| Previous changeset 5:d87ecbc477d8 (2018-11-21) Next changeset 7:caaea0a5c425 (2018-11-22) |
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Commit message:
Advanced options: threads and memory configuration |
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modified:
span.xml span_wrapper.py |
| b |
| diff -r d87ecbc477d8 -r 70500fd87b60 span.xml --- a/span.xml Wed Nov 21 06:29:41 2018 -0500 +++ b/span.xml Wed Nov 21 10:31:58 2018 -0500 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="span" name="SPAN" version="0.7.1.4518"> +<tool id="span" name="SPAN" version="0.7.1.4518a"> <description>Semi-supervised Peak Analyzer for ChIP-Seq data</description> <requirements> <requirement type="package" version="0.7.1.4518">package_span_jar</requirement> @@ -11,27 +11,35 @@ <command interpreter="python"> #if str($action.action_selector) == "model" #if str($control_file) != 'None': - span_wrapper.py model_with_control + span_wrapper.py + "${advanced_options.memory}" "${advanced_options.threads}" + model_with_control "${genome_file.name}" "${genome_file}" "${treatment_file.name}" "${treatment_file}" "${control_file.name}" "${control_file}" "${bin}" #else - span_wrapper.py model_without_control + span_wrapper.py + "${advanced_options.memory}" "${advanced_options.threads}" + model_without_control "${genome_file.name}" "${genome_file}" "${treatment_file.name}" "${treatment_file}" "${bin}" #end if #else #if str($control_file) != 'None': - span_wrapper.py peaks_with_control + span_wrapper.py + "${advanced_options.memory}" "${advanced_options.threads}" + peaks_with_control "${genome_file.name}" "${genome_file}" "${treatment_file.name}" "${treatment_file}" "${control_file.name}" "${control_file}" "${bin}" "${action.fdr}" "${action.gap}" #else - span_wrapper.py peaks_without_control + span_wrapper.py + "${advanced_options.memory}" "${advanced_options.threads}" + peaks_without_control "${genome_file.name}" "${genome_file}" "${treatment_file.name}" "${treatment_file}" "${bin}" @@ -57,21 +65,29 @@ <option value="peaks">Compute SPAN model and produce peaks file</option> </param> <when value="peaks"> - <param name="fdr" size="5" type="float" value="0.0001" label="FDR" argument="--fdr" + <param name="fdr" size="5" type="float" value="0.0001" min="0" label="FDR" argument="--fdr" help="Minimum FDR cutoff to call significant regions, default value is 1.0E-6. SPAN reports p- and q- values for the null hypothesis that a given bin is not enriched with a histone modification. Peaks are formed from a list of truly (in the FDR sense) enriched bins for the analyzed biological condition by thresholding the Q-value with a cutoff FDR and merging spatially close peaks using GAP option to broad ones. This is equivalent to controlling FDR. q-values are are calculated from p-values using Benjamini-Hochberg procedure."/> - <param name="gap" size="5" type="integer" value="5" label="GAP" argument="--gap" + <param name="gap" size="3" type="integer" value="5" min="0" label="GAP" argument="--gap" help="Gap size to merge spatially close peaks. Useful for wide histone modifications. Default value is 5, i.e. peaks separated by 5*BIN distance or less are merged."/> </when> </conditional> - <param name="bin" size="5" type="integer" value="200" label="Bin size" argument="--bin" + <param name="bin" size="5" type="integer" value="200" min="50" label="Bin size" argument="--bin" help="Peak analysis is performed on read coverage tiled into consequent bins, with size being configurable. Default value is 200bp, approximately the length of one nucleosome."/> + + <section name="advanced_options" title="Advanced Options"> + <param name="memory" size="6" type="integer" value="2048" min="1024" + label="Memory limit in megabytes" help="Default value is 2048 megabytes"/> + <param name="threads" argument="--threads" size="2" type="integer" value="2" min="1" + label="Threads number" + help="Default value is 2 threads. SPAN utilizes both multithreading and specialized processor extensions like SSE2, AVX, etc."/> + </section> </inputs> <outputs> <data name="model.span" format="span" from_work_dir="*.span" |
| b |
| diff -r d87ecbc477d8 -r 70500fd87b60 span_wrapper.py --- a/span_wrapper.py Wed Nov 21 06:29:41 2018 -0500 +++ b/span_wrapper.py Wed Nov 21 10:31:58 2018 -0500 |
| [ |
| @@ -11,37 +11,10 @@ SPAN_JAR = os.environ.get("SPAN_JAR") print 'Using SPAN Peak Analyzer distributive file {0}'.format(SPAN_JAR) -# #if str($action.action_selector) == "model" -# #if str($control_file) != 'None': -# span_wrapper.py model_with_control -# "${genome_identifier}" "${genome_file}" -# "${treatment_identifier}" "${treatment_file}" -# "${control_identifier}" "${control_file}" -# "${bin}" -# -# #else -# span_wrapper.py model without_control -# "${genome_identifier}" "${genome_file}" -# "${treatment_identifier}" "${treatment_file}" -# "${bin}" -# #end if -# #else -# #if str($control_file) != 'None': -# span_wrapper.py peaks_with_control -# "${genome_identifier}" "${genome_file}" -# "${treatment_identifier}" "${treatment_file}" -# "${control_identifier}" "${control_file}" -# "${bin}" -# "${action.fdr}" "${action.gap}" -# #else -# span_wrapper.py peaks_without_control -# "${genome_identifier}" "${genome_file}" -# "${treatment_identifier}" "${treatment_file}" -# "${bin}" -# "${action.fdr}" "${action.gap}" -# #end if -# #end if -action = argv[0] +MEMORY = argv[0] +THREADS = argv[1] +ACTION = argv[2] +argv = argv[3:] working_dir = os.path.abspath('.') print 'WORKING DIRECTORY: {}'.format(working_dir) @@ -55,54 +28,64 @@ return result -if action == 'model_with_control': +if ACTION == 'model_with_control': (chrom_sizes, chrom_sizes_file, treatment, treatment_file, control, control_file, - bin) = argv[1:] - cmd = 'java -jar {} analyze --chrom.sizes {} --treatment {} --control {} --bin {}'.format( - SPAN_JAR, + bin) = argv + cmd = 'java -Xmx{}m -jar {} analyze --threads {} ' \ + '--chrom.sizes {} --treatment {} --control {} --bin {}'.format( + MEMORY, SPAN_JAR, THREADS, link(chrom_sizes, chrom_sizes_file), link(treatment, treatment_file), link(control, control_file), bin) -elif action == 'model_without_control': + +elif ACTION == 'model_without_control': (chrom_sizes, chrom_sizes_file, treatment, treatment_file, - bin) = argv[1:] - cmd = 'java -jar {} analyze --chrom.sizes {} --treatment {} --bin {}'.format( - SPAN_JAR, + bin) = argv + cmd = 'java -Xmx{}m -jar {} analyze --threads {} ' \ + '--chrom.sizes {} --treatment {} --bin {}'.format( + MEMORY, SPAN_JAR, THREADS, link(chrom_sizes, chrom_sizes_file), link(treatment, treatment_file), bin) -elif action == "peaks_with_control": + +elif ACTION == "peaks_with_control": (chrom_sizes, chrom_sizes_file, treatment, treatment_file, control, control_file, bin, - fdr, gap) = argv[1:] - cmd = 'java -jar {} analyze --chrom.sizes {} --treatment {} --control {} ' \ - '--bin {} --fdr {} --gap {} --peaks {}'.format( - SPAN_JAR, + fdr, gap) = argv + cmd = 'java -Xmx{}m -jar {} analyze --threads {} ' \ + '--chrom.sizes {} --treatment {} --control {} --bin {} --fdr {} --gap {} --peaks {}'.format( + MEMORY, SPAN_JAR, THREADS, link(chrom_sizes, chrom_sizes_file), link(treatment, treatment_file), link(control, control_file), bin, fdr, gap, os.path.join(working_dir, 'result.peak')) -elif action == 'peaks_without_control': + +elif ACTION == 'peaks_without_control': (chrom_sizes, chrom_sizes_file, treatment, treatment_file, bin, - fdr, gap) = argv[1:] - cmd = 'java -jar {} analyze --chrom.sizes {} --treatment {} -' \ - '-bin {} --fdr {} --gap {} --peaks {}'.format( - SPAN_JAR, + fdr, gap) = argv + cmd = 'java -Xmx{}m -jar {} analyze --threads {} ' \ + '--chrom.sizes {} --treatment {} -bin {} --fdr {} --gap {} --peaks {}'.format( + MEMORY, SPAN_JAR, THREADS, link(chrom_sizes, chrom_sizes_file), link(treatment, treatment_file), bin, fdr, gap, os.path.join(working_dir, 'result.peak')) + (chrom_sizes, chrom_sizes_file, + treatment, treatment_file, + bin, + fdr, gap) = argv + else: - raise Exception("Unknown action command {}".format(action)) + raise Exception("Unknown action command {}".format(ACTION)) print 'Launching SPAN: {}'.format(cmd) subprocess.check_call(cmd, cwd=None, shell=True) |