changeset 1:639c0edb7e64 draft

planemo upload for repository https://github.com/kavonrtep/galaxy_packages commit 248ffeb6792d5807820b664eae3e88306f3f395e-dirty

--- 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)