Mercurial > repos > iuc > multigsea
diff multigsea.xml @ 0:28e29a3d0eda draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea commit 5c1b8a2b105a80e236f88e71a743147d79925ac4
| author | iuc |
|---|---|
| date | Wed, 07 Jun 2023 19:48:50 +0000 |
| parents | |
| children | e48b10ce08b8 |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/multigsea.xml Wed Jun 07 19:48:50 2023 +0000 @@ -0,0 +1,295 @@ +<tool id="multigsea" name="multiGSEA" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@" profile="@PROFILE@"> + <description>GSEA-based pathway enrichment analysis for multi-omics data</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro='xrefs'/> + <expand macro='requirements'/> + <stdio> + <regex match="Execution halted" + source="both" + level="fatal" + description="Execution halted." /> + <regex match="Error in" + source="both" + level="fatal" + description="An undefined error occurred, please check your input carefully and contact your administrator." /> + <regex match="Fatal error" + source="both" + level="fatal" + description="An undefined error occurred, please check your input carefully and contact your administrator." /> + </stdio> + <command><![CDATA[ + + Rscript '${__tool_directory__}/multiGSEA.R' + #if $transcriptomics_data.selector == "true" + --transcriptomics '${transcriptomics_data.transcriptomics}' + --transcriptome_ids $transcriptomics_data.transcriptome_ids + #end if + #if $proteomics_data.selector == "true" + --proteomics '${proteomics}' + --proteome_ids $proteomics_data.proteome_ids + #end if + #if $metabolomics_data.selector == "true" + --metabolomics '${metabolomics}' + --metabolome_ids $metabolomics_data.metabolome_ids + #end if + --organism $organism + --databases $databases + --combine_pvalues $combine_pvalues + --padj_method $padj_method + + ]]></command> + <inputs> + <conditional name="transcriptomics_data"> + <param name="selector" type="select" label="Select transcriptomics data"> + <option value="true">Enabled</option> + <option value="false">Disabled</option> + </param> + <when value="true"> + <param name="transcriptomics" type="data" format="tabular" label="Transcriptomics data" + help="String specifying the returned gene ID format." /> + <expand macro="macro_IDs" name="transcriptome_ids" label="Gene ID format in transcriptomics data"/> + </when> + <when value="false"/> + </conditional> + <conditional name="proteomics_data"> + <param name="selector" type="select" label="Select proteomics data"> + <option value="true">Enabled</option> + <option value="false">Disabled</option> + </param> + <when value="true"> + <param name="proteomics" type="data" format="tabular" label="Proteomics data" + help="String specifying the returned gene ID format" /> + <expand macro="macro_IDs" name="proteome_ids" label="Gene ID format in proteomics data"/> + </when> + <when value="false"/> + </conditional> + <conditional name="metabolomics_data"> + <param name="selector" type="select" label="Select metabolomics data"> + <option value="true">Enabled</option> + <option value="false">Disabled</option> + </param> + <when value="true"> + <param name="metabolomics" type="data" format="tabular" label="Metabolomics data" + help="String specifying the returned metabolite ID format." /> + <param name="metabolome_ids" type="select" label="Metabolite ID format" + help="String specifying the returned metabolite ID format."> + <option value="HMDB">HMDB</option> + <option value="CAS">CAS</option> + <option value="DTXCID">DTXCID</option> + <option value="DTXSID">DTXSID</option> + <option value="SID">SID</option> + <option value="CID">CID</option> + <option value="ChEBI">ChEBI</option> + <option value="KEGG">KEGG</option> + <option value="Drugbank">Drugbank</option> + </param> + </when> + <when value="false"/> + </conditional> + <param name="organism" type="select" label="Supported organisms"> + <option value="hsapiens">Homo sapiens (Human)</option> + <option value="mmusculus">Mus musculus (Mouse)</option> + <option value="rnorvegicus">Rattus Norvegicus (Rat)</option> + <option value="cfamiliaris">Canis lupus familiaris (Dog)</option> + <option value="btaurus">Bos taurus (Cow)</option> + <option value="sscrofa">Sus scrofa (Pig)</option> + <option value="ggallus">Gallus gallus (Chicken)</option> + <option value="xlaevis">Xenopus laevis (Flog)</option> + <option value="drerio">Danio rerio (Zebrafish)</option> + <option value="dmelanogaster">Drosophila melanogaster (Fruit fly)</option> + <option value="celegans">Caenorabditis elegans (Roundworm)</option> + </param> + <param name="databases" type="select" multiple="true" label="Pathway databases" help="Available pathway databases"> + <option value="all" selected="true">All available databases</option> + <option value="kegg">KEGG</option> + <option value="reactome">REACTOME</option> + <option value="wikipathways">WIKIPATHWAYS</option> + <option value="pathbank">PATHBANK</option> + <option value="smpdb">SMPDB (Human only)</option> + <option value="panther">PANTHER (Human only)</option> + <option value="pharmgkb">PHARMGKB (Human only)</option> + </param> + <param name="combine_pvalues" type="select" label="Combine p-values method" help="It specifies the method to combine multiple p-values "> + <option value="stouffer">Stouffer</option> + <option value="fisher">Fisher</option> + <option value="edgington">Edgington</option> + </param> + <param name="padj_method" type="select" label="P-values correction method" help=" Multiple testing corrections adjust + p-values derived from multiple statistical tests to correct for occurrence of false positives"> + <option value="holm">Holm</option> + <option value="hochberg">Hochberg</option> + <option value="hommel">Hommel</option> + <option value="bonferroni">Bonferroni</option> + <option value="BH" selected="true">BH</option> + <option value="BY">BY</option> + </param> + </inputs> + <outputs> + <data name="output" format="tabular" from_work_dir="results.tsv" label="${tool.name} on ${on_string}: pathway enrichment"/> + </outputs> + <tests> + <!-- Test only with transcriptomics data --> + <test expect_num_outputs="1"> + <param name="organism" value="hsapiens"/> + <param name="databases" value="kegg"/> + <param name="combine_pvalues" value="stouffer"/> + <param name="padj_method" value="holm"/> + <conditional name="transcriptomics_data"> + <param name="selector" value="true"/> + <param name="transcriptomics" value="transcriptome.tsv"/> + <param name="transcriptome_ids" value="SYMBOL"/> + </conditional> + <output name="output"> + <assert_contents> + <has_size value="43574" delta="300"/> + <has_text text="Ubiquinone and other terpenoid-quinone biosynthesis"/> + </assert_contents> + </output> + </test> + <!-- Test all inputs --> + <test expect_num_outputs="1"> + <param name="organism" value="hsapiens"/> + <param name="databases" value="kegg"/> + <param name="combine_pvalues" value="stouffer"/> + <param name="padj_method" value="holm"/> + <conditional name="transcriptomics_data"> + <param name="selector" value="true"/> + <param name="transcriptomics" value="transcriptome.tsv"/> + <param name="transcriptome_ids" value="SYMBOL"/> + </conditional> + <conditional name="proteomics_data"> + <param name="selector" value="true"/> + <param name="proteomics" value="proteome.tsv"/> + <param name="proteome_ids" value="SYMBOL"/> + </conditional> + <conditional name="metabolomics_data"> + <param name="selector" value="true"/> + <param name="metabolomics" value="metabolome.tsv"/> + <param name="metabolome_ids" value="HMDB"/> + </conditional> + <output name="output"> + <assert_contents> + <has_size value="42541" delta="300"/> + <has_text text="Ubiquinone and other terpenoid-quinone biosynthesis"/> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ + +.. class:: infomark + +Purpose +======= + +The multiGSEA allows to perform robust GSEA-based pathway enrichment for +multiple omics layers. The enrichment is calculated for each omics layer +separately and aggregated p-values are calculated afterwards to derive a +composite multi-omics pathway enrichment. + +Input requirements +================== + +``multiGSEA`` can be applied with up to three different omics layers. In +principle, the input format is similar between those layers, containing +the feature IDs, the log2 fold change, and the p-Value. + +The columns have to be named as follows: + +:: + + - Symbol (feature ID) + - logFC (log2 fold change) + - pValue + +Two example omics data sets is shown below: + +**Trancriptomics input data** + +================== ========= ============ +Symbol logFC pValue +================== ========= ============ +ENSRNOG00000009450 -3.447792 1.063839e-24 +ENSRNOG00000011858 -2.604610 4.928870e-36 +ENSRNOG00000005438 -2.743588 8.085929e-15 +ENSRNOG00000005697 -3.575947 5.721265e-34 +ENSRNOG00000011130 -2.507097 2.931514e-11 +ENSRNOG00000002265 -2.647413 9.085615e-26 +================== ========= ============ + +**Proteomics input data** + +======== ====== ============ +Symbol logFC pValue +======== ====== ============ +B1WBW4 -4.080 6.027171e-04 +B2RYC9 -2.860 2.937084e-06 +F1LPV8 3.370 2.930764e-13 +F1LR66 5.310 3.580927e-16 +P06685 5.030 1.890405e-18 +P06761 0.324 4.833296e-01 +======== ====== ============ + +Organisms +========= + +``multiGSEA`` can be applied to 11 model organisms: + +- *Homo sapiens* (hsapiens) +- *Mus musculus* (mmusculus) +- *Rattus norvegicus* (rnorvegicus) +- *Canis familiaris* (cfamiliaris) +- *Sus scrofa* (sscrofa) +- *Bos taurus* (btaurus) +- *Danio rerio* (drerio) +- *Gallus gallus* (ggallus) +- *Xaenopus laevis* (xlaevis) +- *Caenorhabditis elegans* (celegans) +- *Drosophila melanogaster* (dmelanogaster) + +Databases +========= + +Depending on the selected organism, several pathway databases can be +queried. + +**H.sapiens** + + - kegg, reactome, wikipathways, panther, pathbank, pharmgkb, smpdb + +**M.musculus, R.norvegicus, B.taurus, C.elegans, D.melanogaster** + + - kegg, reactome, pathbank, wikipathways + +**C.familiaris, S.scrofa, D.rerio, G.gallus** + + - kegg, reactome, wikipathways + +**X.laevis** + + - kegg + +Combining p-values +================== + +multiGSEA provided three different methods to aggregate p-values. These +methods differ in their way how they weight either small or large +p-values. By default, combinePvalues will apply the Z-method or +Stouffer’s method (Stouffer *et al.*, 1949) which has no bias towards +small or large p-values. The widely used Fisher’s combined probability +test (Fisher, 1932) can also be applied but is known for its bias +towards small p-values. Edgington’s method goes the opposite direction +by favoring large p-values (Edgington, 1972). + + +Output format +============= + +The calculated pathway enrichment is sorted based on their combined adjusted p-values. For each individual pathway, the single omics p-Value and adjusted p-Values are collected as well as the combined p-Value and adjusted p-Value. + + + ]]></help> + <expand macro="citations" /> +</tool>