# HG changeset patch
# User mvdbeek
# Date 1456398574 18000
# Node ID 15ce6435ab8395f4477a416f8a9b95b6dffd5640
# Parent  d4b5942ed347e37e2600f4b0f873b68264b7c563
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty

diff -r d4b5942ed347 -r 15ce6435ab83 get_length_and_gc_content.r
--- a/get_length_and_gc_content.r	Thu Feb 25 05:49:08 2016 -0500
+++ b/get_length_and_gc_content.r	Thu Feb 25 06:09:34 2016 -0500
@@ -21,9 +21,9 @@
 
 #Load the annotation and reduce it
 GTF <- import.gff(GTFfile, format="gtf", genome=NA, feature.type="exon")
-grl <- reduce(split(GTF, elementMetadata(GTF)$gene_name))
+grl <- reduce(split(GTF, elementMetadata(GTF)$gene_id))
 reducedGTF <- unlist(grl, use.names=T)
-elementMetadata(reducedGTF)$gene_name <- rep(names(grl), elementLengths(grl))
+elementMetadata(reducedGTF)$gene_id <- rep(names(grl), elementLengths(grl))
 
 #Open the fasta file
 FASTA <- FaFile(FASTAfile)
@@ -39,7 +39,7 @@
     width = sum(elementMetadata(x)$widths)
     c(width, nGCs/width)
 }
-output <- t(sapply(split(reducedGTF, elementMetadata(reducedGTF)$gene_name), calc_GC_length))
+output <- t(sapply(split(reducedGTF, elementMetadata(reducedGTF)$gene_id), calc_GC_length))
 colnames(output) <- c("Length", "GC")
 
 write.table(output, file="GC_lengths.tsv", sep="\t")
\ No newline at end of file
diff -r d4b5942ed347 -r 15ce6435ab83 get_length_and_gc_content.xml
--- a/get_length_and_gc_content.xml	Thu Feb 25 05:49:08 2016 -0500
+++ b/get_length_and_gc_content.xml	Thu Feb 25 06:09:34 2016 -0500
@@ -6,7 +6,10 @@
     </requirements>
     <command interpreter="Rscript">
         get_length_and_gc_content.r --gtf "$gtf"
-        --fasta "$fastaSource.fasta"
+        #if $fastaSource.genomeSource == "indexed":
+            --fasta "$fastaSource.fasta.fields.path"
+        #else:
+            --fasta "$fastaSource.fasta"
         --output "output"
     </command>
     <inputs>