Mercurial > repos > petr-novak > various_galaxy_tools
changeset 1:639c0edb7e64 draft
planemo upload for repository https://github.com/kavonrtep/galaxy_packages commit 248ffeb6792d5807820b664eae3e88306f3f395e-dirty
| author | petr-novak |
|---|---|
| date | Mon, 26 Feb 2024 12:59:20 +0000 |
| parents | 696e702ebf74 |
| children | 90c46e40d222 |
| files | extract_GFF_Features.xml gff2bed.xml gff2tabular.R |
| diffstat | 3 files changed, 13 insertions(+), 3 deletions(-) [+] |
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--- a/extract_GFF_Features.xml Mon May 09 08:26:30 2022 +0000 +++ b/extract_GFF_Features.xml Mon Feb 26 12:59:20 2024 +0000 @@ -1,6 +1,7 @@ <tool id="Extract_features1" name="Extract features" version="1.0.0"> <description>from GFF data</description> - <command interpreter="python">extract_GFF_Features.py $input1 $out_file1 ${column_choice.col} ${column_choice.feature}</command> + <command> + python '$__tool_directory__'/extract_GFF_Features.py $input1 $out_file1 ${column_choice.col} ${column_choice.feature}</command> <inputs> <param format="gff" name="input1" type="data" label="Select GFF data"/> <conditional name="column_choice">
--- a/gff2bed.xml Mon May 09 08:26:30 2022 +0000 +++ b/gff2bed.xml Mon Feb 26 12:59:20 2024 +0000 @@ -1,9 +1,11 @@ -<tool id="gff2bed1" name="GFF-to-BED" version="1.0.1"> +<tool id="gff2bed1" name="GFF-to-BED" version="1.0.2"> <description>converter</description> <edam_operations> <edam_operation>operation_3434</edam_operation> </edam_operations> - <command interpreter="python">gff_to_bed_converter.py $input $out_file1</command> + <command> + python '$__tool_directory__'/gff_to_bed_converter.py $input $out_file1 + </command> <inputs> <param format="gff" name="input" type="data" label="Convert this dataset"/> </inputs>
--- a/gff2tabular.R Mon May 09 08:26:30 2022 +0000 +++ b/gff2tabular.R Mon Feb 26 12:59:20 2024 +0000 @@ -2,5 +2,12 @@ library(rtracklayer) gff <- import(commandArgs(T)[1], format='GFF') tabular <- as.data.frame(gff) +head(tabular) +# some columns are lists, we need to convert them to vectors before writing to file +for (i in 1:ncol(tabular)){ + if (is.list(tabular[[i]])){ + tabular[[i]] <- sapply(tabular[[i]], function(x) paste(x, collapse = ";")) + } +} write.table(tabular, file = commandArgs(T)[2], quote=FALSE, sep="\t", row.names=FALSE)