Mercurial > repos > azomics > fcs_merge_downsample
changeset 0:8e568997abda draft
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
| author | azomics |
|---|---|
| date | Mon, 22 Jun 2020 20:35:09 -0400 |
| parents | |
| children | 04afe468b234 |
| files | FCSMergeDownsample.R FCSMergeDownsample.xml test-data/input1.fcs test-data/input2.fcs test-data/input3.fcs test-data/merge1.flowframe test-data/merge2.fcs |
| diffstat | 7 files changed, 264 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/FCSMergeDownsample.R Mon Jun 22 20:35:09 2020 -0400 @@ -0,0 +1,115 @@ +#!/usr/bin/Rscript +# Aggregate FCS files Module for Galaxy +# with FlowSOM AggregateFlowFrames +###################################################################### +# Copyright (c) 2017 Northrop Grumman. +# All rights reserved. +###################################################################### +# +# Version 1 +# Cristel Thomas +# +# +library(FlowSOM) +library(flowCore) + +downsampleMergeFCS <- function(fcs_files, nb_cells, output="", flag_fcs=FALSE) { + ff <- AggregateFlowFrames(fcs_files, nb_cells, writeOutput = FALSE) + n <- length(colnames(ff)) - 2 + exprs(ff) <- exprs(ff)[,1:n] + if (flag_fcs) { + write.FCS(ff, output) + } else { + saveRDS(ff, file=output) + } +} + +checkFCSfiles <- function(fcsfiles, ds_factor=0.1, out_file ="", + flag_fcs=FALSE) { + isValid <- F + nb_events <- 0 + markerCheck <- T + + for (i in 1:length(fcsfiles)){ + is_file_valid <- F + tryCatch({ + fcs <- read.FCS(fcsfiles[i], transformation=FALSE) + is_file_valid <- T + nb_events <- nb_events + as.numeric(fcs@description$`$TOT`) + }, error = function(ex) { + print(paste(ex)) + }) + if (is_file_valid){ + if (i == 1) { + m1 <- as.vector(pData(parameters(fcs))$desc) + } else { + m2 <- as.vector(pData(parameters(fcs))$desc) + if (is.na(all(m1==m2))) { + mm1 <- is.na(m1) + mm2 <- is.na(m2) + if (all(mm1==mm2)){ + if (!all(m1==m2, na.rm=TRUE)){ + markerCheck <- F + } + } else { + markerCheck <- F + } + } else if (!all(m1==m2)) { + markerCheck <- F + } + } + } else { + quit(save = "no", status = 10, runLast = FALSE) + } + } + + if (markerCheck) { + isValid <- T + } else { + quit(save = "no", status = 12, runLast = FALSE) + } + + ## translate ds_factor to nb of events + nb_cell <- floor(ds_factor*nb_events) + + if (isValid) { + downsampleMergeFCS(fcsfiles, nb_cell, out_file, flag_fcs) + } else { + quit(save = "no", status = 10, runLast = FALSE) + } +} + +args <- commandArgs(trailingOnly = TRUE) +flag_fcs <- FALSE + +if (args[2] == "FCS"){ + flag_fcs <- TRUE +} + +if (args[3] == "" || args[3] == "i.e.:0.1 or 10X") { + factor <- 0.1 +} else { + #rm last X if it's there + ds <- gsub("X", "", args[3]) + if (!is.na(as.numeric(ds))) { + factor <- as.numeric(ds) + if (factor > 1 && factor <= 100) { + factor <- as.numeric(ds) / 100 + } else if (factor > 100){ + quit(save = "no", status = 11, runLast = FALSE) + } + } else { + quit(save = "no", status = 11, runLast = FALSE) + } +} + +nb_files <- (length(args) - 3) +fcsfiles <- character(nb_files) +j <- 1 +## get files and file names +for (i in 4:length(args)) { + fcsfiles[[j]] <- args[i] + j <- j + 1 +} + +checkFCSfiles(fcsfiles, factor, args[1], flag_fcs)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/FCSMergeDownsample.xml Mon Jun 22 20:35:09 2020 -0400 @@ -0,0 +1,149 @@ +<tool id="fcs_merge_downsample" name="Merge and downsample" version="1.0+galaxy1"> + <description>FCS files with FlowSOM</description> + <requirements> + <requirement type="package" version="1.18.0">bioconductor-flowsom</requirement> + </requirements> + <stdio> + <exit_code range="10" level="fatal" description="One or more FCS files is not valid. See stderr for more details." /> + <exit_code range="11" level="fatal" description="Please provide a numeric value [0,1] for the downsampling factor." /> + <exit_code range="12" level="fatal" description="There are inconsistencies in marker names between FCS files." /> + </stdio> + <command><![CDATA[ + FCSMergeDownsample.R '${output_file}' '${outformat}' '${factorDS}' + #for $f in $input + '${f}' + #end for + ]]> + </command> + <inputs> + <param format="fcs" name="input" type="data_collection" collection_type="list" label="FCS files Collection"/> + <param name="factorDS" type="text" label="Downsample by:" value="i.e.:0.1 or 10%" optional="true" help="By default 0.1"/> + <param name="outformat" type="select" label="Output Format"> + <option value="flowFrame">R Data, flowFrame</option> + <option value="FCS">FCS 3.0</option> + </param> + </inputs> + <outputs> + <data format="flowframe" name="output_file" label="Merged FCS from ${input.name} in ${outformat}"> + <change_format> + <when input="outformat" value="FCS" format="fcs" /> + </change_format> + </data> + </outputs> + <tests> + <test> + <param name="input"> + <collection type="list"> + <element name="input1.fcs" value="input1.fcs"/> + <element name="input2.fcs" value="input2.fcs"/> + <element name="input3.fcs" value="input3.fcs"/> + </collection> + </param> + <param name="factorDS" value=".8"/> + <param name="outformat" value="flowFrame"/> + <output name="output_file" file="merge1.flowframe" compare="sim_size" delta="1000000"/> + </test> + <test> + <param name="input"> + <collection type="list"> + <element name="input1.fcs" value="input1.fcs"/> + <element name="input2.fcs" value="input2.fcs"/> + <element name="input3.fcs" value="input3.fcs"/> + </collection> + </param> + <param name="factorDS" value="i.e.:0.1 or 10%"/> + <param name="outformat" value="FCS"/> + <output name="output_file" file="merge2.fcs" compare="sim_size" delta="1000000"/> + </test> + </tests> + <help><![CDATA[ +Merge and downsample using FlowSOM +------------------- + +This tool merges and downsamples multiple FCS files into one flowframe or FCS file using FlowSOM. + +**Input files** + +This tool requires a collection of FCS files as input. + +.. class:: warningmark + +Input files **MUST** have the same markers *and* channels. The following tools in the FCS Files tool section can help harmonize channels and/or markers in the FCS files collection: + +- Get list of markers or channels in FCS files. +- Edit markers or channels in FCS files + +**Downsampling** + +By default, files are downsampled to 10% of the total number of events across input files. If a downsampling factor is provided, each file in the input dataset collection will be downsampled randomly without replacement as follows: + +- If n is between 0 and 1, the size of the output will be n times that of the input files. +- If n is between 1 and 100, the size of the output will be n% that of the input files. + +.. class:: infomark + +Downsampling is implemented such that each file will contribute an equal number of event to the aggregate. + +.. class:: warningmark + +At this time, up-sampling is not supported. If the number provided is greater than 100, the tool will exit. + +**Output file** + +The output file contains an aggregation of events from the input files provided all are valid FCS files. If a downsampling factor is provided, the corresponding proportion of each input file ONLY will be read in. Output can be provided in FCS format or in a RData object containing a flowFrame. + +.. class:: infomark + +The output generated contains data for all markers present in the original files. No information is added, or removed. + +----- + +**Example** + +*File1*: 20K events:: + + Marker1 Marker2 Marker3 ... + 34 45 12 ... + 33 65 10 ... + 87 26 76 ... + 24 56 32 ... + 95 83 53 ... + ... ... ... ... + +*File2*: 20K events:: + + Marker1 Marker2 Marker3 ... + 19 62 98 ... + 12 36 58 ... + 41 42 68 ... + 76 74 53 ... + 62 34 45 ... + ... ... ... ... + +*Output*: 4K events:: + + Marker1 Marker2 Marker3 ... + 34 45 12 ... + 87 26 76 ... + 12 36 58 ... + 62 34 45 ... + ... ... ... ... + +.. class:: infomark + +With a downsampling factor of 0.5: 20K events:: + + Marker1 Marker2 Marker3 ... + 34 45 12 ... + 24 56 32 ... + 95 83 53 ... + 19 62 98 ... + 12 36 58 ... + 62 34 45 ... + ... ... ... ... + ]]> + </help> + <citations> + <citation type="doi">10.1002/cyto.a.22625</citation> + </citations> +</tool>