Mercurial > repos > iuc > mothur_anosim
comparison anosim.xml @ 2:d83e7e498f31 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 22:09:48 -0400 |
parents | 08ccc12f2a3a |
children | 652d2803062c |
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1:f228c52a3978 | 2:d83e7e498f31 |
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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 "$dist" dist.dat && | 13 ln -s '$phylip' phylip.dat && |
14 ln -s "$design" design.dat && | 14 ln -s '$design' design.dat && |
15 | 15 |
16 echo 'anosim( | 16 echo 'anosim( |
17 phylip=dist.dat, | 17 phylip=phylip.dat, |
18 iters=$iters, | 18 iters=$iters, |
19 alpha=$alpha, | 19 alpha=$alpha, |
20 design=design.dat | 20 design=design.dat |
21 )' | 21 )' |
22 | sed 's/ //g' ## mothur trips over whitespace | 22 | sed 's/ //g' ## mothur trips over whitespace |
23 | mothur | 23 | mothur |
24 | tee mothur.out.log | 24 | tee mothur.out.log |
25 ]]></command> | 25 ]]></command> |
26 <inputs> | 26 <inputs> |
27 <param name="dist" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/> | 27 <param argument="phylip" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/> |
28 <param name="design" type="data" format="tabular" label="design - assign groups to new grouping" help="design has 2 columns: group(col 1) and grouping(col 2) (separated by a TAB character)"/> | 28 <param argument="design" type="data" format="tabular" label="design - assign groups to new grouping" |
29 <param name="alpha" type="float" optional="true" value="0.05" min="0" label="alpha - acceptable stopping precision (default 0.05)"/> | 29 help="design has 2 columns: group(col 1) and grouping(col 2) (separated by a TAB character)"/> |
30 <param name="iters" type="integer" value="1000" min="0" label="iters - Number of random configuration to try (default 1000)"/> | 30 <param argument="alpha" type="float" optional="true" value="0.05" min="0" label="alpha - acceptable stopping precision" help="default: 0.05"/> |
31 <param argument="iters" type="integer" value="1000" min="0" label="iters - Number of random configuration to try" help="default: 1000"/> | |
32 <expand macro="param-savelog"/> | |
31 </inputs> | 33 </inputs> |
32 <outputs> | 34 <outputs> |
33 <expand macro="logfile-output"/> | 35 <expand macro="logfile-output"/> |
34 <data name="anosim" format="tabular" from_work_dir="dist.anosim" label="${tool.name} on ${on_string}: anosim"/> | 36 <data name="anosim" format="tabular" from_work_dir="phylip.anosim" label="${tool.name} on ${on_string}: anosim"/> |
35 </outputs> | 37 </outputs> |
36 <tests> | 38 <tests> |
37 <test> | 39 <test> |
38 <param name="dist" value="amazon.dist"/> | 40 <param name="phylip" value="amazon.dist"/> |
39 <param name="design" value="amazon.design"/> | 41 <param name="design" value="amazon.design"/> |
40 <output name="anosim" ftype="tabular"> | 42 <output name="anosim" ftype="tabular"> |
41 <assert_contents> | 43 <assert_contents> |
42 <has_line_matching expression="^comparison\tR-value\tP-value$"/> | 44 <has_line_matching expression="^comparison\tR-value\tP-value$"/> |
43 <has_line_matching expression="^A-B\t[0-9\.\-]+\t[0-9\.]+$"/> | 45 <has_line_matching expression="^A-B\t[0-9\.\-]+\t[0-9\.]+$"/> |
44 </assert_contents> | 46 </assert_contents> |
45 </output> | 47 </output> |
48 <param name="savelog" value="true"/> | |
46 <expand macro="logfile-test"/> | 49 <expand macro="logfile-test"/> |
47 </test> | 50 </test> |
48 </tests> | 51 </tests> |
49 <help> | 52 <help><![CDATA[ |
50 <![CDATA[ | |
51 | 53 |
52 @MOTHUR_OVERVIEW@ | 54 @MOTHUR_OVERVIEW@ |
53 | 55 |
54 **Command Documentation** | 56 **Command Documentation** |
55 | 57 |
68 | 70 |
69 | 71 |
70 .. _phylip_distance_matrix: https://www.mothur.org/wiki/Phylip-formatted_distance_matrix | 72 .. _phylip_distance_matrix: https://www.mothur.org/wiki/Phylip-formatted_distance_matrix |
71 .. _anosim: https://www.mothur.org/wiki/Anosim | 73 .. _anosim: https://www.mothur.org/wiki/Anosim |
72 | 74 |
73 ]]> | 75 ]]></help> |
74 </help> | |
75 <expand macro="citations"/> | 76 <expand macro="citations"/> |
76 </tool> | 77 </tool> |