Mercurial > repos > anmoljh > candidate_compound_select
changeset 0:639d350de274 draft
planemo upload commit a1f4dd8eb560c649391ada1a6bb9505893a35272-dirty
| author | anmoljh |
|---|---|
| date | Fri, 01 Jun 2018 04:38:30 -0400 |
| parents | |
| children | 843adfe71ce2 |
| files | select_compound.R select_compound.xml tool_dependencies.xml |
| diffstat | 3 files changed, 63 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/select_compound.R Fri Jun 01 04:38:30 2018 -0400 @@ -0,0 +1,19 @@ +args <- commandArgs(T) +arg1 <- args[1] ## Reae Input prediction file +arg2 <- args[2] ## Less Than +arg3 <- args[3] ## Greater Than or equal too +arg4 <- args[4] ## Active / Inactive +arg5 <- args[5] ## define output file name +asd <- read.table(arg1,row.names=1,header=T) +if (arg4 == "Active") { +refined <- asd[asd[,1] >= as.numeric(arg3) & asd[,1] <= as.numeric(arg2),] +compound <- rownames(refined) +refined <- cbind(compound,refined) +} else if((arg4 == "Inactive") ){ +#refined <- asd[asd[,1] <= as.numeric(arg2),] +refined <- asd[asd[,2] >= as.numeric(arg3) & asd[,2] <= as.numeric(arg2),] +compound <- rownames(refined) +refined <- cbind(compound,refined)} +###write.table(dw,file=args3,row.names=FALSE,sep="\t") +write.table(refined,file=arg5,row.names=FALSE,sep="\t") +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/select_compound.xml Fri Jun 01 04:38:30 2018 -0400 @@ -0,0 +1,38 @@ +<?xml version="1.0"?> +<tool id="select_compound" name="Compound Selector" version="1.0"> +<description>This tool selects compounds from prediction result based on score</description> + +<requirements> + <requirement type="package" version="3.2.1">R</requirement> +</requirements> + +<stdio> + <exit_code range="1:" /> +</stdio> + +<command interpreter="Rscript">select_compound.R $predictionfile $LT $GT $type $SelectedCompound </command> + +<inputs> + <param name="predictionfile" type="data" format="txt,tabular,csv" label="Predition Result File" help ="upload gcac prediction result file " /> + <param name="type" type="select" label="Active/Positive or Inactive/Negative" help ="select type of molecule"> + <option value="Active" selected="True">Active/Positive</option> + <option value="Inactive">Inactive/Negative</option> + </param> + <param name="GT" type="float" value="0.5" label="Score greater than and equal to" help ="define value above which compound selected default is 0.5" /> + <param name="LT" type="float" value="1.0" label="Score less than and equal to" help ="define value below which compound selected default is 1" /> +</inputs> + +<outputs> + <data name="SelectedCompound" format="txt" label="Refind-${predictionfile.name}" /> +</outputs> +<tests> + <test> + <param name="predictionfile" value="prediction_set_result.txt" /> + <param name="type" value="Active" /> + <param name="GT" value="0.5" /> + <param name="LT" value="1.0" /> + <output name="SelectedCompound" file="selected_prediction_set_result.txt" compare="sim_size" delta="4000" /> + </test> +</tests> +<help></help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Fri Jun 01 04:38:30 2018 -0400 @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="R" version="3.2.1"> + <repository changeset_revision="d9f7d84125b7" name="package_r_3_2_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu/" /> + </package> +</tool_dependency>