Mercurial > repos > azomics > flow_compensate
comparison flow-compensate.xml @ 0:ca7ba337b727 draft
"planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/flow_compensate commit 386fcc6286d3e2d2769ac9856a653b04d5c6b0ad"
| author | azomics |
|---|---|
| date | Tue, 25 May 2021 00:07:44 +0000 |
| parents | |
| children | ffc083c86d44 |
comparison
equal
deleted
inserted
replaced
| -1:000000000000 | 0:ca7ba337b727 |
|---|---|
| 1 <tool id="flow-compensate" name="Flow compensate" version="0.1.0+galaxy0" profile="19.01" python_template_version="3.5"> | |
| 2 <description> | |
| 3 compensates a set of FCS objects through a compensation matrix | |
| 4 </description> | |
| 5 <requirements> | |
| 6 <requirement type="package" version="2.2.0">bioconductor-flowcore</requirement> | |
| 7 </requirements> | |
| 8 <command detect_errors="exit_code"><![CDATA[ | |
| 9 mkdir -p input_dir; | |
| 10 #for $fcs in $fcs_list: | |
| 11 ln -s '$fcs' input_dir/'$fcs.element_identifier'; | |
| 12 #end for | |
| 13 mkdir -p output_dir; | |
| 14 Rscript '$compensate_script' '$compensation_matrix' input_dir output_dir | |
| 15 ]]></command> | |
| 16 <configfiles> | |
| 17 <configfile name="compensate_script"><![CDATA[ | |
| 18 library(flowCore) | |
| 19 | |
| 20 args <- commandArgs( TRUE ) | |
| 21 | |
| 22 if ( length( args ) != 3 ) { | |
| 23 cat( "ERROR: no arguments with directory, matrix file for compensation and out_dir", | |
| 24 file = stderr() ) | |
| 25 stop() | |
| 26 } | |
| 27 | |
| 28 comp_matrix <- read.table(file=args[[ 1 ]], sep="\t", header=TRUE, check.names = FALSE) | |
| 29 comp_matrix<-as.matrix(comp_matrix[,-1]) | |
| 30 ## Square matrix, reuse colnames into rownames | |
| 31 rownames(comp_matrix)<-colnames(comp_matrix) | |
| 32 fcs_dir <- args[[ 2 ]] | |
| 33 | |
| 34 samp<-read.flowSet(files=list.files(path=fcs_dir, pattern=".*.fcs\$"), path=fcs_dir) | |
| 35 | |
| 36 samp<-compensate(samp, comp_matrix) | |
| 37 | |
| 38 write.flowSet(samp, outdir=args[[ 3 ]]) | |
| 39 | |
| 40 ]]></configfile> | |
| 41 </configfiles> | |
| 42 <inputs> | |
| 43 <param type="data" name="fcs_list" format="fcs" multiple="true" label="FCS files" help="FCS files to compensate using the provided matrix"/> | |
| 44 <param type="data" name="compensation_matrix" format="tabular" label="Matrix to use for compensation" /> | |
| 45 </inputs> | |
| 46 <outputs> | |
| 47 <collection name="compensated_fcs" format="fcs" label="${tool.name} compensated FCS files on ${on_string}" type="list"> | |
| 48 <discover_datasets pattern="__designation_and_ext__" directory="output_dir" visible="true" /> | |
| 49 </collection> | |
| 50 </outputs> | |
| 51 <help><![CDATA[ | |
| 52 TODO: Fill in help. | |
| 53 ]]></help> | |
| 54 </tool> |