Mercurial > repos > azomics > metacyto_checkpanel
changeset 0:67d79ba0f7aa draft default tip
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14b2e4d834a9856236affb7b77debecca360c542"
| author | azomics |
|---|---|
| date | Tue, 27 Jul 2021 21:47:56 +0000 |
| parents | |
| children | |
| files | images/checkpanel.png images/h metacyto_checkpanel.R metacyto_checkpanel.xml test-data/mc_preprocesss_summary.metacyto_summary.txt |
| diffstat | 5 files changed, 126 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/images/h Tue Jul 27 21:47:56 2021 +0000 @@ -0,0 +1,1 @@ +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/metacyto_checkpanel.R Tue Jul 27 21:47:56 2021 +0000 @@ -0,0 +1,37 @@ +#!/usr/bin/env Rscript +###################################################################### +# Copyright (c) 2018 Northrop Grumman. +# All rights reserved. +###################################################################### +# +# Version 1 - January 2018 +# Author: Cristel Thomas +# +# + +library(MetaCyto) + +check_panel <- function(df, outfile = "") { + report <- panelSummary(df, ".", cluster = F, width = 30, height = 20) + markers <- data.frame("Markers" = row.names(report)) + s <- cbind(markers, report) + write.table(s, file = outfile, quote = F, row.names = F, col.names = T, sep = "\t") +} + +check_input_format <- function(infile = "", outfile = "") { + df <- read.table(infile, sep = "\t", header = T, colClasses = "character") + nm <- colnames(df) + check_ab <- if ("antibodies" %in% nm) TRUE else FALSE + check_sdy <- if ("study_id" %in% nm) TRUE else FALSE + + if (check_sdy && check_ab) { + check_panel(df, outfile) + } else { + quit(save = "no", status = 10, runLast = FALSE) + } +} + +################################################################################ +args <- commandArgs(trailingOnly = TRUE) + +check_input_format(args[1], args[2])
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/metacyto_checkpanel.xml Tue Jul 27 21:47:56 2021 +0000 @@ -0,0 +1,81 @@ +<tool id="metacyto_checkpanel" name="Check markers in analysis panels" version="1.0+galaxy0" profile="18.01"> + <description>for MetaCyto</description> + <requirements> + <requirement type="package" version="1.4.0">bioconductor-metacyto</requirement> + </requirements> + <stdio> + <exit_code range="1:9" /> + <exit_code range="10" level="fatal" description="The input file cannot be used. Please check input format." /> + <exit_code range="11:" /> + </stdio> + <command><![CDATA[ + Rscript --slave --vanilla '$__tool_directory__/metacyto_checkpanel.R' '${input_file}' '${output_file}'; + #if $graph=="TRUE" + mv panel_summary.pdf '${pdf_out}' + #end if + ]]> + </command> + <inputs> + <param format="metacyto_summary.txt" name="input_file" type="data" label="MetaCyto preprocessing summary"/> + <param name="graph" type="boolean" label="Output visual summary?" checked="false" truevalue="TRUE" falsevalue="FALSE" /> + </inputs> + <outputs> + <data format="tabular" name="output_file" label="Panel Summary of ${input_file.name}"/> + <data format="pdf" name="pdf_out" label="Visual Panel Summary of ${input_file.name}"> + <filter>(graph)</filter> + </data> + </outputs> + <tests> + <test> + <param name="input_file" value="mc_preprocesss_summary.metacyto_summary.txt"/> + <param name="graph" value="True"/> + <output name="output_file" ftype="tabular"> + <assert_contents> + <has_n_columns n="3" /> + <has_text text="CD95" /> + <has_n_lines n="14" /> + </assert_contents> + </output> + <output name="pdf_out" ftype="pdf"> + <assert_contents> + <has_size value="4569" delta="500" /> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ + Metacyto Check Markers in analysis panels + ----------------------------------------- + + This tool uses MetaCyto's panel summary function to compare marker names between groups of FCS files. + + **Input** + This tool requires the MetaCyto pre-processing Summary as input. + + **Output** + This tool generates a table and an optional visual representation in PDF of how markers are distributed in the FCS file sets. + + + **Example** + + *Input* - Summary Table:: + + study_id antibodies filenames + group1 Marker1|Marker2|Marker3|... file1.fcs + group2 Marker1|Marker2|Marker3|... file2.fcs + ... ... ... + + *Output* - Panel Summary:: + + Markers group1 group2 ... + Marker1 1 1 ... + Marker2 1 1 ... + Marker3 0 1 ... + ... ... ... ... + + *Graphical output* + + .. image:: ./images/checkpanel.png + ]]> + </help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mc_preprocesss_summary.metacyto_summary.txt Tue Jul 27 21:47:56 2021 +0000 @@ -0,0 +1,7 @@ +study_id antibodies filenames +group 1 FSC-A|SSC-A|CD11A|CD4|CD16|CD28|CD95|CD3|CD62L|CD8B|CCR7|TIME|SAMPLE_ID Hs90208Bd_C20090205_00.583331.fcs +group 1 FSC-A|SSC-A|CD11A|CD4|CD16|CD28|CD95|CD3|CD62L|CD8B|CCR7|TIME|SAMPLE_ID Hs90210Bd_C20090205_00.583065.fcs +group 1 FSC-A|SSC-A|CD11A|CD4|CD16|CD28|CD95|CD3|CD62L|CD8B|CCR7|TIME|SAMPLE_ID Hs90211Bd_C20090205_00.583066.fcs +group 2 FSC-A|SSC-A|CD11A|CD4|CD16|CD28|CD95|CD3|CD62L|CD8B|CCR7|TIME|SAMPLE_ID T_Hs60003Bd_C200900407A_00.581924.fcs +group 2 FSC-A|SSC-A|CD11A|CD4|CD16|CD28|CD95|CD3|CD62L|CD8B|CCR7|TIME|SAMPLE_ID T_Hs60011Bd_C200900505A_00.581822.fcs +group 2 FSC-A|SSC-A|CD11A|CD4|CD16|CD28|CD95|CD3|CD62L|CD8B|CCR7|TIME|SAMPLE_ID T_Hs60012Bd_C200900505A_00.581833.fcs