Mercurial > repos > mbernt > proteomicsr_msigdb_workflow
diff macros.xml @ 0:0fbb062e0cf5 draft default tip
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty
| author | mbernt |
|---|---|
| date | Tue, 19 Dec 2023 15:51:04 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Tue Dec 19 15:51:04 2023 +0000 @@ -0,0 +1,174 @@ +<macros> + <token name="@TOOL_VERSION@">0.1.0</token> + <token name="@VERSION_SUFFIX@">0</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">r-proteomicsr</requirement> + <!-- <requirement type="package" version="2.58.0">bioconductor-biomart</requirement> + <requirement type="package" version="4.10.0">bioconductor-clusterprofiler</requirement> + <requirement type="package" version="1.24.0">bioconductor-dep</requirement> + <requirement type="package" version="2.18.0">bioconductor-complexheatmap</requirement> + <requirement type="package" version="1.20.0">bioconductor-kinswingr</requirement> + <requirement type="package" version="0.4.15">r-circlize</requirement> + <requirement type="package" version="3.4.0">r-classdiscovery</requirement> + <requirement type="package" version="0.92">r-corrplot</requirement> + <requirement type="package" version="0.3.4">r-dendsort</requirement> + <requirement type="package" version="1.63_1">r-dynamictreecut</requirement> + <requirement type="package" version="3.4.2">r-ggplot2</requirement> + <requirement type="package" version="0.6.0">r-ggpubr</requirement> + <requirement type="package" version="6.3.2">r-mixomics</requirement> + <requirement type="package" version="7.5.1">r-msigdbr</requirement> + <requirement type="package" version="1.0.12">r-pheatmap</requirement> + <requirement type="package" version="1.8.9">r-plyr</requirement> + <requirement type="package" version="2.1.4">r-readr</requirement> + <requirement type="package" version="1.4.4">r-reshape2</requirement> + <requirement type="package" version="1.2.1">r-scales</requirement> + <requirement type="package" version="1.4.8">r-splitstackshape</requirement> + <requirement type="package" version="1.3.0">r-tidyr</requirement> + <requirement type="package" version="1.71">r-wgcna</requirement> + <requirement type="package" version="2.3.4">r-dbplyr</requirement> --> + + <!-- conda create -y \-\-quiet \-\-strict-channel-priority \-\-solver libmamba \-\-override-channels \-\-channel conda-forge \-\-channel bioconda \-\-channel defaults \-\-name + __r-proteomicsr@0.1.0 + "bioconductor-biomart=2.58.0" # needed update https://github.com/grimbough/biomaRt/issues/87 + "bioconductor-clusterprofiler=4.10.0" #(newer needed, otherwise conflict with bioconductor-biomart) + "bioconductor-dep=1.24.0" # same + bioconductor-complexheatmap=2.18.0 + bioconductor-kinswingr + r-circlize=0.4.15 + r-classdiscovery=3.4.0 + r-corrplot=0.92 r-dendsort=0.3.4 + r-dynamictreecut=1.63_1 + r-ggplot2=3.4.2 + r-ggpubr=0.6.0 + r-mixomics=6.3.2 + r-msigdbr=7.5.1 + r-pheatmap=1.0.12 + r-plyr=1.8.9 + r-readr=2.1.4 + r-reshape2=1.4.4 + r-scales=1.2.1 + r-splitstackshape=1.4.8 + r-tidyr=1.3.0 + r-wgcna=1.71 + "r-dbplyr<2.4" + --> + <!-- <requirement type="package" version="3.0.0">r-ggsci</requirement> --> + <!-- <requirement type="package" version="2.3">r-gridextra</requirement> --> + + <yield/> + </requirements> + </xml> + + <token name="@READ_INPUTS@"><![CDATA[ +#if $sampleTable.ext == 'csv' + sampleTable <- read.csv("$sampleTable", row.names = 1) +#else + sampleTable <- read.delim("$sampleTable", header = TRUE, row.names = 1, sep = "\t") +#end if +@READ_SAMPLE_GENES_MAPPING@ + ]]></token> + + <token name="@READ_SAMPLE_GENES_MAPPING@"><![CDATA[ +#if $sampleGenes + #if $sampleGenes.ext == 'csv' + sampleGenes <- read.csv("$sampleGenes", row.names = 1) + #else + sampleGenes <- read.delim("$sampleGenes", header = TRUE, row.names = 1, sep = "\t") + #end if +#else + sampleGenes <- NULL +#end if +#if $sampleMapping + #if $sampleMapping.ext == 'csv' + sampleMapping <- read.csv("$sampleMapping", row.names = 1) + #else + sampleMapping <- read.delim("$sampleMapping", header = TRUE, row.names = 1, sep = "\t") + #end if +#else + sampleMapping <- NULL +#end if + ]]></token> + + <token name="@COMMON_WF_PARAMETERS@"><![CDATA[ + sampleTable, + sampleGenes = sampleGenes, ## this implies more output data sets! + sampleMapping = sampleMapping, + remove_outliers = $remove_outliers, + median_normalize = $median_normalize, + number_replicates_reliable = $number_replicates_reliable, + reliable_all_comparisons = $reliable_all_comparisons, + alternative = "$alternative", + var.equal = $var_equal, + paired = $paired, + pvalue_decision = "$pvalue_decision", + pvalue_adjustment = "$pvalue_adjustment", + significance_cutoff = $significance_cutoff, + color_up = "${color_up}FF", + color_none = "${color_none}FF", + color_down = "${color_down}FF" + ]]></token> + <xml name="common_wf_paramerters"> + <param argument="sampleTable" type="data" format="csv,tabular" label="Sample table" help="Rows: unique identifiers (e.g. uniprot accessions), Columns: samples. Replicates should be indicated using _1, _2, .... Content should be numeric."/> + <expand macro="sample_genes_mapping"/> + <param argument="remove_outliers" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Remove outliers" help="Identified by the function identify_outliers() based on Mahalanobis distances"/> + <param argument="median_normalize" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Apply median normalization" help=""/> + + <yield/> + + <param argument="number_replicates_reliable" type="integer" min="1" value="3" label="Number of replicates for reliable identification" help="Number of replicates for which quantitation data should be available to consider a protein reliably identified under the particular condition (i.e. in a sample)"/> + <!--TODO formulation unclear, comparisons between what? Samples? --> + <param argument="reliable_all_comparisons" type="select" label="Required comparisons" help="Candidates are returned that are identified in the given number of replicates (number_replicates_reliable) in all/at least one comparison."> + <option value="FALSE">At least one</option> + <option value="TRUE">All</option> + </param> + <!-- TODO which variances? --> + <param argument="var.equal" name="var_equal" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Treat variances as equal" help="for t-test"/> + <param argument="paired" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Use paired t-test" help=""/> + <param argument="alternative" type="select" label="Alternative hypothesis" help=""> + <option value="two.sided">two.sided</option> + <option value="greater">greater</option> + <option value="less">less</option> + </param> + <param argument="pvalue_adjustment" type="select" label="Method for p-value adjustment" help=""> + <option value="holm">Holm</option> + <option value="hochberg">Hochberg</option> + <option value="hommel">Hommel</option> + <option value="bonferroni">Bonferroni</option> + <option value="BY">Benjamini & Yekutieli (BY)</option> + <option value="fdr" selected="true">Benjamini & Hochberg (BH/fdr)</option> + <option value="none">None</option> + </param> + <param argument="pvalue_decision" type="select" label="Choose whether to extract and visualize data based on adjusted p-values or raw p-values" help=""> + <option value="pvalueadj" selected="true">adjusted p-values</option> + <option value="pvalue">raw p-values</option> + </param> + <param argument="significance_cutoff" type="float" value="0.05" min="0" max="1" label="Significance cutoff" help="All candidates with lower value are considered significantly affected"/> + <param argument="color_up" type="color" value="#DC0000" label="Color for up-regulated candidates"/> + <param argument="color_down" type="color" value="#3C5488" label="Color for down-regulated candidates"/> + <param argument="color_none" type="color" value="#000000" label="Color for not significantly altered candidates"/> + </xml> + + <xml name="sample_genes_mapping"> + <param argument="sampleGenes" type="data" format="csv,tabular" optional="true" label="Accession - Gene name mapping" help="An optional table conatining columns Accession and Gene"/> + <param argument="sampleMapping" type="data" format="csv,tabular" optional="true" label="Sample mapping" help="An optional table that is used to relate different conditions to ggplot facets. See help."/> + </xml> + + <xml name="citations"> + <citations> + <citation type="bibtex">@UNPUBLISHED{Linnarsson2016, + author = "Isabel Karkossa", + title = "proteomicsr", + publisher = {UFZ GitLab}, + journal = {Git repository}, + year = "2023" + note = "https://git.ufz.de/kratochv/proteomicsr" + } + </citation> + </citations> + </xml> + <!-- TODO citations: helmholz codebase / doi --> + + + +</macros> \ No newline at end of file