# HG changeset patch # User charles-bernard # Date 1479547542 18000 # Node ID c8acc8808b529225dfebfff84806b3a9dbab20ad # Parent 2496883e588b68bc502aaaa894db2cb106a3809d Uploaded diff -r 2496883e588b -r c8acc8808b52 ALFA/.shed.yml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ALFA/.shed.yml Sat Nov 19 04:25:42 2016 -0500 @@ -0,0 +1,14 @@ +categories: +- Graphics +- Next Gen Mappers +- Sequence Analysis +- Visualization +description: A tool to Compute and display distribution of reads by genomic categories +long_description: | + ALFA provides a global overview of features distribution composing New Generation Sequencing dataset(s). + Given a set of aligned reads (BAM files) and an annotation file (GTF format), the tool produces plots of the raw and normalized distributions of those reads among genomic categories (stop codon, 5'-UTR, CDS, intergenic, etc.) and biotypes (protein coding genes, miRNA, tRNA, etc.). Whatever the sequencing technique, whatever the organism. + https://github.com/biocompibens/ALFA.git +name: alfa +owner: charles_bernard +remote_repository_url: https://github.com/charles-bernard/Galaxy_tools/tree/master/ALFA +type: unrestricted \ No newline at end of file diff -r 2496883e588b -r c8acc8808b52 ALFA/ALFA_wrapper.py --- a/ALFA/ALFA_wrapper.py Fri Nov 04 06:12:07 2016 -0400 +++ b/ALFA/ALFA_wrapper.py Sat Nov 19 04:25:42 2016 -0500 @@ -48,8 +48,6 @@ index='index' os.symlink(stranded_index, index + '.stranded.index') os.symlink(unstranded_index, index + '.unstranded.index') - #shutil.copy(stranded_index, index + '.stranded.index') - #shutil.copy(unstranded_index, index + '.unstranded.index') return index def get_input2_args(reads_list, format): @@ -57,14 +55,14 @@ if n%2 != 0: exit_and_explain('Problem with pairing reads filename and reads label') input2_args='-i' - k = 0 + k = 1 reads_filenames = [''] * (n/2) reads_labels = [''] * (n/2) for i in range(0, n, 2): reads_filenames[k] = reads_list[i].split('__fname__')[1] reads_labels[k] = reads_list[i+1].split('__label__')[1] if not reads_labels[k]: - reads_labels[k] = 'sample_%s' % str(k+1) + reads_labels[k] = 'sample_%s' % str(k) input2_args='%s %s %s' % (input2_args, reads_filenames[k], reads_labels[k]) k += 1 if format == 'bedgraph': @@ -88,8 +86,7 @@ merged_count_file = open('count_file.txt', 'wb') for i in range(0, len(reads_labels)): current_count_file = open(reads_labels[i] + '.categories_counts', 'r') - reads_label = reads_labels[i] - merged_count_file.write('##LABEL: %s\n\n' % reads_label) + merged_count_file.write('##LABEL: %s\n\n' % reads_label[i]) merged_count_file.write(current_count_file.read()) merged_count_file.write('__________________________________________________________________\n') current_count_file.close() @@ -180,4 +177,4 @@ shutil.move(args.bi_indexes[1] + '.unstranded.index', args.output_index[1]) cleanup_before_exit(tmp_dir) -main() \ No newline at end of file +main() diff -r 2496883e588b -r c8acc8808b52 ALFA/alfa_wrapper.xml --- a/ALFA/alfa_wrapper.xml Fri Nov 04 06:12:07 2016 -0400 +++ b/ALFA/alfa_wrapper.xml Sat Nov 19 04:25:42 2016 -0500 @@ -16,37 +16,37 @@ ##__INPUT 1__## #if str ( $annotation.annotationSource['annotationSourceSelection'] ) == "index" - --index $annotation.annotationSource['strandedIndex'] $annotation.annotationSource['unstrandedIndex'] + --index "$annotation.annotationSource['strandedIndex']" "$annotation.annotationSource['unstrandedIndex']" #else if str ( $annotation.annotationSource['annotationSourceSelection'] ) == "built_in_index" - --bi_index $annotation.annotationSource.built_in_index_prefix.fields.prefix + --bi_index "$annotation.annotationSource.built_in_index_prefix.fields.prefix" #else - --annotation $annotation.annotationSource['annotationFile'] + --annotation "$annotation.annotationSource['annotationFile']" #end if ##__INPUT 2__## --reads_format $reads.readsType['readsTypeSelection'] --reads #for $i, $r in enumerate ( $reads.readsType['readsList'] ) - __fname__$r.readsFile - __label__$r.readsLabel + "__fname__$r.readsFile" + "__label__$r.readsLabel" #end for --strandness $reads['strandness'] ##__OUTPUT FILES__## #if str ( $outputFiles['plot'] ) == "True" #if str ( $outputOptions['plotFormat'] ) == "pdf" - --output_pdf $outputPdf + --output_pdf "$outputPdf" #else if str ( $outputOptions['plotFormat'] ) == "png" - --output_png $outputCategoriesPng $outputBiotypesPng + --output_png "$outputCategoriesPng" "$outputBiotypesPng" #else - --output_svg $outputCategoriesSvg $outputBiotypesSvg + --output_svg "$outputCategoriesSvg" "$outputBiotypesSvg" #end if #end if #if str ( $outputFiles['countFile'] ) == "True" - --output_count $outputCountFile + --output_count "$outputCountFile" #end if #if str ( $outputFiles['index'] ) == "True" - --output_index $outputStrandedIndex $outputUnstrandedIndex + --output_index "$outputStrandedIndex" "$outputUnstrandedIndex" #end if ##__OUTPUT OPTIONS__## @@ -58,8 +58,8 @@ #end if #end if - --log_report $logReport - --tool_dir $__tool_directory__ + --log_report "$logReport" + --tool_dir "$__tool_directory__" ]]> @@ -326,4 +326,4 @@ } - \ No newline at end of file + diff -r 2496883e588b -r c8acc8808b52 ALFA/tool_dependencies.xml --- a/ALFA/tool_dependencies.xml Fri Nov 04 06:12:07 2016 -0400 +++ b/ALFA/tool_dependencies.xml Sat Nov 19 04:25:42 2016 -0500 @@ -2,10 +2,10 @@ - - - - - - - \ No newline at end of file + + + + + + +