# HG changeset patch
# User jackcurragh
# Date 1652875054 0
# Node ID 49e8fcbaaa72c01190ed4cfb59ab69559e86361c
# Parent  dfed3b7be399391812ef591af83b516befa13e56
Uploaded

diff -r dfed3b7be399 -r 49e8fcbaaa72 create_ribosome_profile/bam_to_ribosome_profile.py
--- a/create_ribosome_profile/bam_to_ribosome_profile.py	Thu Apr 28 12:08:08 2022 +0000
+++ b/create_ribosome_profile/bam_to_ribosome_profile.py	Wed May 18 11:57:34 2022 +0000
@@ -119,15 +119,20 @@
 if __name__ == '__main__':
 	bam_path = str(argv[1]) 
 	offset = int(argv[2])
-	fasta_path = str(argv[3])
-	mode = argv[4]
-	output = argv[5]
+	fasta_source = str(argv[3])
+	fasta_path = str(argv[4])
+	builtin = str(argv[5])
+	mode = argv[6]
+	output = argv[7]
 
 	if not os.path.exists(bam_path + ".bai"): 
 		print(bam_path)
 		pysam.index(bam_path)
 	
-	main(bam_path = bam_path, fasta_path = fasta_path, output=output, mode=mode, offset=offset)
+	if fasta_source == 'history':
+		main(bam_path = bam_path, fasta_path = fasta_path, output=output, mode=mode, offset=offset)
+	else:
+		main(bam_path = bam_path, fasta_path = builtin, output=output, mode=mode, offset=offset)
 
 
 
diff -r dfed3b7be399 -r 49e8fcbaaa72 create_ribosome_profile/create_ribosome_profile.xml
--- a/create_ribosome_profile/create_ribosome_profile.xml	Thu Apr 28 12:08:08 2022 +0000
+++ b/create_ribosome_profile/create_ribosome_profile.xml	Wed May 18 11:57:34 2022 +0000
@@ -1,13 +1,34 @@
-<tool id="create_ribosome_profiles" name="Create Ribosome Profiles" version="1.a">
-    <description>Produce a sorted bed file from a sorted BAM file with the option of introducing an offset to the A-Site of a ribosome protected fragment.</description>
+<tool id="create_ribosome_profiles" name="Create Ribosome Profiles" version="1.1">
+    <description>Produce a sorted bed file of A-Site profiles of RPFs.</description>
     <requirements>
-        <requirement type="package" version="1.73">biopython</requirement>
+        <requirement type="package" version="1.79">biopython</requirement>
         <requirement type="package" version="0.19.0">pysam</requirement>
     </requirements>
-    <command>python $__tool_directory__/bam_to_ribosome_profile.py ${input1} ${input2} ${input3} ${input4} ${output1}</command>
+    <command>python $__tool_directory__/bam_to_ribosome_profile.py ${input1} ${input2} $refGenomeSource.genomeSource
+            #if $refGenomeSource.genomeSource == "builtin":
+                none ${refGenomeSource.input1_builtin.fields.path} ${input4} ${output1}
+            #else:
+                ${refGenomeSource.input1_file} none ${input4} ${output1}
+            #end if
+    </command>
     <inputs>
         <param name="input1" type="data" format="bam" label="BAM file to process"/>
         <param name="input2" type="integer" value="15" label="Offset to use" help="Use 15 for elongating ribosomes, 12 for initiating and 0 form RNA-seq reads"/>
+        <param name="genomeSource" type="select" label="Will you select a reference from your history or use a built-in FASTA?">
+            <option value="builtin">Use a built-in FASTA</option>
+            <option value="history">Use one from the history</option>
+        </param>
+        <when value="builtin">
+            <param name="input1_builtin" type="select" format="fasta" label="Select a reference" help="if your reference of interest is not listed - contact RiboGalaxy team">
+                <options from_data_table="builtin_fastas">
+                    <filter type="sort_by" column="2" />
+                    <validator type="no_options" message="No built-ins are available" />
+                </options>
+            </param>
+        </when>
+        <when value="history">
+            <param name="input1_file" type="data" format="fasta" label="FASTA File" />
+        </when>
         <param name="input3" type="data" format="fasta" label="FASTA file to which the reads were aligned"/>
         <param name="input4" type="select" label="Approach" help ="Use Offset for RNase and Weight for MNase">
             <option value="offset" selected="true">Use offset approach</option>
diff -r dfed3b7be399 -r 49e8fcbaaa72 create_ribosome_profile/tool-data/builtin_fastas.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/create_ribosome_profile/tool-data/builtin_fastas.loc.sample	Wed May 18 11:57:34 2022 +0000
@@ -0,0 +1,8 @@
+mus_musculus_m28	m28	Mus musculus (m28) Genome	/data2/indices/bowtie/genome/mus_musculus_m28/mus_musculus_m28.fa
+drosophila_melanogaster_dm6	dm6	Drosophila melanogaster (dm6) Genome	/data2/indices/bowtie/genome/drosophila_melanogater_dm6/dm6.fa
+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
+Arabidopsis	araThal	Arabidopsis thaliana (TAIR10) Genome	/data2/indices/bowtie/genome/Arabidopsis/GCF_000001735.4_TAIR10.1_genomic.fna
+homo_sapiens_hg19	hg19	Homo sapiens (hg19) Genome	/data2/indices/bowtie/genome/homo_sapiens_hg19/hg19.fa
+homo_sapiens_hg38	hg38	Homo sapiens (hg38) Genome	/data2/indices/bowtie/genome/homo_sapiens_hg38/hg38.fa
\ No newline at end of file
diff -r dfed3b7be399 -r 49e8fcbaaa72 create_ribosome_profile/tool_data_table_conf.xml.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/create_ribosome_profile/tool_data_table_conf.xml.sample	Wed May 18 11:57:34 2022 +0000
@@ -0,0 +1,8 @@
+<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc-->
+<tables>
+    <!-- Locations of indexes in the Bowtie mapper format -->
+    <table name="builtin_fastas" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="tool-data/builtin_fastas.loc" />
+    </table>
+</tables>
\ No newline at end of file