MOTHUR_OVERVIEW@
111
112 .. _Mothur: http://www.mothur.org/wiki/Main_Page
113
114 **Command Documenation**
115
116 The pairwise.seqs_ command will calculate uncorrected pairwise distances between sequencesi as a column-formatted_distance_matrix_ or phylip-formatted_distance_matrix_.
117
118 .. _column-formatted_distance_matrix: http://www.mothur.org/wiki/Column-formatted_distance_matrix
119 .. _phylip-formatted_distance_matrix: http://www.mothur.org/wiki/Phylip-formatted_distance_matrix
120 .. _pairwise.seqs: http://www.mothur.org/wiki/Pairwise.seqs
121
122 ]]>
123 </help>
124 <expand macro="citations"/>
125 </tool>