| Previous changeset 1:34397a84faf1 (2020-06-23) Next changeset 3:dd00eee6cd06 (2023-09-29) |
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Commit message:
planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 2482f9499096cc780cf1bf688ea07de150191be5 |
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modified:
FCSflowAI.R FCSflowAI.xml |
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| diff -r 34397a84faf1 -r fab7c5deeb65 FCSflowAI.R --- a/FCSflowAI.R Tue Jun 23 18:34:02 2020 -0400 +++ b/FCSflowAI.R Tue Sep 26 23:19:04 2023 +0000 |
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| @@ -7,7 +7,7 @@ # Gianni Monaco, Hao Chen, Michael Poidinger, Jinmiao Chen, # Joao Pedro de Magalhaes and Anis Larbi # Bioinformatics (2016) -# doi: 10.1093/bioinformatics/btw191 +# doi 10.1093/bioinformatics/btw191 # library(flowAI) @@ -17,22 +17,22 @@ args <- commandArgs(trailingOnly = TRUE) -remFS <- if(args[4]) c("FSC", "SSC") else NULL +rem_fs <- if (args[4]) c("FSC", "SSC") else NULL flow_auto_qc( - fcsfiles = args[1], - remove_from = args[2], - alphaFR = as.numeric(args[3]), - ChRemoveFS = remFS, - outlierFS = args[5], - pen_valueFS = as.numeric(args[6]), - sideFM = args[7], - fcs_QC = ifelse(args[9] == "None", FALSE, "_QC"), - fcs_highQ = ifelse(args[10] == "None", FALSE, "_highQ"), - fcs_lowQ = ifelse(args[11] == "None", FALSE, "_lowQ"), - folder_results = FALSE) + fcsfiles = args[1], + remove_from = args[2], + alphaFR = as.numeric(args[3]), + ChRemoveFS = rem_fs, + outlierFS = args[5], + pen_valueFS = as.numeric(args[6]), + sideFM = args[7], + fcs_QC = ifelse(args[9] == "None", FALSE, "_QC"), + fcs_highQ = ifelse(args[10] == "None", FALSE, "_highQ"), + fcs_lowQ = ifelse(args[11] == "None", FALSE, "_lowQ"), + folder_results = FALSE) -try(file.rename(dir(".", pattern = ".*_QC.html"), args[8]), silent =TRUE) -try(file.rename(dir(".", pattern = ".*_QC.fcs"), args[9]), silent =TRUE) -try(file.rename(dir(".", pattern = ".*_highQ.fcs"), args[10]), silent =TRUE) -try(file.rename(dir(".", pattern = ".*_lowQ.fcs"), args[11]), silent =TRUE) +try(file.rename(dir(".", pattern = ".*_QC.html"), args[8]), silent = TRUE) +try(file.rename(dir(".", pattern = ".*_QC.fcs"), args[9]), silent = TRUE) +try(file.rename(dir(".", pattern = ".*_highQ.fcs"), args[10]), silent = TRUE) +try(file.rename(dir(".", pattern = ".*_lowQ.fcs"), args[11]), silent = TRUE) |
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| diff -r 34397a84faf1 -r fab7c5deeb65 FCSflowAI.xml --- a/FCSflowAI.xml Tue Jun 23 18:34:02 2020 -0400 +++ b/FCSflowAI.xml Tue Sep 26 23:19:04 2023 +0000 |
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| @@ -1,14 +1,24 @@ -<tool id="flowAI" name="flowAI" version="1.0+galaxy0"> +<tool id="flowAI" name="flowAI" version="1.0+galaxy1"> <description> automatic quality control</description> <requirements> <requirement type="package" version="1.42.0">bioconductor-flowcore</requirement> <requirement type="package" version="1.2.9">bioconductor-flowai</requirement> </requirements> <stdio> - <exit_code range="2:" level="fatal" description="See stderr for more details." /> + <exit_code range="1:" level="fatal" description="See stderr for more details."/> </stdio> <command><![CDATA[ - Rscript $__tool_directory__/FCSflowAI.R '${input}' '${remove}' $alphaFR $chremFS $outFS $penFS '${sideFM}' '${full_rep}' $highfcs $lowfcs $qcfcs + Rscript $__tool_directory__/FCSflowAI.R '${input}' '${remove}' $alphaFR $chremFS $outFS $penFS '${sideFM}' report.html high.fcs low.fcs qc.fcs && + cp report.html $full_rep + #if $highQ_FCS: + && cp high.fcs $highfcs + #end if + #if $lowQ_FCS: + && cp low.fcs $lowfcs + #end if + #if $QC_FCS: + && cp qc.fcs $qcfcs + #end if ]]> </command> <inputs> @@ -49,7 +59,7 @@ </data> </outputs> <tests> - <test> + <test expect_num_outputs="2"> <param name="input" value="input.fcs"/> <param name="remove" value="all"/> <param name="alphaFR" value="0.01"/> @@ -60,10 +70,18 @@ <param name="highQ_FCS" value="TRUE"/> <param name="lowQ_FCS" value="FALSE"/> <param name="QC_FCS" value="FALSE"/> - <output name="full_rep" file="std/QCreport.html" compare="sim_size"/> + <output name="full_rep"> + <assert_contents> + <has_n_lines min="100" max="500"/> + <has_text text="data:image/png;base64"/> + <has_text text="Dynamic range check"/> + <has_text text="total_UNIQUE"/> + <has_size value="267939" delta="30000"/> + </assert_contents> + </output> <output name="highfcs" file="std/hqdata.fcs" compare="sim_size"/> </test> - <test> + <test expect_num_outputs="4"> <param name="input" value="input.fcs"/> <param name="remove" value="all"/> <param name="alphaFR" value="0.01"/> @@ -74,12 +92,20 @@ <param name="highQ_FCS" value="TRUE"/> <param name="lowQ_FCS" value="TRUE"/> <param name="QC_FCS" value="TRUE"/> - <output name="full_rep" file="std/QCreport.html" compare="sim_size"/> + <output name="full_rep"> + <assert_contents> + <has_n_lines min="100" max="500"/> + <has_text text="data:image/png;base64"/> + <has_text text="Dynamic range check"/> + <has_text text="total_UNIQUE"/> + <has_size value="267939" delta="30000"/> + </assert_contents> + </output> <output name="highfcs" file="std/hqdata.fcs" compare="sim_size"/> <output name="lowfcs" file="std/lqdata.fcs" compare="sim_size"/> <output name="qcfcs" file="std/alldata.fcs" compare="sim_size"/> </test> - <test> + <test expect_num_outputs="2"> <param name="input" value="input.fcs"/> <param name="remove" value="all"/> <param name="alphaFR" value="0.01"/> @@ -90,10 +116,17 @@ <param name="highQ_FCS" value="TRUE"/> <param name="lowQ_FCS" value="FALSE"/> <param name="QC_FCS" value="FALSE"/> - <output name="full_rep" file="nooutliers/QCreport_nooutliers.html" compare="sim_size"/> + <output name="full_rep"> + <assert_contents> + <has_n_lines min="100" max="500"/> + <has_text text="data:image/png;base64"/> + <has_text text="Dynamic range check"/> + <has_size value="268106" delta="30000"/> + </assert_contents> + </output> <output name="highfcs" file="nooutliers/hqdata_nooutliers.fcs" compare="sim_size"/> </test> - <test> + <test expect_num_outputs="2"> <param name="input" value="input.fcs"/> <param name="remove" value="all"/> <param name="alphaFR" value="0.01"/> @@ -104,7 +137,15 @@ <param name="highQ_FCS" value="TRUE"/> <param name="lowQ_FCS" value="FALSE"/> <param name="QC_FCS" value="FALSE"/> - <output name="full_rep" file="withsfsc/QCreport_sfsc.html" compare="sim_size"/> + <output name="full_rep"> + <assert_contents> + <has_n_lines min="100" max="500"/> + <has_text text="data:image/png;base64"/> + <has_text text="Dynamic range check"/> + <has_text text="total_UNIQUE"/> + <has_size value="267894" delta="30000"/> + </assert_contents> + </output> <output name="highfcs" file="withsfsc/hqdata_sfsc.fcs" compare="sim_size"/> </test> </tests> |