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add pgxRpi tool #6805

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add pgxRpi tool #6805

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724fd7b
add tool pgxRpi
hangjiaz Feb 27, 2025
8c62e93
delete environment yaml
hangjiaz Feb 27, 2025
f766baf
Update tools/pgxRpi/pgxFreqplot.xml
hangjiaz Feb 27, 2025
e9b56c2
Update tools/pgxRpi/.shed.yml
hangjiaz Feb 27, 2025
8245dbd
Update tools/pgxRpi/pgxLoader.xml
hangjiaz Feb 27, 2025
0218c58
modify shed
hangjiaz Feb 27, 2025
a6cd1e5
add macro & more tests
hangjiaz Feb 28, 2025
f37ffff
Update tools/pgxRpi/.shed.yml
hangjiaz Feb 28, 2025
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10 changes: 10 additions & 0 deletions tools/pgxRpi/.shed.yml
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name: pgxrpi
owner: iuc
description: pgxLoader and pgxFreqplot functions from pgxRpi 1.2.0
homepage_url: https://github.com/progenetix/pgxRpi
long_description: |
pgxRpi is an R wrapper package for the Progenetix REST API that leverages the capabilities of the Beacon v2 specification. It also provides functions to enhance the visualisation of the retrieved genomic variation data.
remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/pgxrpi
type: unrestricted
categories:
- Variant Analysis
80 changes: 80 additions & 0 deletions tools/pgxRpi/pgxFreqplot.xml
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<tool id="pgx_freqplot" name="pgxRpi pgxFreqplot" version="0.1.0+galaxy0" profile="21.05">
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should the version 1.20 and maybe a macro?

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Thank you for pointing this out. I have included it in a macro.

<requirements>
<requirement type="package" version="4.4.2">r-base</requirement>
<requirement type="package" version="1.20">bioconductor-pgxrpi</requirement>
<requirement type="package" version="1.58.0">bioconductor-genomicranges</requirement>
</requirements>
<command detect_errors="exit_code"><![CDATA[
Rscript '$run_pgxFreqplot'
]]></command>
<configfiles>
<configfile name='run_pgxFreqplot'><![CDATA[
## Setup R error handling to go to stderr
options(show.error.messages=F, error = function () { cat(geterrmessage(), file=stderr()); q("no", 1, F) })

library(pgxRpi)
library(GenomicRanges)
data <- readLines("$freqdata")
metacolumn <- which(grepl("#",data))
metadata <- data[which(grepl("#",data))]
metadata <- lapply(seq_len(length(metadata)), function(i){
indmeta <- metadata[i]
indmeta <- unlist(strsplit(indmeta,split = ";"))
indmeta <- data.frame(filter=gsub("#group_id=","",indmeta[1]),label=gsub("label=","",indmeta[2]),sample_count=gsub("sample_count=","",indmeta[3]))
return(indmeta)
})
metadata <- do.call(rbind,metadata)
data <- read.csv("$freqdata",sep="\t",skip = max(metacolumn),header = T)
freq <- makeGRangesListFromDataFrame(data,split.field = 'group_name',keep.extra.columns=TRUE)
S4Vectors::mcols(freq) <- metadata

process_input_parameter <- function(param, if_numeric=FALSE){
if (param == ""){
param <- NULL
}
else{
param <- trimws(unlist(strsplit(param,split=',')))
if (if_numeric) param <- as.numeric(param)
}
return(param)
}


chrom <- process_input_parameter('$chrom',TRUE)
filters <- process_input_parameter('$filters')
layout <- process_input_parameter('$layout',TRUE)

pdf("$pgxplot",width=$plotwidth,height=$plotheight)
pgxFreqplot(freq,filters=filters,chrom=chrom,layout=layout,assembly="$assembly")
dev.off()
]]></configfile>
</configfiles>
<inputs>
<param type='data' name='freqdata' format='txt' label='CNV frequency data' help='CNV frequency data returned by pgxLodaer'/>
<param name='chrom' type='text' optional='true' label='Chromosomes to plot' help='Use commas to separate multiple chromosomes (e.g. 1,3,5). If not specified, the plot will cover the entire genome.' />
<param name='layout' type='text' optional='true' label='Number of rows and columns in plot' help='Use commas to separate rows and columns (e.g. 3,1). Only used in plot by chromosome.'/>
<param name='filters' type='text' optional='true' label='Filter to plot' help='Only support one filter.' />
<param name='assembly' type='select' label='Genome assembly version'>
<option value="hg38" selected="true">hg38</option>
<option value="hg19">hg19</option>
</param>
<param name='plotwidth' type='integer' value='8' label='Width of the plot in inches.' />
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Can we use a proper metric system here ;) I propose cm or mm ;)

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I have changed it to cm.

<param name='plotheight' type='integer' value='4' label='Height of the plot in inches.' />
</inputs>
<outputs>
<data name='pgxplot' format='pdf' label='CNV frequency plot'/>
</outputs>
<tests>
<test>
<param name='freqdata' value='cnv-frequency.txt'/>
<param name="filters" value="NCIT:C3058"/>
<output name="pgxplot" file="cnv-frequency.pdf" />
</test>
</tests>
<help><![CDATA[
Thie function plots the CNV frequency loaded from pgxRpi
]]></help>
<citations>
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maybe put this into a macro?

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I have placed the citation in a macro. However, since the help text varies across different functions, I have not included it in a macro.

<citation type='doi'>10.18129/B9.bioc.pgxRpi</citation>
</citations>
</tool>
103 changes: 103 additions & 0 deletions tools/pgxRpi/pgxLoader.xml
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<tool id="pgx_loader" name="pgxRpi pgxLodaer" version="0.1.0+galaxy0" profile="21.05">
<requirements>
<requirement type="package" version="4.4.2">r-base</requirement>
<requirement type="package" version="1.20">bioconductor-pgxrpi</requirement>
</requirements>
<command detect_errors="exit_code"><![CDATA[
Rscript '$run_pgxLoader'
]]></command>
<configfiles>
<configfile name='run_pgxLoader'><![CDATA[
## Setup R error handling to go to stderr
options(show.error.messages=F, error = function () { cat(geterrmessage(), file=stderr()); q("no", 1, F) })

library('pgxRpi')

real_output <- '$advanced_settings.output'

if ('$type' != "g_variants" | real_output == "Default"){
real_output <- NULL
}

process_input_parameter <- function(param){
if (param == ""){
param <- NULL
}
else{
param <- trimws(unlist(strsplit(param,split=',')))
}
return(param)
}

biosample_ids <- process_input_parameter('$biosample_id')
individual_ids <- process_input_parameter('$individual_id')
filters <- process_input_parameter('$filters')
dataset <- process_input_parameter('$advanced_settings.dataset')

## adapt to old version of this package (1.2.0)
if ('$type' == "filtering_terms"){
result <- data.frame(filters=pgxFilter())
} else{
result <- pgxLoader(type='$type',output=real_output,biosample_id=biosample_ids,individual_id=individual_ids,filters=filters,codematches='$codematches',skip=as.numeric($advanced_settings.skip),limit=as.numeric('$advanced_settings.limit'),dataset=dataset,domain='$advanced_settings.domain',entry_point='$advanced_settings.entry_point')
}

append <- FALSE

## adapt to tsv format
if ('$type' == "cnv_frequency"){
metadata <- S4Vectors::mcols(result)
metadata_lines <- paste0("#group_id=",metadata[['filter']],";label=",metadata[['label']],";sample_count=",metadata[['sample_count']])
write.table(metadata_lines,file='$pgxdata', quote=FALSE, col.names=FALSE, row.names=FALSE)
append <- TRUE
} else if ('$type' == "cnv_fraction"){
result <- cbind(analysis_id=rownames(result[["genome_cnv_frac"]]),result[["genome_cnv_frac"]],result[["chr_cnv_frac"]],result[["arm_cnv_frac"]])
}

suppressWarnings(write.table(result, file='$pgxdata', append=append, quote=FALSE, col.names=TRUE, row.names=FALSE, sep = '\t'))
]]></configfile>
</configfiles>
<inputs>
<param name='type' type='select' label='Output data type'>
<option value="individuals">individuals</option>
<option value="biosamples">biosamples</option>
<option value="analyses">analyses</option>
<option value="g_variants">genomic variations</option>
<option value="cnv_frequency">precomputed CNV frequency data from Progenetix</option>
<option value="cnv_fraction">CNV fraction per sample based on Progenetix data</option>
<option value="sample_count">count of samples in Progenetix</option>
<option value="filtering_terms">All available filters in Progenetix</option>
</param>
<param name='biosample_id' type='text' optional='true' label='Identifiers of biosamples' help='Use commas to separate multiple IDs (e.g. pgxbs-m3io46hq,pgxbs-m3io41c2). If the output data type is "genomic variations", only this search condition is supported.' />
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it would be nice to add some validators to all those text inputs

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Please refer to my response above

<param name='individual_id' type='text' optional='true' label='Identifiers of individuals' help='Use commas to separate multiple IDs (e.g. pgxind-m3io3pzi,pgxind-m3io3mi3).'/>
<param name='filters' type='text' optional='true' label='Filters' help='Use commas to combine filters (e.g. NCIT:C3512,PMID:37084736) using AND logic when the output data type is "individuals", "biosamples", "analyses"; OR logic when the output data type is "precomputed CNV frequency", "count of samples". Do not use multiple filters when the output data type is "CNV fraction".' />
<param name='codematches' type='boolean' checked='false' label='Whether to exclude samples from child concepts of the specified filters' />
<section name="advanced_settings" title="Advanced settings" expanded="false">
<param name='output' type='select' value="Default" optional="true" label='Variant data format'>
<option value="Default" selected="true">Default</option>
<option value="pgxseg">pgxseg</option>
<option value="seg">seg</option>
</param>
<param name='limit' type='integer' value='0' optional='true' label='Integer to specify the number of returned profiles' />
<param name='skip' type='integer' value='0' optional='true' label='Integer specifying the number of profiles to skip' />
<param name='dataset' type='text' optional='true' label='Dataset to query from the Beacon response' help='Use commas to separate multiple datasets to enter' />
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How should such a text look like? Is it really a dataset?

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This parameter is used to select specific datasets for Progenetix. Currently, Progenetix returns data using only one dataset ID, "progenetix." I have updated the default value of this parameter to "progenetix."

The reason for keeping this parameter is that the package can also query data from other resources via the Beacon API, where "dataset" is a standard query parameter. This allows for more flexible queries across different resources and supports future expansions of Progenetix.

<param name='domain' type='text' value="http://progenetix.org" optional='true' label='Domain of the query data resource' />
<param name='entry_point' type='text' value="beacon" optional='true' label='Entry point of the Beacon v2 API' />
</section>
</inputs>
<outputs>
<data name="pgxdata" format="txt" label="${tool.name} for $type data" />
</outputs>
<tests>
<test>
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please add tests with more options, especially from the advanced settings

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Thank you for your suggestions! I have included several tests covering different input types and advanced settings.

However, a few input types, such as “sample_counts,” are not included because these queries return aggregated results. Since Progenetix data is continuously expanding, the results may change over time, causing test failures despite the tool functioning correctly.

Similarly, some parameters, such as “filters,” are not included because their queries return multiple records in a non-fixed order, which could lead to test failures.

<param name="type" value="biosamples"/>
<param name="biosample_id" value="pgxbs-kftvki7h"/>
<output name="pgxdata" file="biosamples.txt" />
</test>
</tests>
<help><![CDATA[
pgxRpi is an R wrapper package for Progenetix REST API that leverages the capabilities of Beacon v2 specification.
]]></help>
<citations>
<citation type='doi'>10.18129/B9.bioc.pgxRpi</citation>
</citations>
</tool>
2 changes: 2 additions & 0 deletions tools/pgxRpi/test-data/biosamples.txt
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biosample_id individual_id biosample_status_id biosample_status_label sample_origin_type_id sample_origin_type_label histological_diagnosis_id histological_diagnosis_label sampled_tissue_id sampled_tissue_label pathological_stage_id pathological_stage_label tnm_id tnm_label tumor_grade_id tumor_grade_label age_iso notes icdo_morphology_id icdo_morphology_label icdo_topography_id icdo_topography_label pubmed_id cellosaurus_id cbioportal_id tcga_project_id analysis_info_experiment_id analysis_info_series_id analysis_info_platform_id cohort_ids biosample_legacy_id geoprov_city geoprov_country geoprov_iso_alpha3 geoprov_long_latitude geoprov_long_longitude updated
pgxbs-kftvki7h pgxind-kftx6ltd EFO:0009656 neoplastic sample OBI:0001479 specimen from organism NCIT:C3512 Lung Adenocarcinoma UBERON:0002048 lung NCIT:C27976 Stage Ib NCIT:C48706,NCIT:C48714,NCIT:C48724 N1 Stage Finding,N3 Stage Finding,T2 Stage Finding NA NA P56Y adenocarcinoma [lung] pgx:icdom-81403 Adenocarcinoma, NOS pgx:icdot-C34.9 Lung, NOS PMID:19607727 NA NA NA geo:GSM417055 geo:GSE16597 geo:GPL8690 pgx:cohort-arraymap,pgx:cohort-2021progenetix,pgx:cohort-carriocordo2021heterogeneity NA New York City United States of America USA 40.71 -74.01 2020-09-10 17:46:45.105000
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