Mercurial > repos > artbio > small_rna_maps
changeset 15:82fedc576024 draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c1d96f7f028512aa4d8fcae3dd5f967cd445708e
| author | artbio |
|---|---|
| date | Sat, 06 Oct 2018 05:24:15 -0400 |
| parents | cd75c72e1d75 |
| children | 600e2498bd21 |
| files | small_rna_maps.py small_rna_maps.xml test-data/input1_input2new_norm_1_2_counts.tab test-data/input1_input2new_norm_1_2_single_plot_counts.pdf test-data/input1_min20_max30_single_plot_size.pdf test-data/input1_min20_max30_size.tab test-data/input_new2.bam |
| diffstat | 7 files changed, 661 insertions(+), 28 deletions(-) [+] |
line wrap: on
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--- 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):
--- 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 @@ -<tool id="small_rna_maps" name="small_rna_maps" version="2.5.2"> +<tool id="small_rna_maps" name="small_rna_maps" version="2.6.0"> <description></description> <requirements> <requirement type="package" version="1.11.2=py27_0">numpy</requirement> @@ -7,19 +7,20 @@ <requirement type="package" version="0.6_28=r3.3.2_0">r-latticeextra</requirement> <requirement type="package" version="2.2.1=r3.3.2_0">r-gridextra</requirement> <requirement type="package" version="1.4.2=r3.3.2_0">r-reshape2</requirement> - + <requirement type="package" version="0.6.6">sambamba</requirement> </requirements> <stdio> <exit_code range="1:" level="fatal" description="Tool exception" /> </stdio> <command detect_errors="exit_code"><![CDATA[ #for $file in $series - samtools index '$file.inputs'; + sambamba view -t \${GALAXY_SLOTS} -F "not unmapped and sequence_length >= ${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 @@ <param name="plots_options_selector" type="select" display="radio" label="Plot Options"> <option value="one_plot">Just one plot per chromosome</option> <option value="two_plot" selected="True">Two plots per chromosome</option> - <option value="global">Global read size distributions of aligned reads</option> + <option value="global">Global read size distributions of aligned reads</option> </param> <when value="two_plot"> <param name="first_plot" type="select" display="radio" label="Select the type of the top plot"> - <option value="Counts">Counts</option> - <option value="Coverage">Coverage</option> - <option value="Mean">Mean Sizes</option> + <option value="Counts">Counts</option> + <option value="Coverage">Coverage</option> + <option value="Mean">Mean Sizes</option> <option value="Median">Median Sizes</option> <option value="Size">Size Distributions</option> </param> <param name="extra_plot" type="select" display="radio" label="Select the type of the bottom plot"> - <option value="Counts">Counts</option> - <option value="Coverage">Coverage</option> - <option value="Mean">Mean Sizes</option> + <option value="Counts">Counts</option> + <option value="Coverage">Coverage</option> + <option value="Mean">Mean Sizes</option> <option value="Median">Median Sizes</option> <option value="Size">Size Distributions</option> </param> </when> <when value="one_plot"> <param name="first_plot" type="select" display="radio" label="select the type of plot"> - <option value="Counts">Counts</option> - <option value="Coverage">Coverage</option> - <option value="Mean">Mean Sizes</option> + <option value="Counts">Counts</option> + <option value="Coverage">Coverage</option> + <option value="Mean">Mean Sizes</option> <option value="Median">Median Sizes</option> <option value="Size">Size Distributions</option> </param> @@ -134,7 +135,7 @@ <data format="tabular" name="output_tab" label="$plots_options.first_plot dataframe" /> <data format="tabular" name="extra_output_tab" label="$plots_options.extra_plot dataframe"> <filter>plots_options['plots_options_selector'] == 'two_plot'</filter> - </data> + </data> <data format="pdf" name="output_pdf" label="small RNA maps" /> </outputs> @@ -144,6 +145,23 @@ <param name="inputs" value="input1.bam" ftype="bam" /> <param name="normalization" value="1.0" /> </repeat> + <repeat name="series"> + <param name="inputs" value="input_new2.bam" ftype="bam" /> + <param name="normalization" value="2.0" /> + </repeat> + <param name="minsize" value="0" /> + <param name="maxsize" value="10000" /> + <param name="cluster" value="0" /> + <param name="plots_options_selector" value="one_plot" /> + <param name="first_plot" value="Counts" /> + <output file="input1_input2new_norm_1_2_counts.tab" name="output_tab" /> + <output file="input1_input2new_norm_1_2_single_plot_counts.pdf" name="output_pdf" /> + </test> + <test> + <repeat name="series"> + <param name="inputs" value="input1.bam" ftype="bam" /> + <param name="normalization" value="1.0" /> + </repeat> <param name="minsize" value="0" /> <param name="maxsize" value="10000" /> <param name="cluster" value="0" /> @@ -377,4 +395,3 @@ }</citation> </citations> </tool> -
--- /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 F 1 +input1.bam FBtr0070001 72 27 F 2 +input1.bam FBtr0070001 72 30 F 1 +input1.bam FBtr0070001 72 31 F 11 +input1.bam FBtr0070001 72 32 F 27 +input1.bam FBtr0070001 72 34 F 1 +input1.bam FBtr0070001 72 72 F 0 +input1.bam FBtr0070533 72 1 F 1 +input1.bam FBtr0070533 72 12 F 2 +input1.bam FBtr0070533 72 15 F 1 +input1.bam FBtr0070533 72 19 F 5 +input1.bam FBtr0070533 72 20 F 1 +input1.bam FBtr0070533 72 21 F 1 +input1.bam FBtr0070533 72 22 F 1 +input1.bam FBtr0070533 72 25 F 1 +input1.bam FBtr0070533 72 26 F 1 +input1.bam FBtr0070533 72 28 F 1 +input1.bam 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