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comparison dist.seqs.xml @ 0:2b4254acee00 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 16:29:54 -0400
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-1:000000000000 0:2b4254acee00
1 <tool profile="16.07" id="mothur_dist_seqs" name="Dist.seqs" version="@WRAPPER_VERSION@.0">
2 <description>calculate uncorrected pairwise distances between aligned 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 'dist.seqs(
13 fasta=fasta.dat,
14 #if $calc:
15 calc=$calc,
16 #end if
17 countends=$countends,
18 #if $cutoff:
19 cutoff=$cutoff,
20 #end if
21 #if $output:
22 output=$output,
23 #end if
24 processors='\${GALAXY_SLOTS:-8}'
25 )'
26 | sed 's/ //g' ## mothur trips over whitespace
27 | mothur
28 ]]></command>
29 <inputs>
30 <param name="fasta" type="data" format="mothur.align" label="fasta - Alignment Fasta"/>
31 <param name="calc" type="select" label="calc - Calc Method - Gap Penality">
32 <option value="" selected="true">use default</option>
33 <option value="onegap">onegap - counts a string of gaps as a single gap</option>
34 <option value="nogaps">nogaps - ignores gaps</option>
35 <option value="eachgap ">eachgap - penalize each gap</option>
36 </param>
37 <param name="countends" type="boolean" checked="true" truevalue="true" falsevalue="false" label="countends - Penalize terminal gaps"/>
38 <param name="cutoff" type="float" value="" min="0.0" optional="true" 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"/>
39 <param name="output" type="select" label="output - Distance Matrix Output Format" help="">
40 <option value="" selected="true">Default Column-Formatted Matrix</option>
41 <option value="lt">Phylip formatted Lower Triangle Matrix</option>
42 <option value="square">Phylip formatted Square Matrix</option>
43 </param>
44 </inputs>
45 <outputs>
46 <expand macro="logfile-output"/>
47 <data name="out_dist" format="mothur.pair.dist" from_work_dir="fasta*.dist" label="${tool.name} on ${on_string}: dist">
48 <change_format>
49 <when input="output" value="lt" format="mothur.lower.dist"/>
50 <when input="output" value="square" format="mothur.square.dist"/>
51 </change_format>
52 </data>
53 </outputs>
54 <tests>
55 <test><!-- test with default params -->
56 <param name="fasta" value="HMP_MOCK.v35.align" ftype="mothur.align"/>
57 <output name="out_dist" md5="2c4817bb8657b4df2dcb1f2a019f505e" ftype="mothur.pair.dist"/>
58 <expand macro="logfile-test"/>
59 </test>
60 <test><!-- test with all params custom -->
61 <param name="fasta" value="HMP_MOCK.v35.align" ftype="mothur.align"/>
62 <param name="calc" value="nogaps"/>
63 <param name="countends" value="false"/>
64 <param name="cutoff" value="0.3"/>
65 <param name="output" value="lt"/>
66 <output name="out_dist" md5="8a5ccf1ad8f1c344cf4d3e2c97d4cdc6" ftype="mothur.lower.dist"/>
67 <expand macro="logfile-test"/>
68 </test>
69 </tests>
70 <help>
71 <![CDATA[
72
73 @MOTHUR_OVERVIEW@
74
75 **Command Documenation**
76
77 The dist.seqs_ command will calculate uncorrected pairwise distances between aligned sequences. The command will generate a column-formatted_distance_matrix_ that is compatible with the column option in the read.dist command. The command is also able to generate a phylip-formatted_distance_matrix_. There are several options for how to handle gap comparisons and terminal gaps.
78
79 .. _column-formatted_distance_matrix: http://www.mothur.org/wiki/Column-formatted_distance_matrix
80 .. _phylip-formatted_distance_matrix: http://www.mothur.org/wiki/Phylip-formatted_distance_matrix
81 .. _dist.seqs: http://www.mothur.org/wiki/Dist.seqs
82
83 v.1.20.0: Updated to Mothur 1.33
84
85 ]]>
86 </help>
87 <expand macro="citations"/>
88 </tool>