Mercurial > repos > iuc > mothur_dist_seqs

comparison dist.seqs.xml @ 2:189b742d2434 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 22:23:36 -0400
parents d103727775eb
children 57eb5df69242
comparison
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1:efc735bcc806 2:189b742d2434
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 "$fasta" fasta.dat && 13 ln -s '$fasta' fasta.dat &&
14 14
15 echo 'dist.seqs( 15 echo 'dist.seqs(
16 fasta=fasta.dat, 16 fasta=fasta.dat,
17 #if $calc: 17 #if $calc:
18 calc=$calc, 18 calc=$calc,
19 #end if 19 #end if
20 countends=$countends, 20 countends=$countends,
21 #if $cutoff: 21 #if $cutoff:
22 cutoff=$cutoff, 22 cutoff=$cutoff,
23 #end if 23 #end if
24 #if $output: 24 #if $output:
25 output=$output, 25 output=$output,
26 #end if 26 #end if
27 processors='\${GALAXY_SLOTS:-8}' 27 processors='\${GALAXY_SLOTS:-8}'
28 )' 28 )'
29 | sed 's/ //g' ## mothur trips over whitespace 29 | sed 's/ //g' ## mothur trips over whitespace
30 | mothur 30 | mothur
31 | tee mothur.out.log 31 | tee mothur.out.log
32 ]]></command> 32 ]]></command>
33 <inputs> 33 <inputs>
34 <param name="fasta" type="data" format="mothur.align,fasta" label="fasta - Alignment Fasta"/> 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"> 35 <param name="calc" type="select" label="calc - Calc Method - Gap Penality">
36 <option value="" selected="true">use default</option> 36 <option value="" selected="true">use default</option>
37 <option value="onegap">onegap - counts a string of gaps as a single gap</option> 37 <option value="onegap">onegap - counts a string of gaps as a single gap</option>
38 <option value="nogaps">nogaps - ignores gaps</option> 38 <option value="nogaps">nogaps - ignores gaps</option>
39 <option value="eachgap ">eachgap - penalize each gap</option> 39 <option value="eachgap ">eachgap - penalize each gap</option>
40 </param> 40 </param>
41 <param name="countends" type="boolean" checked="true" truevalue="true" falsevalue="false" label="countends - Penalize terminal gaps"/> 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"/> 42 <param name="cutoff" type="float" value="" min="0.0" optional="true" label="cutoff - Distance Cutoff threshold - ignored if not > 0"
43 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 <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="" selected="true">Default Column-Formatted Matrix</option>
45 <option value="lt">Phylip formatted Lower Triangle Matrix</option> 46 <option value="lt">Phylip formatted Lower Triangle Matrix</option>
46 <option value="square">Phylip formatted Square Matrix</option> 47 <option value="square">Phylip formatted Square Matrix</option>
47 </param> 48 </param>
49 <expand macro="param-savelog"/>
48 </inputs> 50 </inputs>
49 <outputs> 51 <outputs>
50 <expand macro="logfile-output"/> 52 <expand macro="logfile-output"/>
51 <data name="out_dist" format="mothur.pair.dist" from_work_dir="fasta*.dist" label="${tool.name} on ${on_string}: dist"> 53 <data name="out_dist" format="mothur.pair.dist" from_work_dir="fasta*.dist" label="${tool.name} on ${on_string}: dist">
52 <change_format> 54 <change_format>
57 </outputs> 59 </outputs>
58 <tests> 60 <tests>
59 <test><!-- test with default params --> 61 <test><!-- test with default params -->
60 <param name="fasta" value="HMP_MOCK.v35.align" ftype="mothur.align"/> 62 <param name="fasta" value="HMP_MOCK.v35.align" ftype="mothur.align"/>
61 <output name="out_dist" md5="2c4817bb8657b4df2dcb1f2a019f505e" ftype="mothur.pair.dist"/> 63 <output name="out_dist" md5="2c4817bb8657b4df2dcb1f2a019f505e" ftype="mothur.pair.dist"/>
64 <param name="savelog" value="true"/>
62 <expand macro="logfile-test"/> 65 <expand macro="logfile-test"/>
63 </test> 66 </test>
64 <test><!-- test with all params custom --> 67 <test><!-- test with all params custom -->
65 <param name="fasta" value="HMP_MOCK.v35.align" ftype="mothur.align"/> 68 <param name="fasta" value="HMP_MOCK.v35.align" ftype="mothur.align"/>
66 <param name="calc" value="nogaps"/> 69 <param name="calc" value="nogaps"/>
67 <param name="countends" value="false"/> 70 <param name="countends" value="false"/>
68 <param name="cutoff" value="0.3"/> 71 <param name="cutoff" value="0.3"/>
69 <param name="output" value="lt"/> 72 <param name="output" value="lt"/>
70 <output name="out_dist" md5="8a5ccf1ad8f1c344cf4d3e2c97d4cdc6" ftype="mothur.lower.dist"/> 73 <output name="out_dist" md5="8a5ccf1ad8f1c344cf4d3e2c97d4cdc6" ftype="mothur.lower.dist"/>
74 <param name="savelog" value="true"/>
71 <expand macro="logfile-test"/> 75 <expand macro="logfile-test"/>
72 </test> 76 </test>
73 </tests> 77 </tests>
74 <help> 78 <help><![CDATA[
75 <![CDATA[
76 79
77 @MOTHUR_OVERVIEW@ 80 @MOTHUR_OVERVIEW@
78 81
79 **Command Documentation** 82 **Command Documentation**
80 83
84 .. _phylip-formatted_distance_matrix: https://www.mothur.org/wiki/Phylip-formatted_distance_matrix 87 .. _phylip-formatted_distance_matrix: https://www.mothur.org/wiki/Phylip-formatted_distance_matrix
85 .. _dist.seqs: https://www.mothur.org/wiki/Dist.seqs 88 .. _dist.seqs: https://www.mothur.org/wiki/Dist.seqs
86 89
87 v.1.20.0: Updated to Mothur 1.33 90 v.1.20.0: Updated to Mothur 1.33
88 91
89 ]]> 92 ]]></help>
90 </help>
91 <expand macro="citations"/> 93 <expand macro="citations"/>
92 </tool> 94 </tool>