# HG changeset patch
# User artbio
# Date 1525042633 14400
# Node ID de227b7307cfe41882098de40fbb54c1c3cedea1
# Parent  2a08a6eb471cf4926a74dcb83f33540d23207d62
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit af0f70b8156c078cc0d832c54ebb678af10c42a0

diff -r 2a08a6eb471c -r de227b7307cf format_fasta_hairpins.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/format_fasta_hairpins.py	Sun Apr 29 18:57:13 2018 -0400
@@ -0,0 +1,61 @@
+import argparse
+import gzip
+
+
+def Parser():
+    the_parser = argparse.ArgumentParser()
+    the_parser.add_argument(
+        '--hairpins_path', action="store", type=str,
+        help="BASE url. ex: /pub/mirbase/22/")
+    the_parser.add_argument(
+        '--output', action="store", type=str,
+        help="parsed hairpin output in fasta format")
+    the_parser.add_argument(
+        '--basename', action="store", type=str,
+        help="genome basename of the parsed fasta")
+    args = the_parser.parse_args()
+    return args
+
+
+def get_fasta_dic(gzipfile):
+    '''
+    gzipfile value example : 'mirbase/22/hairpin.fa.gz'
+    '''
+    item_dic = {}
+    with gzip.open(gzipfile, 'rb') as f:
+        current_item = ''
+        stringlist = []
+        for line in f:
+            line = line.decode('utf-8').strip('\n')
+            if (line[0] == ">"):
+                # dump the sequence of the previous item
+                if current_item and stringlist:
+                    item_dic[current_item] = "".join(stringlist)
+                # take first word of item '''
+                current_item = line[1:].split()[0]
+                stringlist = []
+            else:
+                stringlist.append(line)
+        item_dic[current_item] = "".join(stringlist)  # for the last item
+    return item_dic
+
+
+def convert_and_print_hairpins(gzipfile, basename, fasta_output):
+    raw_fasta_dict = get_fasta_dic(gzipfile)
+    parsed_fasta_dict = {}
+    trs = str.maketrans("uU", "tT")
+    for head in raw_fasta_dict:
+        if basename in head:
+            parsed_fasta_dict[head] = raw_fasta_dict[head].translate(trs)
+    with open(fasta_output, "w") as output:
+        for head in sorted(parsed_fasta_dict):
+            output.write('>%s\n%s\n' % (head, parsed_fasta_dict[head]))
+
+
+def main(hairpins_path, basename, outfile):
+    convert_and_print_hairpins(hairpins_path, basename, outfile)
+
+
+if __name__ == "__main__":
+    args = Parser()
+    main(args.hairpins_path, args.basename, args.output)
diff -r 2a08a6eb471c -r de227b7307cf format_fasta_hairpins.sh
--- a/format_fasta_hairpins.sh	Wed Apr 25 12:48:27 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,19 +0,0 @@
-GENOME_KEY=$1
-        
-gunzip hairpin.fa.gz
-sed -i.bak '/^[^>]/ y/uU/tT/' hairpin.fa ## replace U by tT
-sed -i.bak2 -E 's/ .+//' hairpin.fa ## just leaves mir name as one word header
-awk '/^>/ {printf("\n%s\n",$0);next; } { printf("%s",$0);}  END {printf("\n");}' < hairpin.fa > hairpin.fa.bak3
-tail -n +2 hairpin.fa.bak3 > hairpin.fa ## generate single line sequences
-awk 'BEGIN{RS=">"}{gsub("\n","\t",$0); print ">"$0}' < hairpin.fa > hairpin.fa.tmp
-mv hairpin.fa hairpin.bak4 && tail -n +2 hairpin.fa.tmp > hairpin.fa
-rm hairpin.fa.tmp ## tabular sequences
-sed -i.bak5 -E $'s/\t$//g' hairpin.fa ## remove tab before end line leaved by previous awk
-grep ">${GENOME_KEY}-" hairpin.fa > hairpin.fa.tmp
-mv hairpin.fa hairpin.fa.bak6
-mv hairpin.fa.tmp hairpin.fa ## filter tabular hairpins with proper genomeKey
-tr '\t' '\n' < hairpin.fa > hairpin.fa.tmp
-mv hairpin.fa hairpin.fa.bak7
-mv hairpin.fa.tmp hairpin.fa ## terminate parsing by regenerating fasta format, bowtie-build ready
-rm ./*.bak* ## cleaning job directory
-
diff -r 2a08a6eb471c -r de227b7307cf mature_mir_gff_translation.py
--- a/mature_mir_gff_translation.py	Wed Apr 25 12:48:27 2018 -0400
+++ b/mature_mir_gff_translation.py	Sun Apr 29 18:57:13 2018 -0400
@@ -5,10 +5,14 @@
 def Parser():
     the_parser = argparse.ArgumentParser()
     the_parser.add_argument(
-        '--input', action="store", type=str, help="input miRBase GFF3 file")
+        '--gff_path', action="store", type=str,
+        help="path to miRBase GFF3 file")
     the_parser.add_argument(
         '--output', action="store", type=str,
         help="output GFF3 file with converted mature mir coordinates")
+    the_parser.add_argument(
+        '--basename', action="store", type=str,
+        help="basename of the parsed gff file returned")
     args = the_parser.parse_args()
     return args
 
@@ -95,10 +99,10 @@
         output.write('\n')
 
 
-def main(infile, outfile):
-    convert_and_print_gff(infile, outfile)
+def main(gff_path, outfile):
+    convert_and_print_gff(gff_path, outfile)
 
 
 if __name__ == "__main__":
     args = Parser()
-    main(args.input, args.output)
+    main(args.gff_path, args.output)
diff -r 2a08a6eb471c -r de227b7307cf mirbase.tar.gz
Binary file mirbase.tar.gz has changed
diff -r 2a08a6eb471c -r de227b7307cf mircounts.xml
--- a/mircounts.xml	Wed Apr 25 12:48:27 2018 -0400
+++ b/mircounts.xml	Sun Apr 29 18:57:13 2018 -0400
@@ -1,18 +1,24 @@
-<tool id="mircounts" name="miRcounts" version="1.2.6">
+<tool id="mircounts" name="miRcounts" version="1.3.0">
     <description> Counts miRNA alignments from small RNA sequence data</description>
     <requirements>
-        <requirement type="package" version="1.18">gnu-wget</requirement>
         <requirement type="package" version="1.2.0">bowtie</requirement>
         <requirement type="package" version="1.6.0">samtools</requirement>
         <requirement type="package" version="0.11.2.2">pysam</requirement>
         <requirement type="package" version="1.3.2=r3.3.2_0">r-optparse</requirement>
         <requirement type="package" version="0.20_34=r3.3.2_0">r-lattice</requirement>
     </requirements>
+    <stdio>
+        <exit_code range="1:" level="warning" description="Tool exception" />
+    </stdio>
     <command detect_errors="exit_code"><![CDATA[
-        wget --quiet ftp://mirbase.org/pub/mirbase/${mirbase_version}/genomes/${genomeKey}.gff3 && ## download the gff3 file specified by the variable genomeKey
-        python '$__tool_directory__'/mature_mir_gff_translation.py --input ${genomeKey}.gff3 --output $gff3 && ## transcode the mature miR genome coordinates into coordinates relative to the corresponding "miRNA_primary_transcript".
-        wget --quiet ftp://mirbase.org/pub/mirbase/${mirbase_version}/hairpin.fa.gz &&
-        sh '$__tool_directory__'/format_fasta_hairpins.sh $genomeKey &&
+        tar -xvzf  '$__tool_directory__'/mirbase.tar.gz &&
+        python '$__tool_directory__'/mature_mir_gff_translation.py
+                                                --gff_path mirbase/${mirbase_version}/genomes/${genomeKey}.gff3
+                                                --output $gff3 && ## transcode the mature miR genome coordinates into coordinates relative to the corresponding "miRNA_primary_transcript".
+        python '$__tool_directory__'/format_fasta_hairpins.py
+                                                --hairpins_path mirbase/${mirbase_version}/hairpin.fa.gz
+                                                --basename ${genomeKey}
+                                                --output hairpin.fa &&
         #if $cutadapt.cutoption == "yes":
             python '$__tool_directory__'/yac.py --input $cutadapt.input
                                                 --output clipped_input.fastq
@@ -21,15 +27,15 @@
                                                 --min $cutadapt.min
                                                 --max $cutadapt.max
                                                 --Nmode $cutadapt.Nmode &&
-        #else
+        #else:
             ln -f -s '$cutadapt.clipped_input' clipped_input.fastq &&
         #end if
-        bowtie-build hairpin.fa hairpin >/dev/null &&
-        bowtie -v $v -M 1 --best --strata --norc -p \${GALAXY_SLOTS:-4} --sam hairpin -q clipped_input.fastq | samtools sort -O bam -o '$output' 2>&1 &&
+        bowtie-build hairpin.fa hairpin &&
+        bowtie -v $v -M 1 --best --strata --norc -p \${GALAXY_SLOTS:-4} --sam hairpin -q clipped_input.fastq | samtools sort -O bam -o '$output' &&
         samtools index $output &&
-        python '$__tool_directory__'/mircounts.py -pm --alignment $output --gff $gff3 --quality_threshold 10 --pre_mirs $pre_mir_count_file --mirs $mir_count_file --lattice $coverage_dataframe;
+        python '$__tool_directory__'/mircounts.py --alignment $output --gff $gff3 --quality_threshold 10 --pre_mirs $pre_mir_count_file --mirs $mir_count_file --lattice $coverage_dataframe
         #if $plotting.plottingOption == 'yes':
-            Rscript '$__tool_directory__'/coverage_plotting.R --dataframe $coverage_dataframe --type $plotting.display --output $latticePDF
+            && Rscript '$__tool_directory__'/coverage_plotting.R --dataframe $coverage_dataframe --type $plotting.display --output $latticePDF
         #end if
     ]]></command>
     <inputs>
@@ -141,8 +147,8 @@
             <param name="plottingOption" value="no"/>
             <param name="output_premir_counts" value="True"/>
             <param name="output_mir_counts" value="True"/>
-            <output name="output" file="unclipped.out.22.bam" ftype="bam"/>
-            <output name="gff3" file="translated_dme.22.gff3" ftype="gff3" lines_diff="22"/>
+            <output name="output" file="unclipped.out.22.bam"/>
+            <output name="gff3" file="translated_dme.22.gff3" lines_diff="22"/>
             <output name="pre_mir_count_file" file="pre_mirs_unclipped_count.22.tab"/>
             <output name="mir_count_file" file="mirs_unclipped_count.22.tab"/>
         </test>
@@ -159,8 +165,8 @@
             <param name="plottingOption" value="no"/>
             <param name="output_premir_counts" value="True"/>
             <param name="output_mir_counts" value="True"/>
-            <output name="output" file="unclipped.out.bam" ftype="bam"/>
-            <output name="gff3" file="translated_dme.gff3" ftype="gff3" lines_diff="22"/>
+            <output name="output" file="unclipped.out.bam" />
+            <output name="gff3" file="translated_dme.gff3" lines_diff="22"/>
             <output name="pre_mir_count_file" file="pre_mirs_unclipped_count.tab"/>
             <output name="mir_count_file" file="mirs_unclipped_count.tab"/>
         </test>
@@ -178,11 +184,11 @@
             <param name="display" value="relative"/>
             <param name="output_premir_counts" value="True"/>
             <param name="output_mir_counts" value="True"/>
-            <output name="output" file="unclipped.out.bam" ftype="bam"/>
-            <output name="gff3" file="translated_dme.gff3" ftype="gff3"  lines_diff="22"/>
+            <output name="output" file="unclipped.out.bam"/>
+            <output name="gff3" file="translated_dme.gff3"  lines_diff="22"/>
             <output name="pre_mir_count_file" file="pre_mirs_unclipped_count.tab"/>
             <output name="mir_count_file" file="mirs_unclipped_count.tab"/>
-            <output name="latticePDF" file="mir_unclipped_coverage.pdf" ftype="pdf"/>
+            <output name="latticePDF" file="mir_unclipped_coverage.pdf"/>
             <output name="coverage_dataframe" file="lattice_unclipped_dataframe.tab"/>
         </test>
         <test>
@@ -195,11 +201,11 @@
             <param name="display" value="absolute"/>
             <param name="output_premir_counts" value="True"/>
             <param name="output_mir_counts" value="True"/>
-            <output name="output" file="clipped.out.bam" ftype="bam"/>
-            <output name="gff3" file="translated_dme.gff3" ftype="gff3"  lines_diff="22"/>
+            <output name="output" file="clipped.out.bam"/>
+            <output name="gff3" file="translated_dme.gff3" lines_diff="22"/>
             <output name="pre_mir_count_file" file="pre_mirs_clipped_count.tab"/>
             <output name="mir_count_file" file="mirs_clipped_count.tab"/>
-            <output name="latticePDF" file="mir_clipped_coverage.pdf" ftype="pdf"/>
+            <output name="latticePDF" file="mir_clipped_coverage.pdf"/>
             <output name="coverage_dataframe" file="lattice_clipped_dataframe.tab"/>
         </test>
     </tests>
diff -r 2a08a6eb471c -r de227b7307cf test-data/clipped.out.bam
Binary file test-data/clipped.out.bam has changed
diff -r 2a08a6eb471c -r de227b7307cf test-data/unclipped.out.22.bam
Binary file test-data/unclipped.out.22.bam has changed
diff -r 2a08a6eb471c -r de227b7307cf test-data/unclipped.out.bam
Binary file test-data/unclipped.out.bam has changed