# HG changeset patch # User artbio # Date 1538817855 14400 # Node ID 82fedc57602484982cbf3890bcef7c47fe4e24b3 # Parent cd75c72e1d7558eeeb9f9ded826223de60b5ceab planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c1d96f7f028512aa4d8fcae3dd5f967cd445708e diff -r cd75c72e1d75 -r 82fedc576024 small_rna_maps.py --- a/small_rna_maps.py Tue Apr 10 10:13:04 2018 -0400 +++ b/small_rna_maps.py Sat Oct 06 05:24:15 2018 -0400 @@ -54,15 +54,13 @@ map_dictionary[(chrom, 1, 'F')] = [] map_dictionary[(chrom, self.chromosomes[chrom], 'F')] = [] for read in bam_object.fetch(chrom): - if (read.query_alignment_length >= minsize and - read.query_alignment_length <= maxsize): - positions = read.positions # a list of covered positions - if read.is_reverse: - map_dictionary[(chrom, positions[-1]+1, 'R')].append( - read.query_alignment_length) - else: - map_dictionary[(chrom, positions[0]+1, 'F')].append( - read.query_alignment_length) + positions = read.positions # a list of covered positions + if read.is_reverse: + map_dictionary[(chrom, positions[-1]+1, 'R')].append( + read.query_alignment_length) + else: + map_dictionary[(chrom, positions[0]+1, 'F')].append( + read.query_alignment_length) return map_dictionary def grouper(self, iterable, clust_distance): diff -r cd75c72e1d75 -r 82fedc576024 small_rna_maps.xml --- a/small_rna_maps.xml Tue Apr 10 10:13:04 2018 -0400 +++ b/small_rna_maps.xml Sat Oct 06 05:24:15 2018 -0400 @@ -1,4 +1,4 @@ - + numpy @@ -7,19 +7,20 @@ r-latticeextra r-gridextra r-reshape2 - + sambamba = ${minsize} and sequence_length <= ${maxsize}" -f bam '$file.inputs' >'$file.inputs.name'; + samtools index '$file.inputs.name'; #end for - python '$__tool_directory__'/small_rna_maps.py + python '$__tool_directory__'/small_rna_maps.py --inputs #for $file in $series - '$file.inputs' + '$file.inputs.name' #end for --sample_names #for $sample in $series @@ -39,9 +40,9 @@ --outputs '$output_tab' ; #end if Rscript '$__tool_directory__'/small_rna_maps.r - --first_dataframe '$output_tab' + --first_dataframe '$output_tab' --extra_dataframe '$extra_output_tab' - --normalization + --normalization #set $norm = "" #for $file in $series #set $norm += str($file.normalization)+' ' @@ -83,29 +84,29 @@ - + - - - + + + - - - + + + - - - + + + @@ -134,7 +135,7 @@ plots_options['plots_options_selector'] == 'two_plot' - + @@ -144,6 +145,23 @@ + + + + + + + + + + + + + + + + + @@ -377,4 +395,3 @@ } - diff -r cd75c72e1d75 -r 82fedc576024 test-data/input1_input2new_norm_1_2_counts.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input1_input2new_norm_1_2_counts.tab Sat Oct 06 05:24:15 2018 -0400 @@ -0,0 +1,616 @@ +Dataset Chromosome Chrom_length Coordinate Polarity Counts +input1.bam FBtr0070001 72 1 F 1 +input1.bam FBtr0070001 72 7 F 6 +input1.bam FBtr0070001 72 8 F 3 +input1.bam FBtr0070001 72 11 F 2 +input1.bam FBtr0070001 72 16 F 1 +input1.bam FBtr0070001 72 17 F 1 +input1.bam FBtr0070001 72 18 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