Mercurial > repos > iuc > mothur_pairwise_seqs

comparison pairwise.seqs.xml @ 0:fe6e11f9f639 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 05:12:33 -0400
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-1:000000000000 0:fe6e11f9f639
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="stdio"/>
8 <expand macro="version_command"/>
9 <command><![CDATA[
10 @SHELL_OPTIONS@
11
12 ## create symlinks to input datasets
13 ln -s "$fasta" fasta.dat &&
14
15 echo 'pairwise.seqs(
16 fasta=fasta.dat,
17 align=$align,
18 #if $calc:
19 calc=$calc,
20 #end if
21 $countends
22 #if float($cutoff) > 0.0:
23 cutoff=$cutoff,
24 #end if
25 #if $scoring.setby == "user":
26 match=$scoring.match,
27 mismatch=$scoring.mismatch,
28 gapopen=$scoring.gapopen,
29 gapextend=$scoring.gapextend,
30 #end if
31 #if $output:
32 output=$output,
33 #end if
34 processors='\${GALAXY_SLOTS:-8}'
35 )'
36 | sed 's/ //g' ## mothur trips over whitespace
37 | mothur
38 | tee mothur.out.log
39 ]]></command>
40 <inputs>
41 <param name="fasta" type="data" format="fasta" label="fasta - Fasta"/>
42 <param name="align" type="select" label="align - Select a pairwise alignment method" help="">
43 <option value="needleman" selected="true">needleman (default)</option>
44 <option value="gotoh">gotoh</option>
45 <option value="blast">blast</option>
46 </param>
47 <param name="calc" type="select" label="calc - Calc Method - Gap Penality" help="">
48 <option value="" selected="true">use default</option>
49 <option value="onegap">onegap - counts a string of gaps as a single gap</option>
50 <option value="nogaps">nogaps - ignores gaps</option>
51 <option value="eachgap">eachgap - penalize each gap</option>
52 </param>
53 <param name="countends" type="boolean" checked="true" truevalue="" falsevalue="countends=false," label="countends - Countends" help="Penalize terminal gaps"/>
54 <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"/>
55 <conditional name="scoring">
56 <param name="setby" type="select" label="Scoring match, mismatch, gapopen, and gapextend" help="">
57 <option value="default" selected="true">Use default settings</option>
58 <option value="user">Manually set scoring values</option>
59 </param>
60 <when value="default"/>
61 <when value="user">
62 <param name="match" type="integer" value="1" label="match - Pairwise alignment reward for a match"/>
63 <param name="mismatch" type="integer" value="-1" label="mismatch - Pairwise alignment penalty for a mismatch"/>
64 <param name="gapopen" type="integer" value="-2" label="gapopen - Pairwise alignment penalty for opening a gap"/>
65 <param name="gapextend" type="integer" value="-1" label="gapextend - Pairwise alignment penalty for extending a gap"/>
66 </when>
67 </conditional>
68 <param name="output" type="select" label="output - Distance Matrix Output Format" help="">
69 <option value="" selected="true">Column-Formatted Matrix (Default)</option>
70 <option value="lt">Phylip formatted Lower Triangle Matrix</option>
71 <option value="square">Phylip formatted Square Matrix</option>
72 </param>
73 </inputs>
74 <outputs>
75 <expand macro="logfile-output"/>
76 <data name="out_dist" format="mothur.pair.dist" from_work_dir="fasta*.dist" label="${tool.name} on ${on_string}: dist">
77 <change_format>
78 <when input="output" value="lt" format="mothur.lower.dist"/>
79 <when input="output" value="square" format="mothur.square.dist"/>
80 </change_format>
81 </data>
82 </outputs>
83 <tests>
84 <test>
85 <param name="fasta" value="amazon.unique.fasta"/>
86 <param name="align" value="needleman"/>
87 <param name="calc" value=""/>
88 <param name="countends" value=""/>
89 <param name="cutoff" value="0.0"/>
90 <param name="setby" value="default"/>
91 <param name="output" value=""/>
92 <expand macro="logfile-test"/>
93 <output name="out_dist" md5="bb2fefcda217604cd0e985f676168379"/>
94 </test>
95 <test>
96 <param name="fasta" value="amazon.unique.fasta"/>
97 <param name="align" value="gotoh"/>
98 <param name="calc" value="onegap"/>
99 <param name="countends" value="countends=false,"/>
100 <param name="cutoff" value="0.01"/>
101 <param name="setby" value="user"/>
102 <param name="match" value="2"/>
103 <param name="mismatch" value="-1"/>
104 <param name="gapopen" value="-2"/>
105 <param name="gapextend" value="-1"/>
106 <param name="output" value="lt"/>
107 <expand macro="logfile-test"/>
108 <output name="out_dist" md5="945c494bee1700c7f9a4ce5d87355190"/>
109 </test>
110 </tests>
111 <help>
112 <![CDATA[
113
114 @MOTHUR_OVERVIEW@
115
116 .. _Mothur: https://www.mothur.org/wiki/Main_Page
117
118 **Command Documentation**
119
120 The pairwise.seqs_ command will calculate uncorrected pairwise distances between sequencesi as a column-formatted_distance_matrix_ or phylip-formatted_distance_matrix_.
121
122 .. _column-formatted_distance_matrix: https://www.mothur.org/wiki/Column-formatted_distance_matrix
123 .. _phylip-formatted_distance_matrix: https://www.mothur.org/wiki/Phylip-formatted_distance_matrix
124 .. _pairwise.seqs: https://www.mothur.org/wiki/Pairwise.seqs
125
126 ]]>
127 </help>
128 <expand macro="citations"/>
129 </tool>