# HG changeset patch
# User jackcurragh
# Date 1650537558 0
# Node ID cfdf764b9226e61b6a90c6b8a053dc1c1e63f24d
# Parent  a244b29ce89a90736552b91780f3f7ed662f3a48
Uploaded

diff -r a244b29ce89a -r cfdf764b9226 get_chrom_sizes/calculating_chrom.sizes.py
--- a/get_chrom_sizes/calculating_chrom.sizes.py	Wed Apr 20 15:20:33 2022 +0000
+++ b/get_chrom_sizes/calculating_chrom.sizes.py	Thu Apr 21 10:39:18 2022 +0000
@@ -3,7 +3,8 @@
 from sys import argv
 # python calculating_chrom.sizes.py genome_input.fa output.chrom.sizes
 genome = str(argv[1])
-output = str(argv[2])
+prefix = str(argv[2])
+output = str(argv[3])
 # genome = 'test-data/test.fasta'
 # output = "test-data/test_chrom.sizes"
 
@@ -20,9 +21,12 @@
 	else:
 		sequence = line.strip('\n')
 		record[1] += len(sequence)
-		
+
+if record not in records:
+	records.append(record)
+
 for seq_record in records:
-	output_line = '%s\t%i\n' % (seq_record[0], seq_record[1])
+	output_line = f"{prefix}{seq_record[0]}\t{seq_record[1]}\n"
 	chromSizesoutput.write(output_line)
 
 chromSizesoutput.close()
diff -r a244b29ce89a -r cfdf764b9226 get_chrom_sizes/get_chrom_sizes.xml
--- a/get_chrom_sizes/get_chrom_sizes.xml	Wed Apr 20 15:20:33 2022 +0000
+++ b/get_chrom_sizes/get_chrom_sizes.xml	Thu Apr 21 10:39:18 2022 +0000
@@ -1,10 +1,12 @@
 <tool id="get_chrom_sizes" name="Get Chromosome Sizes" version="2.0">
     <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} ${output1}
+        python $__tool_directory__/calculating_chrom.sizes.py ${input1} ${input2} ${output1}
     </command>
     <inputs>
         <param name="input1" type="data" format="fasta" label="FASTA File" />
+        <param name="input2" type="text" label="Chromosome Column Prefix (eg. chr)" />
+
     </inputs>
     <outputs>
        <data name="output1" format="tabular"/>
@@ -12,6 +14,7 @@
     <tests>
         <test>
             <param name="input1" value="test.fasta" ftype="fasta" />
+            <param name="input2" value="chr"/>
             <output name="output1" file="test.fasta.sizes" ftype="tabular" lines_diff="4" />
         </test>
     </tests>
diff -r a244b29ce89a -r cfdf764b9226 get_chrom_sizes/test-data/test.fasta.sizes
--- a/get_chrom_sizes/test-data/test.fasta.sizes	Wed Apr 20 15:20:33 2022 +0000
+++ b/get_chrom_sizes/test-data/test.fasta.sizes	Thu Apr 21 10:39:18 2022 +0000
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