Mercurial > repos > caleb-easterly > peca
comparison peca.xml @ 11:19bb06146c2e draft
planemo upload for repository https://github.com/caleb-easterly/galaxytools/peca
author | caleb-easterly |
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date | Thu, 08 Mar 2018 18:27:44 -0500 |
parents | f0de83932f9e |
children | 5c3b60c36c66 |
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10:f0de83932f9e | 11:19bb06146c2e |
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7 </requirements> | 7 </requirements> |
8 <command detect_errors="exit_code"><![CDATA[ | 8 <command detect_errors="exit_code"><![CDATA[ |
9 ## write groups to file | 9 ## write groups to file |
10 echo '$group1' > group1.txt && | 10 echo '$group1' > group1.txt && |
11 echo '$group2' > group2.txt && | 11 echo '$group2' > group2.txt && |
12 Rscript --vanilla '$__tool_directory__/peca.R' '$input' group1.txt group2.txt '$test_type' '$output' | 12 Rscript --vanilla '$__tool_directory__/peca.R' '$input' group1.txt group2.txt '$test_type' '$paired' '$output' |
13 ]]></command> | 13 ]]></command> |
14 <inputs> | 14 <inputs> |
15 <param name="input" type="data" format="tabular"/> | 15 <param name="input" type="data" format="tabular"/> |
16 <param name="group1" type="data_column" data_ref="input" multiple="true"/> | 16 <param name="group1" type="data_column" data_ref="input" multiple="true"/> |
17 <param name="group2" type="data_column" data_ref="input" multiple="true"/> | 17 <param name="group2" type="data_column" data_ref="input" multiple="true"/> |
18 <param name="test_type" type="select"> | 18 <param name="test_type" type="select" label="Type of test"> |
19 <option value="t" selected="true">Standard t-test</option> | 19 <option value="t" selected="true">Standard t-test</option> |
20 <option value="modt">Modified t-test</option> | 20 <option value="modt">Modified t-test</option> |
21 <option value="rots">Reproducibility-optimized test statistic</option> | 21 <option value="rots">Reproducibility-optimized test statistic</option> |
22 </param> | 22 </param> |
23 <param name="paired" type="boolean" label="Perform paired t-test" checked="false"/> | |
23 </inputs> | 24 </inputs> |
24 <outputs> | 25 <outputs> |
25 <data format="tabular" name="output"/> | 26 <data format="tabular" name="output"/> |
26 </outputs> | 27 </outputs> |
27 <tests> | 28 <tests> |
28 <test> | 29 <test> |
29 <param name="input" value="test.tab" ftype="tabular"/> | 30 <param name="input" value="test.tab" ftype="tabular"/> |
30 <param name="group1" value="2,3,4"/> | 31 <param name="group1" value="2,3,4"/> |
31 <param name="group2" value="5,6,7"/> | 32 <param name="group2" value="5,6,7"/> |
32 <param name="test_type" value="t"/> | 33 <param name="test_type" value="t"/> |
34 <param name="paired" value="false"/> | |
33 <output name="output" file="out.tab" ftype="tabular"/> | 35 <output name="output" file="out.tab" ftype="tabular"/> |
34 </test> | 36 </test> |
35 </tests> | 37 </tests> |
36 <help><![CDATA[ | 38 <help><![CDATA[ |
37 ]]></help> | 39 ]]></help> |