Mercurial > repos > iuc > mothur_dist_seqs
comparison dist.seqs.xml @ 2:189b742d2434 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
author | iuc |
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date | Tue, 20 Mar 2018 22:23:36 -0400 |
parents | d103727775eb |
children | 57eb5df69242 |
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1:efc735bcc806 | 2:189b742d2434 |
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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> |