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comparison phyloseq_2_deseq2.xml @ 0:1f0569e94be4 draft

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"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_2_deseq2 commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
author qfabrepo
date Mon, 14 Sep 2020 08:20:41 +0000
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1 <tool id="phyloseq_DESeq2" name="DESeq2" version="1.22.3" hidden="false">
2 <description>Differential Analysis</description>
3 <requirements>
4 <requirement type="package" version="3.4.1">r-base</requirement>
5 <requirement type="package" version="1.22.3">bioconductor-phyloseq</requirement>
6 <requirement type="package" version="1.18.1">bioconductor-deseq2</requirement>
7 <requirement type="package" version="1.20.0">r-getopt</requirement>
8 <requirement type="package" version="9.18">ghostscript</requirement>
9 </requirements>
10 <version_command><![CDATA[
11 echo $(R --version | grep version | grep -v GNU)", phyloseq version" $(R --vanilla --slave -e "library(phyloseq); cat(sessionInfo()\$otherPkgs\$phyloseq\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
12 ]]></version_command>
13 <command detect_errors="exit_code"><![CDATA[
14 Rscript '${__tool_directory__}/phyloseq_2_deseq2.r'
15 --biomfile='$biom_input'
16 --metafile='$metadata_input'
17 --factor="${factor}"
18 --test="${test}"
19 --fitType="${fitType}"
20 --cutoff='${cutoff}'
21 --result='$DE_table'
22 --normalisedResult='$normalised_table'
23 ]]></command>
24
25 <inputs>
26 <param format="biom1" name="biom_input" type="data" label="BIOM file"/>
27 <param format="tabular" name="metadata_input" type="data" label="Metadata file"/>
28 <param name="factor" type="data_column" data_ref="metadata_input" use_header_names="TRUE" label="factor for differential analysis testing"/>
29 <param name="test" type="select" display="radio" label="select a test statistic">
30 <option value="Wald" selected="true">Wald</option>
31 <option value="LRT">LRT</option>
32 </param>
33 <param name="fitType" type="select" display="radio" label="select a fit Type for dispersions">
34 <option value="parametric" selected="true">parametric</option>
35 <option value="local">local</option>
36 </param>
37 <param name="cutoff" value="0.05" type="float" label="cutoff value for differential analysis"/>
38 </inputs>
39
40 <outputs>
41 <data format="tabular" name="DE_table" label="${tool.name} DE.txt"/>
42 <data format="tabular" name="normalised_table" type="float" label="${tool.name} Normalised Table.txt"/>
43 </outputs>
44
45 <tests>
46 <test> <!-- Test : Test BIOM format input -->
47 <param name="biom_input" value="test.biom" ftype="biom1" />
48 <param name="metadata_input" value="metadata.txt"/>
49 <param name="factor" value="3" />
50 <param name="test" value="Wald" />
51 <param name="fitType" value="parametric" />
52 <param name="cutoff" value="0.05"/>
53 <output name="DE_table" ftype="tabular" file="DE_table.txt" />
54 <output name="norm_DE_table" ftype="tabular" file="norm_DE_table.txt" />
55 </test>
56 </tests>
57 <help>
58 **What it does**
59 Use BIOM and metadata file as input to perform a differential analysis using R package, DESeq2_ and Phyloseq_.
60
61 .. _DESeq2: https://bioconductor.org/packages/release/bioc/html/DESeq2.html
62 .. _Phyloseq: https://joey711.github.io/phyloseq/index.html
63
64 -----
65
66 **Input**
67
68 - **BIOM file** - select BIOM file
69 - **Metadata file** - metadata file contains experimental information.
70 - **factor for differential analysis testing** - select a factor for differential analysis testing
71 - **Select a test statistic** - e.g. Wald or LRT
72 - **Select a fit Type for dispersions** - e.g. parametric or local
73 - **cutoff value for differential analysis** - e.g. 0.05
74
75 -----
76
77
78 =========
79 Resources
80 =========
81
82 **Wrapper Authors**
83
84 QFAB Bioinformatics (support@qfab.org)
85 </help>
86 <citations>
87 <citation type="doi">10.18129/B9.bioc.phyloseq</citation>
88 <citation type="doi">10.1186/s13059-014-0550-8</citation>
89 </citations>
90 </tool>