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comparison fisher_test.xml @ 3:4b76708c6b95 draft default tip

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/fisher_test commit afc67da70753a5808ade516f71e9bf133efb3268
author artbio
date Sat, 14 Oct 2023 22:59:13 +0000
parents 8052d037517f
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2:8052d037517f 3:4b76708c6b95
1 <tool id="fishertest" name="Fisher's exact test" version="2.22.0+galaxy0"> 1 <tool id="fishertest" name="Fisher's exact test" version="2.32.0+galaxy0">
2 <description>on two gene hit lists</description> 2 <description>on two gene hit lists</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="2.22.0">bioconductor-qvalue</requirement> 4 <requirement type="package" version="2.32.0">bioconductor-qvalue</requirement>
5 </requirements> 5 </requirements>
6 <command><![CDATA[ 6 <command><![CDATA[
7 Rscript '$fisher_test' "\${GALAXY_SLOTS:-1}" 7 Rscript '$fisher_test' "\${GALAXY_SLOTS:-1}"
8 ]]></command> 8 ]]></command>
9 <configfiles> 9 <configfiles>
54 </tests> 54 </tests>
55 <help> 55 <help>
56 56
57 **What it does** 57 **What it does**
58 58
59 Runs Fisher's exact test for testing the null of independence of rows and columns in a contingency table of two columns. 59 Runs Fisher's exact test for testing the null of independence of rows and columns
60 in a contingency table of two columns.
60 61
61 p.pvalues: the chance of getting this data if it is independent between columns (false negative); the p-value. 62 p.pvalues: the chance of getting this data if it is independent between columns
63 (false negative); the p-value.
62 64
63 q.qvalues: FDR (Faslse Detection Rate) adjusted p-values; a q-value of 0.05 implies that 5% of significant tests will result in false positives. 65 q.qvalues: FDR (Faslse Detection Rate) adjusted p-values;
66 a q-value of 0.05 implies that 5% of significant tests will result in false positives.
64 67
65 Be aware that this test does not take into account the biological noise that would be visible if replicates were available. 68 Be aware that this test does not take into account the biological noise
69 that would be visible if replicates were available.
66 70
67 71
68 </help> 72 </help>
69 <citations> 73 <citations>
70 <citation type="doi">10.1111/1467-9868.00346</citation> 74 <citation type="doi">10.1111/1467-9868.00346</citation>