Mercurial > repos > jackcurragh > ribogalaxy_get_chrom_sizes
changeset 17:f87a4b64e6ef draft
Uploaded
| author | jackcurragh |
|---|---|
| date | Tue, 17 May 2022 13:57:39 +0000 |
| parents | ab7b5928faea |
| children | 06c2eaff31e5 |
| files | get_chrom_sizes/calculating_chrom.sizes.py get_chrom_sizes/get_chrom_sizes.xml |
| diffstat | 2 files changed, 4 insertions(+), 4 deletions(-) [+] |
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--- a/get_chrom_sizes/calculating_chrom.sizes.py Tue May 17 13:52:08 2022 +0000 +++ b/get_chrom_sizes/calculating_chrom.sizes.py Tue May 17 13:57:39 2022 +0000 @@ -4,12 +4,12 @@ # python calculating_chrom.sizes.py genome_input.fa output.chrom.sizes fasta_source = str(argv[1]) prefix = str(argv[2]) -genome = str(argv[3]) -builtin = str(argv[4]) +output = str(argv[3]) +genome = str(argv[4]) +builtin = str(argv[5]) # genome = 'test-data/test.fasta' # output = "test-data/test_chrom.sizes" -print(fasta_source, genome, builtin, prefix, output) if fasta_source == 'builtin': genome = builtin
--- a/get_chrom_sizes/get_chrom_sizes.xml Tue May 17 13:52:08 2022 +0000 +++ b/get_chrom_sizes/get_chrom_sizes.xml Tue May 17 13:57:39 2022 +0000 @@ -1,7 +1,7 @@ <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 ${refGenomeSource.genomeSource} ${input2} ${output1} + python $__tool_directory__/calculating_chrom.sizes.py ${refGenomeSource.genomeSource} ${input2} "${output1}" #if $refGenomeSource.genomeSource == "builtin": ${refGenomeSource.input1_builtin.fields.path} #else: