# HG changeset patch
# User jackcurragh
# Date 1652692311 0
# Node ID ec8651ac3d61d42b5f7d79aa472b5a7233ece70f
# Parent  c6a297d05c8e85f3fec1bf9185ab8728b8d4e0c5
Uploaded

diff -r c6a297d05c8e -r ec8651ac3d61 get_chrom_sizes/get_chrom_sizes.xml
--- a/get_chrom_sizes/get_chrom_sizes.xml	Fri May 13 09:17:14 2022 +0000
+++ b/get_chrom_sizes/get_chrom_sizes.xml	Mon May 16 09:11:51 2022 +0000
@@ -1,4 +1,4 @@
-<tool id="get_chrom_sizes" name="Get Chromosome Sizes" version="2.1">
+<tool id="get_chrom_sizes" name="Get Chromosome Sizes" version="2.2">
     <description>Chromosome sizes are needed for the creation of ribosome profiles. This tool generates a tab delimited chrom.sizes file from an inputted fasta</description>
     <command>
         python $__tool_directory__/calculating_chrom.sizes.py ${input1} ${input2} ${output1}
diff -r c6a297d05c8e -r ec8651ac3d61 get_chrom_sizes/tool-data/builtin_fastas.loc.sample
--- a/get_chrom_sizes/tool-data/builtin_fastas.loc.sample	Fri May 13 09:17:14 2022 +0000
+++ b/get_chrom_sizes/tool-data/builtin_fastas.loc.sample	Mon May 16 09:11:51 2022 +0000
@@ -1,8 +1,8 @@
-mus_musculus_m28	m28	Mus musculus (m28) Genome	/data2/indices/bowtie/genome/mus_musculus_m28/mus_musculus_m28_genome.fa
-drosophila_melanogaster_dm6	dm6	Drosophila melanogaster (dm6) Genome	/data2/indices/bowtie/genome/drosophila_melanogater_dm6/drosophila_melanogater_dm6_genome.fa
-sacCer_9	sacCer9	Saccharomyces cerevisiae (v9) Genome	/data2/indices/bowtie/genome/sacCer_9/sacCer_9_genome.fa
-sarCer_3	sacCer3	Saccharomyces cerevisiae (v3) Genome	/data2/indices/bowtie/genome/sacCer_3/sacCer_3_genome.fa
-E_coli_K12_MG1655	e_coli	Escherichia coli (K12 MG1655) Genome	/data2/indices/bowtie/genome/E_coli_K12_MG1655/E_coli_K12_MG1655_genome.fa
-Arabidopsis araThal	Arabidopsis thaliana (TAIR10) Genome	/data2/indices/bowtie/genome/Arabidopsis/Arabidopsis_genome.fa
-homo_sapiens_hg19	hg19	Homo sapiens (hg19) Genome	/data2/indices/bowtie/genome/homo_sapiens_hg19/homo_sapiens_hg19_genome.fa
-homo_sapiens_hg38	hg38	Homo sapiens (hg38) Genome	/data2/indices/bowtie/genome/homo_sapiens_hg38/homo_sapiens_hg38_genome.fa
\ No newline at end of file
+mus_musculus_m28	m28	Mus musculus (m28) Genome	/data2/indices/bowtie/genome/mus_musculus_m28/mus_musculus_m28.fa.gz
+drosophila_melanogaster_dm6	dm6	Drosophila melanogaster (dm6) Genome	/data2/indices/bowtie/genome/drosophila_melanogater_dm6/dm6.fa.gz
+sacCer_9	sacCer9	Saccharomyces cerevisiae (v9) Genome	/data2/indices/bowtie/genome/sacCer_9/S288C_reference_sequence_R9-1-1_19990210.fsa
+sarCer_3	sacCer3	Saccharomyces cerevisiae (v3) Genome	/data2/indices/bowtie/genome/sacCer_3/S288C_reference_sequence_R3-1-1_19970730.fsa
+E_coli_K12_MG1655	e_coli	Escherichia coli (K12 MG1655) Genome	/data2/indices/bowtie/genome/E_coli_K12_MG1655/GCF_003368535.1_ASM336853v1_genomic.fna.gz
+Arabidopsis	araThal	Arabidopsis thaliana (TAIR10) Genome	/data2/indices/bowtie/genome/Arabidopsis/GCF_000001735.4_TAIR10.1_genomic.fna.gz
+homo_sapiens_hg19	hg19	Homo sapiens (hg19) Genome	/data2/indices/bowtie/genome/homo_sapiens_hg19/hg19.fa.gz
+homo_sapiens_hg38	hg38	Homo sapiens (hg38) Genome	/data2/indices/bowtie/genome/homo_sapiens_hg38/hg38.fa.gz
\ No newline at end of file