Mercurial > repos > devteam > cufflinks
changeset 1:b9d29fdd1190 draft
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
| author | devteam |
|---|---|
| date | Tue, 13 Oct 2015 12:37:52 -0400 |
| parents | 1fffcfe2fb35 |
| children | a6f581469476 |
| files | cuff_macros.xml cufflinks_wrapper.py cufflinks_wrapper.xml |
| diffstat | 3 files changed, 67 insertions(+), 63 deletions(-) [+] |
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--- a/cuff_macros.xml Wed Nov 26 13:50:22 2014 -0500 +++ b/cuff_macros.xml Tue Oct 13 12:37:52 2015 -0400 @@ -10,8 +10,8 @@ <stdio> <exit_code range="1:" /> <exit_code range=":-1" /> - <regex match="Error:" /> - <regex match="Exception:" /> + <regex match="Error" /> + <regex match="Exception" /> </stdio> </xml> <xml name="condition_inputs"> @@ -88,4 +88,4 @@ #end for </token> <token name="@HAS_MULTIPLE_INPUTS@">getattr(inputs, "__len__", [].__len__)() >= 2</token> -</macros> \ No newline at end of file +</macros>
--- a/cufflinks_wrapper.py Wed Nov 26 13:50:22 2014 -0500 +++ b/cufflinks_wrapper.py Tue Oct 13 12:37:52 2015 -0400 @@ -1,13 +1,18 @@ #!/usr/bin/env python -import optparse, os, shutil, subprocess, sys, tempfile -from galaxy import eggs +import optparse +import os +import shutil +import subprocess +import sys +import tempfile from galaxy.datatypes.util.gff_util import parse_gff_attributes, gff_attributes_to_str + def stop_err( msg ): - sys.stderr.write( "%s\n" % msg ) - sys.exit() - + sys.exit( "%s\n" % msg ) + + def __main__(): #Parse Command Line parser = optparse.OptionParser() @@ -17,30 +22,30 @@ parser.add_option( '-j', '--pre-mrna-fraction', dest='pre_mrna_fraction', help='Some RNA-Seq protocols produce a significant amount of reads that originate from incompletely spliced transcripts, and these reads can confound the assembly of fully spliced mRNAs. Cufflinks uses this parameter to filter out alignments that lie within the intronic intervals implied by the spliced alignments. The minimum depth of coverage in the intronic region covered by the alignment is divided by the number of spliced reads, and if the result is lower than this parameter value, the intronic alignments are ignored. The default is 5%.' ) parser.add_option( '-p', '--num-threads', dest='num_threads', help='Use this many threads to align reads. The default is 1.' ) parser.add_option( '-G', '--GTF', dest='GTF', help='Tells Cufflinks to use the supplied reference annotation to estimate isoform expression. It will not assemble novel transcripts, and the program will ignore alignments not structurally compatible with any reference transcript.' ) - parser.add_option ("--compatible-hits-norm",dest='compatible_hits_norm',help='Count hits compatible with reference RNAs only') + parser.add_option("--compatible-hits-norm", dest='compatible_hits_norm', action="store_true", help='Count hits compatible with reference RNAs only') parser.add_option( '-g', '--GTF-guide', dest='GTFguide', help='use reference transcript annotation to guide assembly' ) - parser.add_option("--3-overhang-tolerance",dest='three_overhang_tolerance', help='The number of bp allowed to overhang the 3prime end of a reference transcript when determining if an assembled transcript should be merged with it (ie, the assembled transcript is not novel). The default is 600 bp.') - parser.add_option("--intron-overhang-tolerance",dest='intron_overhang_tolerance',help='The number of bp allowed to enter the intron of a reference transcript when determining if an assembled transcript should be merged with it (ie, the assembled transcript is not novel). The default is 50 bp.') - parser.add_option("--no-faux-reads", dest='no_faux_reads',help='This option disables tiling of the reference transcripts with faux reads. Use this if you only want to use sequencing reads in assembly but do not want to output assembled transcripts that lay within reference transcripts. All reference transcripts in the input annotation will also be included in the output.') + parser.add_option("--3-overhang-tolerance", dest='three_overhang_tolerance', help='The number of bp allowed to overhang the 3prime end of a reference transcript when determining if an assembled transcript should be merged with it (ie, the assembled transcript is not novel). The default is 600 bp.') + parser.add_option("--intron-overhang-tolerance", dest='intron_overhang_tolerance', help='The number of bp allowed to enter the intron of a reference transcript when determining if an assembled transcript should be merged with it (ie, the assembled transcript is not novel). The default is 50 bp.') + parser.add_option("--no-faux-reads", dest='no_faux_reads', help='This option disables tiling of the reference transcripts with faux reads. Use this if you only want to use sequencing reads in assembly but do not want to output assembled transcripts that lay within reference transcripts. All reference transcripts in the input annotation will also be included in the output.') parser.add_option( '-u', '--multi-read-correct', dest='multi_read_correct', action="store_true", help='Tells Cufflinks to do an initial estimation procedure to more accurately weight reads mapping to multiple locations in the genome') - + # Normalization options. - parser.add_option( "--no-effective-length-correction", dest="no_effective_length_correction", action="store_true" ) - parser.add_option( "--no-length-correction", dest="no_length_correction", action="store_true" ) + parser.add_option( "--no-effective-length-correction", dest="no_effective_length_correction", action="store_true" ) + parser.add_option( "--no-length-correction", dest="no_length_correction", action="store_true" ) # Wrapper / Galaxy options. parser.add_option( '-A', '--assembled-isoforms-output', dest='assembled_isoforms_output_file', help='Assembled isoforms output file; formate is GTF.' ) - # Advanced Options: - parser.add_option( "--library-type",dest="library_type",help=' library prep used for input reads, default fr-unstranded') - parser.add_option( '-M','--mask-file', dest='mask_file', help='Tells Cufflinks to ignore all reads that could have come from transcripts in this GTF file. \ + # Advanced Options: + parser.add_option( "--library-type", dest="library_type", help=' library prep used for input reads, default fr-unstranded') + parser.add_option( '-M', '--mask-file', dest='mask_file', help='Tells Cufflinks to ignore all reads that could have come from transcripts in this GTF file. \ We recommend including any annotated rRNA, mitochondrial transcripts other abundant transcripts \ you wish to ignore in your analysis in this file. Due to variable efficiency of mRNA enrichment \ methods and rRNA depletion kits, masking these transcripts often improves the overall robustness \ of transcript abundance estimates.') parser.add_option( '-m', '--inner-mean-dist', dest='inner_mean_dist', help='This is the expected (mean) inner distance between mate pairs. \ For, example, for paired end runs with fragments selected at 300bp, \ - where each end is 50bp, you should set -r to be 200. The default is 45bp.') # cufflinks: --frag-len-mean + where each end is 50bp, you should set -r to be 200. The default is 45bp.') # cufflinks: --frag-len-mean parser.add_option( '-s', '--inner-dist-std-dev', dest='inner_dist_std_dev', help='The standard deviation for the distribution on inner distances between mate pairs. The default is 20bp.' ) # cufflinks: --frag-len-std-dev parser.add_option( '--max-mle-iterations', dest='max_mle_iterations', help='Sets the number of iterations allowed during maximum likelihood estimation of abundances. Default: 5000' ) @@ -55,17 +60,16 @@ parser.add_option( '--trim-3-avgcov-thresh', dest='trim_three_avgcov_thresh', help='Minimum average coverage required to attempt 3prime trimming. Default: 10' ) parser.add_option( '--trim-3-dropoff-frac', dest='trim_three_dropoff_frac', help='The fraction of average coverage below which to trim the 3prime end of an assembled transcript. Default: 0.1' ) - # Bias correction options. parser.add_option( '-b', dest='do_bias_correction', action="store_true", help='Providing Cufflinks with a multifasta file via this option instructs it to run our new bias detection and correction algorithm which can significantly improve accuracy of transcript abundance estimates.') parser.add_option( '', '--index', dest='index', help='The path of the reference genome' ) parser.add_option( '', '--ref_file', dest='ref_file', help='The reference dataset from the history' ) - + # Global model (for trackster). parser.add_option( '', '--global_model', dest='global_model_file', help='Global model used for computing on local data' ) - + (options, args) = parser.parse_args() - + # output version # of tool try: tmp = tempfile.NamedTemporaryFile().name @@ -84,7 +88,7 @@ raise Exception except: sys.stdout.write( 'Could not determine Cufflinks version\n' ) - + # If doing bias correction, set/link to sequence file. if options.do_bias_correction: if options.ref_file: @@ -98,27 +102,27 @@ seq_path = options.index # Build command. - + # Base; always use quiet mode to avoid problems with storing log output. cmd = "cufflinks -q --no-update-check" - + # Add options. if options.max_intron_len: - cmd += ( " -I %i" % int ( options.max_intron_len ) ) + cmd += ( " -I %i" % int( options.max_intron_len ) ) if options.min_isoform_fraction: - cmd += ( " -F %f" % float ( options.min_isoform_fraction ) ) + cmd += ( " -F %f" % float( options.min_isoform_fraction ) ) if options.pre_mrna_fraction: - cmd += ( " -j %f" % float ( options.pre_mrna_fraction ) ) + cmd += ( " -j %f" % float( options.pre_mrna_fraction ) ) if options.num_threads: - cmd += ( " -p %i" % int ( options.num_threads ) ) + cmd += ( " -p %i" % int( options.num_threads ) ) if options.GTF: cmd += ( " -G %s" % options.GTF ) if options.compatible_hits_norm: cmd += ( " --compatible-hits-norm" ) if options.GTFguide: cmd += ( " -g %s" % options.GTFguide ) - cmd += ( " --3-overhang-tolerance %i" % int ( options.three_overhang_tolerance ) ) - cmd += ( " --intron-overhang-tolerance %i" % int ( options.intron_overhang_tolerance ) ) + cmd += ( " --3-overhang-tolerance %i" % int( options.three_overhang_tolerance ) ) + cmd += ( " --intron-overhang-tolerance %i" % int( options.intron_overhang_tolerance ) ) if options.no_faux_reads: cmd += ( " --no-faux-reads" ) if options.multi_read_correct: @@ -129,27 +133,27 @@ if options.mask_file: cmd += ( " --mask-file %s" % options.mask_file ) if options.inner_mean_dist: - cmd += ( " -m %i" % int ( options.inner_mean_dist ) ) + cmd += ( " -m %i" % int( options.inner_mean_dist ) ) if options.inner_dist_std_dev: - cmd += ( " -s %i" % int ( options.inner_dist_std_dev ) ) + cmd += ( " -s %i" % int( options.inner_dist_std_dev ) ) if options.max_mle_iterations: - cmd += ( " --max-mle-iterations %i" % int ( options.max_mle_iterations ) ) + cmd += ( " --max-mle-iterations %i" % int( options.max_mle_iterations ) ) if options.junc_alpha: - cmd += ( " --junc-alpha %f" % float ( options.junc_alpha) ) + cmd += ( " --junc-alpha %f" % float( options.junc_alpha) ) if options.small_anchor_fraction: - cmd += ( " --small-anchor-fraction %f" % float (options.small_anchor_fraction ) ) + cmd += ( " --small-anchor-fraction %f" % float(options.small_anchor_fraction ) ) if options.overhang_tolerance: - cmd += ( " --overhang-tolerance %i" % int ( options.overhang_tolerance ) ) + cmd += ( " --overhang-tolerance %i" % int( options.overhang_tolerance ) ) if options.max_bundle_length: - cmd += ( " --max-bundle-length %i" % int ( options.max_bundle_length ) ) + cmd += ( " --max-bundle-length %i" % int( options.max_bundle_length ) ) if options.max_bundle_frags: - cmd += ( " --max-bundle-frags %i" % int ( options.max_bundle_frags ) ) + cmd += ( " --max-bundle-frags %i" % int( options.max_bundle_frags ) ) if options.min_intron_length: - cmd += ( " --min-intron-length %i" % int ( options.min_intron_length ) ) + cmd += ( " --min-intron-length %i" % int( options.min_intron_length ) ) if options.trim_three_avgcov_thresh: - cmd += ( " --trim-3-avgcov-thresh %i" % int ( options.trim_three_avgcov_thresh ) ) + cmd += ( " --trim-3-avgcov-thresh %i" % int( options.trim_three_avgcov_thresh ) ) if options.trim_three_dropoff_frac: - cmd += ( " --trim-3-dropoff-frac %f" % float ( options.trim_three_dropoff_frac ) ) + cmd += ( " --trim-3-dropoff-frac %f" % float( options.trim_three_dropoff_frac ) ) if options.do_bias_correction: cmd += ( " -b %s" % seq_path ) @@ -157,13 +161,13 @@ cmd += ( " --no-effective-length-correction" ) if options.no_length_correction: cmd += ( " --no-length-correction" ) - + # Add input files. cmd += " " + options.input - + # Debugging. print cmd - + # # Run command and handle output. # @@ -176,15 +180,15 @@ proc = subprocess.Popen( args=cmd, shell=True, stderr=tmp_stderr.fileno() ) returncode = proc.wait() tmp_stderr.close() - + # Error checking. if returncode != 0: - raise Exception, "return code = %i" % returncode - + raise Exception("return code = %i" % returncode) + # # Handle output. - # - + # + # Read standard error to get total map/upper quartile mass. total_map_mass = -1 tmp_stderr = open( tmp_name, 'r' ) @@ -193,21 +197,21 @@ total_map_mass = float( line.split(":")[1].strip() ) break tmp_stderr.close() - + # # If there's a global model provided, use model's total map mass # to adjust FPKM + confidence intervals. # - if options.global_model_file: + if options.global_model_file: # Global model is simply total map mass from original run. global_model_file = open( options.global_model_file, 'r' ) global_model_total_map_mass = float( global_model_file.readline() ) global_model_file.close() - + # Ratio of global model's total map mass to original run's map mass is # factor used to adjust FPKM. fpkm_map_mass_ratio = total_map_mass / global_model_total_map_mass - + # Update FPKM values in transcripts.gtf file. transcripts_file = open( "transcripts.gtf", 'r' ) tmp_transcripts = tempfile.NamedTemporaryFile( dir="." ).name @@ -223,11 +227,11 @@ transcripts_file.close() new_transcripts_file.close() shutil.copyfile( tmp_transcripts, "transcripts.gtf" ) - + # TODO: update expression files as well. - + # Set outputs. Transcript and gene expression handled by wrapper directives. - shutil.copyfile( "transcripts.gtf" , options.assembled_isoforms_output_file ) + shutil.copyfile( "transcripts.gtf", options.assembled_isoforms_output_file ) if total_map_mass > -1: f = open( "global_model.txt", 'w' ) f.write( "%f\n" % total_map_mass ) @@ -245,7 +249,7 @@ except OverflowError: pass tmp_stderr.close() - stop_err( 'Error running cufflinks.\n%s\n%s' % ( str( e ), stderr ) ) -if __name__=="__main__": __main__() +if __name__ == "__main__": + __main__()
--- a/cufflinks_wrapper.xml Wed Nov 26 13:50:22 2014 -0500 +++ b/cufflinks_wrapper.xml Tue Oct 13 12:37:52 2015 -0400 @@ -214,8 +214,8 @@ Cufflinks_ assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts. Cufflinks then estimates the relative abundances of these transcripts based on how many reads support each one. Please cite: Trapnell C, Williams BA, Pertea G, Mortazavi AM, Kwan G, van Baren MJ, Salzberg SL, Wold B, Pachter L. Transcript assembly and abundance estimation from RNA-Seq reveals thousands of new transcripts and switching among isoforms. Nature Biotechnology doi:10.1038/nbt.1621 -.. _Cufflinks: http://cufflinks.cbcb.umd.edu/ - +.. _Cufflinks: http://cole-trapnell-lab.github.io/cufflinks/ + ------ **Know what you are doing** @@ -224,7 +224,7 @@ There is no such thing (yet) as an automated gearshift in expression analysis. It is all like stick-shift driving in San Francisco. In other words, running this tool with default parameters will probably not give you meaningful results. A way to deal with this is to **understand** the parameters by carefully reading the `documentation`__ and experimenting. Fortunately, Galaxy makes experimenting easy. -.. __: http://cufflinks.cbcb.umd.edu/manual.html +.. __: http://cole-trapnell-lab.github.io/cufflinks/cufflinks/ ------