Mercurial > repos > iuc > mothur_dist_seqs
comparison dist.seqs.xml @ 0:d103727775eb draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author | iuc |
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date | Fri, 19 May 2017 04:59:45 -0400 |
parents | |
children | 189b742d2434 |
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-1:000000000000 | 0:d103727775eb |
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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="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 'dist.seqs( | |
16 fasta=fasta.dat, | |
17 #if $calc: | |
18 calc=$calc, | |
19 #end if | |
20 countends=$countends, | |
21 #if $cutoff: | |
22 cutoff=$cutoff, | |
23 #end if | |
24 #if $output: | |
25 output=$output, | |
26 #end if | |
27 processors='\${GALAXY_SLOTS:-8}' | |
28 )' | |
29 | sed 's/ //g' ## mothur trips over whitespace | |
30 | mothur | |
31 | tee mothur.out.log | |
32 ]]></command> | |
33 <inputs> | |
34 <param name="fasta" type="data" format="mothur.align,fasta" label="fasta - Alignment Fasta"/> | |
35 <param name="calc" type="select" label="calc - Calc Method - Gap Penality"> | |
36 <option value="" selected="true">use default</option> | |
37 <option value="onegap">onegap - counts a string of gaps as a single gap</option> | |
38 <option value="nogaps">nogaps - ignores gaps</option> | |
39 <option value="eachgap ">eachgap - penalize each gap</option> | |
40 </param> | |
41 <param name="countends" type="boolean" checked="true" truevalue="true" falsevalue="false" label="countends - Penalize terminal gaps"/> | |
42 <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"/> | |
43 <param name="output" type="select" label="output - Distance Matrix Output Format" help=""> | |
44 <option value="" selected="true">Default Column-Formatted Matrix</option> | |
45 <option value="lt">Phylip formatted Lower Triangle Matrix</option> | |
46 <option value="square">Phylip formatted Square Matrix</option> | |
47 </param> | |
48 </inputs> | |
49 <outputs> | |
50 <expand macro="logfile-output"/> | |
51 <data name="out_dist" format="mothur.pair.dist" from_work_dir="fasta*.dist" label="${tool.name} on ${on_string}: dist"> | |
52 <change_format> | |
53 <when input="output" value="lt" format="mothur.lower.dist"/> | |
54 <when input="output" value="square" format="mothur.square.dist"/> | |
55 </change_format> | |
56 </data> | |
57 </outputs> | |
58 <tests> | |
59 <test><!-- test with default params --> | |
60 <param name="fasta" value="HMP_MOCK.v35.align" ftype="mothur.align"/> | |
61 <output name="out_dist" md5="2c4817bb8657b4df2dcb1f2a019f505e" ftype="mothur.pair.dist"/> | |
62 <expand macro="logfile-test"/> | |
63 </test> | |
64 <test><!-- test with all params custom --> | |
65 <param name="fasta" value="HMP_MOCK.v35.align" ftype="mothur.align"/> | |
66 <param name="calc" value="nogaps"/> | |
67 <param name="countends" value="false"/> | |
68 <param name="cutoff" value="0.3"/> | |
69 <param name="output" value="lt"/> | |
70 <output name="out_dist" md5="8a5ccf1ad8f1c344cf4d3e2c97d4cdc6" ftype="mothur.lower.dist"/> | |
71 <expand macro="logfile-test"/> | |
72 </test> | |
73 </tests> | |
74 <help> | |
75 <![CDATA[ | |
76 | |
77 @MOTHUR_OVERVIEW@ | |
78 | |
79 **Command Documentation** | |
80 | |
81 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. | |
82 | |
83 .. _column-formatted_distance_matrix: https://www.mothur.org/wiki/Column-formatted_distance_matrix | |
84 .. _phylip-formatted_distance_matrix: https://www.mothur.org/wiki/Phylip-formatted_distance_matrix | |
85 .. _dist.seqs: https://www.mothur.org/wiki/Dist.seqs | |
86 | |
87 v.1.20.0: Updated to Mothur 1.33 | |
88 | |
89 ]]> | |
90 </help> | |
91 <expand macro="citations"/> | |
92 </tool> |