| Previous changeset 5:67695d7ff787 (2014-01-09) Next changeset 7:b77178f66fc3 (2015-11-11) |
|
Commit message:
Uploaded |
|
modified:
cuffcompare_wrapper.py cuffcompare_wrapper.xml test-data/cuffcompare_out5.gtf test-data/cuffcompare_out6.tracking test-data/cuffcompare_out7.txt tool_dependencies.xml |
|
added:
cuff_macros.xml |
| b |
| diff -r 67695d7ff787 -r 8e534225baa9 cuff_macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cuff_macros.xml Fri Dec 19 11:55:55 2014 -0500 |
| [ |
| @@ -0,0 +1,91 @@ +<macros> + <token name="@VERSION@">2.2.1</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="2.2.1">cufflinks</requirement> + <yield /> + </requirements> + </xml> + <xml name="stdio"> + <stdio> + <exit_code range="1:" /> + <exit_code range=":-1" /> + <regex match="Error:" /> + <regex match="Exception:" /> + </stdio> + </xml> + <xml name="condition_inputs"> + <!-- DEFAULT : use BAM/SAM files --> + <conditional name="in_type"> + <param name="set_in_type" type="select" label="Input data type" + help="CuffNorm supports either CXB (from cuffquant) or SAM/BAM input files. Mixing is not supported. Default: SAM/BAM"> + <option value="BAM">SAM/BAM</option> + <option value="CXB">Cuffquant (CXB)</option> + <option value="CONDITION_LIST">List of single replicate conditions</option> + <option value="CONDITION_REPLICATE_LIST">List of multiple replicate conditions</option> + </param> + <when value="BAM"> + <repeat name="conditions" title="Condition" min="2"> + <param name="name" title="Condition name" type="text" label="Name"/> + <param name="samples" label="Replicates" type="data" format="sam,bam" multiple="true"/> + </repeat> + </when> + <when value="CXB"> + <repeat name="conditions" title="Condition" min="2"> + <param name="name" title="Condition name" type="text" label="Name"/> + <param name="samples" label="Replicates" type="data" format="cxb" multiple="true"/> + </repeat> + </when> + <when value="CONDITION_LIST"> + <param name="conditions" title="List of Conditions" type="data_collection" collection_type="list" /> + </when> + <when value="CONDITION_REPLICATE_LIST"> + <param name="conditions" title="List of Conditions" type="data_collection" collection_type="list:list" /> + </when> + </conditional> + </xml> + <token name="@CONDITION_SAMPLES@"> + #if $in_type.set_in_type in ['BAM', 'CXB'] + #for $condition in $in_type.conditions: + #set samples = ','.join( [ str( $sample ) for $sample in $condition.samples ] ) + $samples + #end for + #elif $in_type.set_in_type == 'CONDITION_LIST' + #for $sample in $in_type.conditions: + $sample + #end for + #elif $in_type.set_in_type == 'CONDITION_REPLICATE_LIST' + #for $condition_list in $in_type.conditions: + #set samples = ','.join( [ str( $sample ) for $sample in $condition_list ] ) + $samples + #end for + #end if + </token> + <token name="@CONDITION_LABELS@"> + #import re + #if $in_type.set_in_type in ['BAM', 'CXB'] + #set labels = '\'' + '\',\''.join( [ str( $condition.name ) for $condition in $in_type.conditions ] ) + '\'' + #elif $in_type.set_in_type in ['CONDITION_LIST', 'CONDITION_REPLICATE_LIST'] + #set labels = '\'' + '\',\''.join( map(lambda x: re.sub('[^\w\-_]', '_', x), $in_type.conditions.keys() ) ) + '\'' + #end if + --labels $labels + </token> + <xml name="cufflinks_gtf_inputs"> + <param format="gtf" name="inputs" type="data" label="GTF file(s) produced by Cufflinks" help="" multiple="true" /> + <repeat name="additional_inputs" title="Additional GTF Inputs (Lists)"> + <param format="gtf" name="additional_inputs" type="data_collection" label="GTF file(s) produced by Cufflinks" help="" /> + </repeat> + </xml> + <token name="@CUFFLINKS_GTF_INPUTS@"> + ## Inputs. + #for $input_file in $inputs: + "${input_file}" + #end for + #for $additional_input in $additional_inputs: + #for $input_file in $additional_input.additional_inputs: + "${input_file}" + #end for + #end for + </token> + <token name="@HAS_MULTIPLE_INPUTS@">getattr(inputs, "__len__", [].__len__)() >= 2</token> +</macros> \ No newline at end of file |
| b |
| diff -r 67695d7ff787 -r 8e534225baa9 cuffcompare_wrapper.py --- a/cuffcompare_wrapper.py Thu Jan 09 14:27:37 2014 -0500 +++ b/cuffcompare_wrapper.py Fri Dec 19 11:55:55 2014 -0500 |
| b |
| @@ -12,9 +12,17 @@ #Parse Command Line parser = optparse.OptionParser() parser.add_option( '-r', dest='ref_annotation', help='An optional "reference" annotation GTF. Each sample is matched against this file, and sample isoforms are tagged as overlapping, matching, or novel where appropriate. See the refmap and tmap output file descriptions below.' ) - parser.add_option( '-R', action="store_true", dest='ignore_nonoverlap', help='If -r was specified, this option causes cuffcompare to ignore reference transcripts that are not overlapped by any transcript in one of cuff1.gtf,...,cuffN.gtf. Useful for ignoring annotated transcripts that are not present in your RNA-Seq samples and thus adjusting the "sensitivity" calculation in the accuracy report written in the transcripts accuracy file' ) + parser.add_option( '-R', action="store_true", dest='ignore_nonoverlap_reference', help='If -r was specified, this option causes cuffcompare to ignore reference transcripts that are not overlapped by any transcript in one of cuff1.gtf,...,cuffN.gtf. Useful for ignoring annotated transcripts that are not present in your RNA-Seq samples and thus adjusting the "sensitivity" calculation in the accuracy report written in the transcripts accuracy file' ) + parser.add_option( '-Q', action="store_true", dest='ignore_nonoverlap_transfrag', help='If -r was specified, this option causes cuffcompare to consider only the input transcripts that overlap any of the reference transcripts (Sp correction); Warning: this will discard all "novel" loci!)' ) + parser.add_option( '-s', dest='use_seq_data', action="store_true", help='Causes cuffcompare to look into for fasta files with the underlying genomic sequences (one file per contig) against which your reads were aligned for some optional classification functions. For example, Cufflinks transcripts consisting mostly of lower-case bases are classified as repeats. Note that <seq_dir> must contain one fasta file per reference chromosome, and each file must be named after the chromosome, and have a .fa or .fasta extension.') + parser.add_option( '-M', action="store_true", dest='discard_single_exon_all', help='discard (ignore) single-exon transfrags and reference transcript') + parser.add_option( '-N', action="store_true", dest='discard_single_exon_ref', help='discard (ignore) single-exon reference transcripts') + parser.add_option( '-e', dest='max_dist_exon', help='Max. Distance for assessing exon accuracy" help="max. distance (range) allowed from free ends of terminal exons of reference transcripts when assessing exon accuracy. Default: 100') + parser.add_option( '-d', dest='max_dist_group', help='Max.Distance for transcript grouping" help="max. distance (range) for grouping transcript start sites. Default: 100') + parser.add_option( '-F', action="store_true", dest='discard_redundant_intron_transfrags', help='Discard intron-redundant transfrags if they share the 5-prime end (if they differ only at the 3-prime end)') + # Wrapper / Galaxy options. 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' ) @@ -63,11 +71,22 @@ # Add options. if options.ref_annotation: cmd += " -r %s " % options.ref_annotation - if options.ignore_nonoverlap: + if options.ignore_nonoverlap_reference: cmd += " -R " + if options.ignore_nonoverlap_transfrag: + cmd += " -Q " if options.use_seq_data: cmd += " -s %s " % seq_path - + if options.discard_single_exon_all: + cmd += " -M " + if options.discard_single_exon_ref: + cmd += " -N " + if options.max_dist_exon: + cmd += " -e %i " % int( options.max_dist_exon ) + if options.max_dist_group: + cmd += " -d %i " % int( options.max_dist_group ) + if options.discard_redundant_intron_transfrags: + cmd += " -F " # Add input files. # Need to symlink inputs so that output files are written to temp directory. |
| b |
| diff -r 67695d7ff787 -r 8e534225baa9 cuffcompare_wrapper.xml --- a/cuffcompare_wrapper.xml Thu Jan 09 14:27:37 2014 -0500 +++ b/cuffcompare_wrapper.xml Fri Dec 19 11:55:55 2014 -0500 |
| b |
| b'@@ -1,19 +1,23 @@\n-<tool id="cuffcompare" name="Cuffcompare" version="0.0.6">\n- <!-- Wrapper supports Cuffcompare versions v1.3.0 and newer -->\n+<tool id="cuffcompare" name="Cuffcompare" version="2.2.1.0">\n <description>compare assembled transcripts to a reference annotation and track Cufflinks transcripts across multiple experiments</description>\n- <requirements>\n- <requirement type="package" version="2.1.1">cufflinks</requirement>\n- </requirements>\n+ <expand macro="requirements" />\n+ <expand macro="stdio" />\n+ <macros>\n+ <import>cuff_macros.xml</import>\n+ </macros>\n <version_command>cuffcompare 2>&1 | head -n 1</version_command>\n <command interpreter="python">\n cuffcompare_wrapper.py \n- \n ## Use annotation reference?\n #if $annotation.use_ref_annotation == "Yes":\n -r $annotation.reference_annotation\n #if $annotation.ignore_nonoverlapping_reference:\n -R\n #end if\n+ #if $annotation.ignore_nonoverlapping_transfrags:\n+ -Q\n+ #end if\n+\n #end if\n \n ## Use sequence data?\n@@ -26,35 +30,38 @@\n #end if\n #end if\n \n+ $discard_single_exon\n+\n+ -e $max_dist_exon\n+ -d $max_dist_group\n+\n+ #if $discard_intron_redundant_transfrags:\n+ -F\n+ #end if \n+\n ## Outputs.\n --combined-transcripts=${transcripts_combined}\n- \n- ## Inputs.\n- ${first_input}\n- #for $input_file in $input_files:\n- ${input_file.additional_input}\n- #end for\n- \n+\n+ @CUFFLINKS_GTF_INPUTS@\n </command>\n <inputs>\n- <param format="gtf" name="first_input" type="data" label="GTF file produced by Cufflinks" help=""/>\n- <repeat name="input_files" title="Additional GTF Input Files">\n- <param format="gtf" name="additional_input" type="data" label="GTF file produced by Cufflinks" help=""/>\n- </repeat>\n+ <expand macro="cufflinks_gtf_inputs" />\n <conditional name="annotation">\n <param name="use_ref_annotation" type="select" label="Use Reference Annotation">\n <option value="No">No</option>\n <option value="Yes">Yes</option>\n </param>\n <when value="Yes">\n- <param format="gff3,gtf" name="reference_annotation" type="data" label="Reference Annotation" help="Requires an annotation file in GFF3 or GTF format."/> \n- <param name="ignore_nonoverlapping_reference" type="boolean" label="Ignore reference transcripts that are not overlapped by any transcript in input files"/>\n+ <param format="gff3,gtf" name="reference_annotation" type="data" label="Reference Annotation" help="Requires an annotation file in GFF3 or GTF format."/>\n+ <param name="ignore_nonoverlapping_reference" type="boolean" label="Ignore reference transcripts that are not overlapped by any input transfrags" help="consider only the reference transcripts that overlap any of the input transfrags (Sn correction)" />\n+ <param name="ignore_nonoverlapping_transfrags" type="boolean" label="Ignore input transcripts that are not overlapped by any reference transcripts" help="consider only the input transcripts that overlap any of the reference transcripts (Sp correction). Warning: this will discard all \'novel\' loci!" />\n </when>\n <when value="No">\n </when>\n </conditional>\n <conditional name="seq_data">\n- <param name="use_seq_data" type="select" label="Use Sequence Data" help="Use sequence data for some optional classification functions, including the addition of the p_id attribute required by Cuffdiff.">\n+ <param name="use_se'..b'ce estimation from RNA-Seq reveals thousands of new transcripts and switching among isoforms. Nature Biotechnology doi:10.1038/nbt.1621\n \n-.. _Cufflinks: http://cufflinks.cbcb.umd.edu/\n- \n+.. _Cufflinks: http://cole-trapnell-lab.github.io/cufflinks/\n+\n ------\n \n **Know what you are doing**\n@@ -143,7 +165,7 @@\n \n 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.\n \n-.. __: http://cufflinks.cbcb.umd.edu/manual.html#cuffcompare\n+.. __: http://cole-trapnell-lab.github.io/cufflinks/cuffcompare/\n \n ------\n \n@@ -174,7 +196,7 @@\n \n Here\'s an example of a line from the tracking file::\n \n- TCONS_00000045 XLOC_000023 Tcea|uc007afj.1\tj\t\\\n+ TCONS_00000045 XLOC_000023 Tcea|uc007afj.1 j \\\n q1:exp.115|exp.115.0|100|3.061355|0.350242|0.350207 \\\n q2:60hr.292|60hr.292.0|100|4.094084|0.000000|0.000000\n \n@@ -197,18 +219,18 @@\n \n If you ran cuffcompare with the -r option, tracking rows will contain the following values. If you did not use -r, the rows will all contain "-" in their class code column::\n \n- Priority\t Code\t Description\n+ Priority Code Description\n ---------------------------------\n- 1\t =\t Match\n- 2\t c\t Contained\t\n- 3\t j\t New isoform\t\n- 4\t e\t A single exon transcript overlapping a reference exon and at least 10 bp of a reference intron, indicating a possible pre-mRNA fragment.\t\n- 5\t i\t A single exon transcript falling entirely with a reference intron\t\n- 6\t r\t Repeat. Currently determined by looking at the reference sequence and applied to transcripts where at least 50% of the bases are lower case\t\n- 7\t p\t Possible polymerase run-on fragment\t\n- 8\t u\t Unknown, intergenic transcript\t\n- 9\t o\t Unknown, generic overlap with reference\t\n- 10 .\t (.tracking file only, indicates multiple classifications)\n+ 1 = Match\n+ 2 c Contained \n+ 3 j New isoform \n+ 4 e A single exon transcript overlapping a reference exon and at least 10 bp of a reference intron, indicating a possible pre-mRNA fragment. \n+ 5 i A single exon transcript falling entirely with a reference intron \n+ 6 r Repeat. Currently determined by looking at the reference sequence and applied to transcripts where at least 50% of the bases are lower case \n+ 7 p Possible polymerase run-on fragment \n+ 8 u Unknown, intergenic transcript \n+ 9 o Unknown, generic overlap with reference \n+ 10 . (.tracking file only, indicates multiple classifications)\n \n -------\n \n@@ -225,4 +247,7 @@\n -r An optional "reference" annotation GTF. Each sample is matched against this file, and sample isoforms are tagged as overlapping, matching, or novel where appropriate. See the refmap and tmap output file descriptions below.\n -R If -r was specified, this option causes cuffcompare to ignore reference transcripts that are not overlapped by any transcript in one of cuff1.gtf,...,cuffN.gtf. Useful for ignoring annotated transcripts that are not present in your RNA-Seq samples and thus adjusting the "sensitivity" calculation in the accuracy report written in the transcripts_accuracy file\n </help>\n+ <citations>\n+ <citation type="doi">10.1038/nbt.1621</citation>\n+ </citations>\n </tool>\n' |
| b |
| diff -r 67695d7ff787 -r 8e534225baa9 test-data/cuffcompare_out5.gtf --- a/test-data/cuffcompare_out5.gtf Thu Jan 09 14:27:37 2014 -0500 +++ b/test-data/cuffcompare_out5.gtf Fri Dec 19 11:55:55 2014 -0500 |
| b |
| b'@@ -22,67 +22,67 @@\n chr1\tCufflinks\texon\t3197247\t3197273\t.\t.\t.\tgene_id "XLOC_000022"; transcript_id "TCONS_00000018"; exon_number "1"; oId "CUFF.57.1"; class_code "u"; tss_id "TSS25";\n chr1\tCufflinks\texon\t3197347\t3197373\t.\t.\t.\tgene_id "XLOC_000023"; transcript_id "TCONS_00000019"; exon_number "1"; oId "CUFF.59.1"; class_code "u"; tss_id "TSS26";\n chr1\tCufflinks\texon\t3197426\t3197452\t.\t.\t.\tgene_id "XLOC_000024"; transcript_id "TCONS_00000060"; exon_number "1"; oId "CUFF.19.1"; class_code "u"; tss_id "TSS27";\n-chr1\tCufflinks\texon\t3200023\t3200191\t.\t.\t.\tgene_id "XLOC_000025"; transcript_id "TCONS_00000020"; exon_number "1"; oId "CUFF.7.1"; class_code "u"; tss_id "TSS28";\n+chr1\tCufflinks\texon\t3200023\t3200191\t.\t.\t.\tgene_id "XLOC_000025"; transcript_id "TCONS_00000020"; exon_number "1"; oId "CUFF.7.1"; class_code "."; tss_id "TSS28";\n chr1\tCufflinks\texon\t3200326\t3200352\t.\t.\t.\tgene_id "XLOC_000026"; transcript_id "TCONS_00000021"; exon_number "1"; oId "CUFF.5.1"; class_code "u"; tss_id "TSS29";\n-chr1\tCufflinks\texon\t3200431\t3200457\t.\t.\t.\tgene_id "XLOC_000027"; transcript_id "TCONS_00000062"; exon_number "1"; oId "CUFF.21.1"; class_code "u"; tss_id "TSS30";\n-chr1\tCufflinks\texon\t3201008\t3201039\t.\t.\t.\tgene_id "XLOC_000028"; transcript_id "TCONS_00000063"; exon_number "1"; oId "CUFF.26.1"; class_code "u"; tss_id "TSS31";\n-chr1\tCufflinks\texon\t3201078\t3201481\t.\t.\t.\tgene_id "XLOC_000029"; transcript_id "TCONS_00000022"; exon_number "1"; oId "CUFF.9.1"; class_code "u"; tss_id "TSS32";\n-chr1\tCufflinks\texon\t3201597\t3201666\t.\t.\t.\tgene_id "XLOC_000030"; transcript_id "TCONS_00000065"; exon_number "1"; oId "CUFF.29.1"; class_code "u"; tss_id "TSS33";\n+chr1\tCufflinks\texon\t3200431\t3200457\t.\t.\t.\tgene_id "XLOC_000027"; transcript_id "TCONS_00000061"; exon_number "1"; oId "CUFF.21.1"; class_code "u"; tss_id "TSS30";\n+chr1\tCufflinks\texon\t3201008\t3201039\t.\t.\t.\tgene_id "XLOC_000028"; transcript_id "TCONS_00000062"; exon_number "1"; oId "CUFF.26.1"; class_code "u"; tss_id "TSS31";\n+chr1\tCufflinks\texon\t3201078\t3201481\t.\t.\t.\tgene_id "XLOC_000029"; transcript_id "TCONS_00000022"; exon_number "1"; oId "CUFF.9.1"; class_code "."; tss_id "TSS32";\n+chr1\tCufflinks\texon\t3201597\t3201666\t.\t.\t.\tgene_id "XLOC_000030"; transcript_id "TCONS_00000063"; exon_number "1"; oId "CUFF.29.1"; class_code "u"; tss_id "TSS33";\n chr1\tCufflinks\texon\t3201673\t3201699\t.\t.\t.\tgene_id "XLOC_000031"; transcript_id "TCONS_00000023"; exon_number "1"; oId "CUFF.11.1"; class_code "u"; tss_id "TSS34";\n-chr1\tCufflinks\texon\t3201726\t3201809\t.\t.\t.\tgene_id "XLOC_000032"; transcript_id "TCONS_00000066"; exon_number "1"; oId "CUFF.31.1"; class_code "u"; tss_id "TSS35";\n-chr1\tCufflinks\texon\t3211522\t3211561\t.\t.\t.\tgene_id "XLOC_000033"; transcript_id "TCONS_00000067"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.33.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS36";\n+chr1\tCufflinks\texon\t3201726\t3201809\t.\t.\t.\tgene_id "XLOC_000032"; transcript_id "TCONS_00000064"; exon_number "1"; oId "CUFF.31.1"; class_code "u"; tss_id "TSS35";\n+chr1\tCufflinks\texon\t3211522\t3211561\t.\t.\t.\tgene_id "XLOC_000033"; transcript_id "TCONS_00000065"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.33.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS36";\n chr1\tCufflinks\texon\t3212214\t3212292\t.\t.\t.\tgene_id "XLOC_000034"; transcript_id "TCONS_00000024"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.15.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS37";\n chr1\tCufflinks\texon\t3212368\t3212439\t.\t.\t.\tgene_id "XLOC_000035"; transcript_id "TCONS_00000025"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.19.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS38";\n-chr1\tCufflinks\texon\t3212718\t3212801\t.\t.\t.\tgene_id "XLOC_000036"; transcript_id "TCONS_00000068"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.35.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS39";\n+chr1\tCufflinks\texon\t3212718\t3212801\t.\t.\t.\tgene_id "XLOC_000036"; transcript_id "TCONS_00000066"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.35.1"; nearest_ref "Xkr4"; class_code "i"; '..b'.\tgene_id "XLOC_000072"; transcript_id "TCONS_00000092"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.87.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS78";\n chr1\tCufflinks\texon\t3363754\t3363849\t.\t.\t.\tgene_id "XLOC_000073"; transcript_id "TCONS_00000042"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.83.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS79";\n-chr1\tCufflinks\texon\t3364872\t3364919\t.\t.\t.\tgene_id "XLOC_000074"; transcript_id "TCONS_00000095"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.89.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS80";\n+chr1\tCufflinks\texon\t3364872\t3364919\t.\t.\t.\tgene_id "XLOC_000074"; transcript_id "TCONS_00000093"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.89.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS80";\n chr1\tCufflinks\texon\t3367136\t3367162\t.\t.\t.\tgene_id "XLOC_000075"; transcript_id "TCONS_00000043"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.85.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS81";\n-chr1\tCufflinks\texon\t3367211\t3367237\t.\t.\t.\tgene_id "XLOC_000076"; transcript_id "TCONS_00000096"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.91.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS82";\n+chr1\tCufflinks\texon\t3367211\t3367237\t.\t.\t.\tgene_id "XLOC_000076"; transcript_id "TCONS_00000094"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.91.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS82";\n chr1\tCufflinks\texon\t3367334\t3367382\t.\t.\t.\tgene_id "XLOC_000077"; transcript_id "TCONS_00000044"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.87.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS83";\n-chr1\tCufflinks\texon\t3369581\t3369607\t.\t.\t.\tgene_id "XLOC_000078"; transcript_id "TCONS_00000097"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.93.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS84";\n-chr1\tCufflinks\texon\t3375002\t3375028\t.\t.\t.\tgene_id "XLOC_000079"; transcript_id "TCONS_00000098"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.95.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS85";\n+chr1\tCufflinks\texon\t3369581\t3369607\t.\t.\t.\tgene_id "XLOC_000078"; transcript_id "TCONS_00000095"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.93.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS84";\n+chr1\tCufflinks\texon\t3375002\t3375028\t.\t.\t.\tgene_id "XLOC_000079"; transcript_id "TCONS_00000096"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.95.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS85";\n chr1\tCufflinks\texon\t3377212\t3377262\t.\t.\t.\tgene_id "XLOC_000080"; transcript_id "TCONS_00000045"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.89.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS86";\n-chr1\tCufflinks\texon\t3379889\t3379915\t.\t.\t.\tgene_id "XLOC_000081"; transcript_id "TCONS_00000099"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.97.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS87";\n-chr1\tCufflinks\texon\t3386740\t3386836\t.\t.\t.\tgene_id "XLOC_000082"; transcript_id "TCONS_00000100"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.99.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS88";\n+chr1\tCufflinks\texon\t3379889\t3379915\t.\t.\t.\tgene_id "XLOC_000081"; transcript_id "TCONS_00000097"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.97.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS87";\n+chr1\tCufflinks\texon\t3386740\t3386836\t.\t.\t.\tgene_id "XLOC_000082"; transcript_id "TCONS_00000098"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.99.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS88";\n chr1\tCufflinks\texon\t3391326\t3391352\t.\t.\t.\tgene_id "XLOC_000083"; transcript_id "TCONS_00000046"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.91.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS89";\n chr1\tCufflinks\texon\t3435842\t3435880\t.\t.\t.\tgene_id "XLOC_000084"; transcript_id "TCONS_00000047"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.93.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS90";\n chr1\tCufflinks\texon\t3447762\t3447788\t.\t.\t.\tgene_id "XLOC_000085"; transcript_id "TCONS_00000048"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.95.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS91";\n' |
| b |
| diff -r 67695d7ff787 -r 8e534225baa9 test-data/cuffcompare_out6.tracking --- a/test-data/cuffcompare_out6.tracking Thu Jan 09 14:27:37 2014 -0500 +++ b/test-data/cuffcompare_out6.tracking Fri Dec 19 11:55:55 2014 -0500 |
| b |
| b'@@ -17,9 +17,9 @@\n TCONS_00000017\tXLOC_000021\t-\tu\tq1:CUFF.55|CUFF.55.1|100|31.293533|0.000000|75.549272|2.000000|-\t-\n TCONS_00000018\tXLOC_000022\t-\tu\tq1:CUFF.57|CUFF.57.1|100|15.646767|0.000000|46.940300|1.000000|-\t-\n TCONS_00000019\tXLOC_000023\t-\tu\tq1:CUFF.59|CUFF.59.1|100|15.646767|0.000000|46.940300|1.000000|-\t-\n-TCONS_00000020\tXLOC_000025\t-\tu\tq1:CUFF.7|CUFF.7.1|100|9.999117|0.000000|19.998234|0.639053|-\t-\n+TCONS_00000020\tXLOC_000025\t-\t.\tq1:CUFF.7|CUFF.7.1|100|9.999117|0.000000|19.998234|0.639053|169\tq2:CUFF.23|CUFF.23.1|100|16.205195|0.000000|34.917342|0.920455|88\n TCONS_00000021\tXLOC_000026\t-\tu\tq1:CUFF.5|CUFF.5.1|100|31.293533|0.000000|75.549272|2.000000|-\t-\n-TCONS_00000022\tXLOC_000029\t-\tu\tq1:CUFF.9|CUFF.9.1|100|17.776896|9.153835|26.399957|1.136139|-\t-\n+TCONS_00000022\tXLOC_000029\t-\t.\tq1:CUFF.9|CUFF.9.1|100|17.776896|9.153835|26.399957|1.136139|404\tq2:CUFF.25|CUFF.25.1|100|35.211287|0.000000|85.007567|2.000000|27\n TCONS_00000023\tXLOC_000031\t-\tu\tq1:CUFF.11|CUFF.11.1|100|31.293533|0.000000|75.549272|2.000000|-\t-\n TCONS_00000024\tXLOC_000034\tXkr4|Xkr4\ti\tq1:CUFF.15|CUFF.15.1|100|10.695258|0.000000|25.820637|0.683544|-\t-\n TCONS_00000025\tXLOC_000035\tXkr4|Xkr4\ti\tq1:CUFF.19|CUFF.19.1|100|29.337687|3.097262|55.578113|1.875000|-\t-\n@@ -58,43 +58,41 @@\n TCONS_00000058\tXLOC_000013\t-\tu\t-\tq2:CUFF.15|CUFF.15.1|100|35.211287|0.000000|85.007567|2.000000|-\n TCONS_00000059\tXLOC_000018\t-\tu\t-\tq2:CUFF.17|CUFF.17.1|100|35.211287|0.000000|85.007567|2.000000|-\n TCONS_00000060\tXLOC_000024\t-\tu\t-\tq2:CUFF.19|CUFF.19.1|100|35.211287|0.000000|85.007567|2.000000|-\n-TCONS_00000061\tXLOC_000025\t-\tu\t-\tq2:CUFF.23|CUFF.23.1|100|16.205195|0.000000|34.917342|0.920455|-\n-TCONS_00000062\tXLOC_000027\t-\tu\t-\tq2:CUFF.21|CUFF.21.1|100|35.211287|0.000000|85.007567|2.000000|-\n-TCONS_00000063\tXLOC_000028\t-\tu\t-\tq2:CUFF.26|CUFF.26.1|100|29.709524|0.000000|71.725135|1.687500|-\n-TCONS_00000064\tXLOC_000029\t-\tu\t-\tq2:CUFF.25|CUFF.25.1|100|35.211287|0.000000|85.007567|2.000000|-\n-TCONS_00000065\tXLOC_000030\t-\tu\t-\tq2:CUFF.29|CUFF.29.1|100|13.581496|0.000000|32.788633|0.771429|-\n-TCONS_00000066\tXLOC_000032\t-\tu\t-\tq2:CUFF.31|CUFF.31.1|100|22.635827|0.000000|45.271655|1.285714|-\n-TCONS_00000067\tXLOC_000033\tXkr4|Xkr4\ti\t-\tq2:CUFF.33|CUFF.33.1|100|23.767619|0.000000|57.380108|1.350000|-\n-TCONS_00000068\tXLOC_000036\tXkr4|Xkr4\ti\t-\tq2:CUFF.35|CUFF.35.1|100|11.317914|0.000000|27.323861|0.642857|-\n-TCONS_00000069\tXLOC_000037\tXkr4|Xkr4\ti\t-\tq2:CUFF.37|CUFF.37.1|100|11.500461|0.000000|24.780049|0.653226|-\n-TCONS_00000070\tXLOC_000038\tXkr4|Xkr4\ti\t-\tq2:CUFF.39|CUFF.39.1|100|52.816931|0.000000|113.804669|3.000000|-\n-TCONS_00000071\tXLOC_000039\tXkr4|Xkr4\ti\t-\tq2:CUFF.41|CUFF.41.1|100|43.213852|0.000000|93.112911|2.454545|-\n-TCONS_00000072\tXLOC_000041\tXkr4|Xkr4\ti\t-\tq2:CUFF.43|CUFF.43.1|100|23.474191|0.000000|46.948383|1.333333|-\n-TCONS_00000073\tXLOC_000043\tXkr4|Xkr4\ti\t-\tq2:CUFF.45|CUFF.45.1|100|20.667495|0.000000|49.895746|1.173913|-\n-TCONS_00000074\tXLOC_000045\tXkr4|Xkr4\ti\t-\tq2:CUFF.47|CUFF.47.1|100|35.211287|0.000000|85.007567|2.000000|-\n-TCONS_00000075\tXLOC_000047\tXkr4|Xkr4\ti\t-\tq2:CUFF.49|CUFF.49.1|100|35.211287|0.000000|85.007567|2.000000|-\n-TCONS_00000076\tXLOC_000049\tXkr4|Xkr4\ti\t-\tq2:CUFF.51|CUFF.51.1|100|14.948188|7.228977|22.667399|0.849057|-\n-TCONS_00000077\tXLOC_000050\tXkr4|Xkr4\ti\t-\tq2:CUFF.53|CUFF.53.1|100|52.816931|0.000000|113.804669|3.000000|-\n-TCONS_00000078\tXLOC_000051\tXkr4|Xkr4\ti\t-\tq2:CUFF.55|CUFF.55.1|100|35.211287|0.000000|85.007567|2.000000|-\n-TCONS_00000079\tXLOC_000053\tXkr4|Xkr4\ti\t-\tq2:CUFF.57|CUFF.57.1|100|35.211287|0.000000|85.007567|2.000000|-\n-TCONS_00000080\tXLOC_000054\tXkr4|Xkr4\ti\t-\tq2:CUFF.59|CUFF.59.1|100|35.211287|0.000000|85.007567|2.000000|-\n-TCONS_00000081\tXLOC_000055\tXkr4|Xkr4\ti\t-\tq2:CUFF.61|CUFF.61.1|100|13.204233|0.000000|31.877838|0.750000|-\n-TCONS_00000082\tXLOC_000056\tXkr4|Xkr4\ti\t-\tq2:CUFF.63|CUFF.63.1|100|35.211287|0.000000|85.007567|2.000000|-\n-TCONS_00000083\tXLOC_000058\tXkr4|Xkr4\ti\t-\tq2:CUFF.65|CUFF.65.1|100|31.170648|0.000000|62.341295|1.770492|-\n-TCONS_00000084\tXLOC_000'..b'UFF.21|CUFF.21.1|100|35.211287|0.000000|85.007567|2.000000|-\n+TCONS_00000062\tXLOC_000028\t-\tu\t-\tq2:CUFF.26|CUFF.26.1|100|29.709524|0.000000|71.725135|1.687500|-\n+TCONS_00000063\tXLOC_000030\t-\tu\t-\tq2:CUFF.29|CUFF.29.1|100|13.581496|0.000000|32.788633|0.771429|-\n+TCONS_00000064\tXLOC_000032\t-\tu\t-\tq2:CUFF.31|CUFF.31.1|100|22.635827|0.000000|45.271655|1.285714|-\n+TCONS_00000065\tXLOC_000033\tXkr4|Xkr4\ti\t-\tq2:CUFF.33|CUFF.33.1|100|23.767619|0.000000|57.380108|1.350000|-\n+TCONS_00000066\tXLOC_000036\tXkr4|Xkr4\ti\t-\tq2:CUFF.35|CUFF.35.1|100|11.317914|0.000000|27.323861|0.642857|-\n+TCONS_00000067\tXLOC_000037\tXkr4|Xkr4\ti\t-\tq2:CUFF.37|CUFF.37.1|100|11.500461|0.000000|24.780049|0.653226|-\n+TCONS_00000068\tXLOC_000038\tXkr4|Xkr4\ti\t-\tq2:CUFF.39|CUFF.39.1|100|52.816931|0.000000|113.804669|3.000000|-\n+TCONS_00000069\tXLOC_000039\tXkr4|Xkr4\ti\t-\tq2:CUFF.41|CUFF.41.1|100|43.213852|0.000000|93.112911|2.454545|-\n+TCONS_00000070\tXLOC_000041\tXkr4|Xkr4\ti\t-\tq2:CUFF.43|CUFF.43.1|100|23.474191|0.000000|46.948383|1.333333|-\n+TCONS_00000071\tXLOC_000043\tXkr4|Xkr4\ti\t-\tq2:CUFF.45|CUFF.45.1|100|20.667495|0.000000|49.895746|1.173913|-\n+TCONS_00000072\tXLOC_000045\tXkr4|Xkr4\ti\t-\tq2:CUFF.47|CUFF.47.1|100|35.211287|0.000000|85.007567|2.000000|-\n+TCONS_00000073\tXLOC_000047\tXkr4|Xkr4\ti\t-\tq2:CUFF.49|CUFF.49.1|100|35.211287|0.000000|85.007567|2.000000|-\n+TCONS_00000074\tXLOC_000049\tXkr4|Xkr4\ti\t-\tq2:CUFF.51|CUFF.51.1|100|14.948188|7.228977|22.667399|0.849057|-\n+TCONS_00000075\tXLOC_000050\tXkr4|Xkr4\ti\t-\tq2:CUFF.53|CUFF.53.1|100|52.816931|0.000000|113.804669|3.000000|-\n+TCONS_00000076\tXLOC_000051\tXkr4|Xkr4\ti\t-\tq2:CUFF.55|CUFF.55.1|100|35.211287|0.000000|85.007567|2.000000|-\n+TCONS_00000077\tXLOC_000053\tXkr4|Xkr4\ti\t-\tq2:CUFF.57|CUFF.57.1|100|35.211287|0.000000|85.007567|2.000000|-\n+TCONS_00000078\tXLOC_000054\tXkr4|Xkr4\ti\t-\tq2:CUFF.59|CUFF.59.1|100|35.211287|0.000000|85.007567|2.000000|-\n+TCONS_00000079\tXLOC_000055\tXkr4|Xkr4\ti\t-\tq2:CUFF.61|CUFF.61.1|100|13.204233|0.000000|31.877838|0.750000|-\n+TCONS_00000080\tXLOC_000056\tXkr4|Xkr4\ti\t-\tq2:CUFF.63|CUFF.63.1|100|35.211287|0.000000|85.007567|2.000000|-\n+TCONS_00000081\tXLOC_000058\tXkr4|Xkr4\ti\t-\tq2:CUFF.65|CUFF.65.1|100|31.170648|0.000000|62.341295|1.770492|-\n+TCONS_00000082\tXLOC_000059\tXkr4|Xkr4\ti\t-\tq2:CUFF.69|CUFF.69.1|100|18.799247|8.750627|28.847866|1.067797|-\n+TCONS_00000083\tXLOC_000060\tXkr4|Xkr4\ti\t-\tq2:CUFF.67|CUFF.67.1|100|15.681351|3.378764|27.983938|0.890700|-\n+TCONS_00000084\tXLOC_000061\tXkr4|Xkr4\ti\t-\tq2:CUFF.71|CUFF.71.1|100|22.635827|0.000000|54.647722|1.285714|-\n+TCONS_00000085\tXLOC_000063\tXkr4|Xkr4\ti\t-\tq2:CUFF.73|CUFF.73.1|100|35.211287|0.000000|85.007567|2.000000|-\n+TCONS_00000086\tXLOC_000064\tXkr4|Xkr4\ti\t-\tq2:CUFF.75|CUFF.75.1|100|52.816931|0.000000|113.804669|3.000000|-\n+TCONS_00000087\tXLOC_000066\tXkr4|Xkr4\ti\t-\tq2:CUFF.77|CUFF.77.1|100|17.605644|0.000000|52.816931|1.000000|-\n+TCONS_00000088\tXLOC_000067\tXkr4|Xkr4\ti\t-\tq2:CUFF.79|CUFF.79.1|100|13.390208|0.000000|32.326821|0.760563|-\n+TCONS_00000089\tXLOC_000068\tXkr4|Xkr4\ti\t-\tq2:CUFF.81|CUFF.81.1|100|11.211141|1.183592|21.238690|0.636792|-\n+TCONS_00000090\tXLOC_000069\tXkr4|Xkr4\ti\t-\tq2:CUFF.83|CUFF.83.1|100|21.126772|0.000000|51.004540|1.200000|-\n+TCONS_00000091\tXLOC_000070\tXkr4|Xkr4\ti\t-\tq2:CUFF.85|CUFF.85.1|100|19.014095|0.000000|38.028190|1.080000|-\n+TCONS_00000092\tXLOC_000072\tXkr4|Xkr4\ti\t-\tq2:CUFF.87|CUFF.87.1|100|24.170460|0.000000|52.080103|1.372881|-\n+TCONS_00000093\tXLOC_000074\tXkr4|Xkr4\ti\t-\tq2:CUFF.89|CUFF.89.1|100|29.709524|0.000000|64.015126|1.687500|-\n+TCONS_00000094\tXLOC_000076\tXkr4|Xkr4\ti\t-\tq2:CUFF.91|CUFF.91.1|100|35.211287|0.000000|85.007567|2.000000|-\n+TCONS_00000095\tXLOC_000078\tXkr4|Xkr4\ti\t-\tq2:CUFF.93|CUFF.93.1|100|35.211287|0.000000|85.007567|2.000000|-\n+TCONS_00000096\tXLOC_000079\tXkr4|Xkr4\ti\t-\tq2:CUFF.95|CUFF.95.1|100|35.211287|0.000000|85.007567|2.000000|-\n+TCONS_00000097\tXLOC_000081\tXkr4|Xkr4\ti\t-\tq2:CUFF.97|CUFF.97.1|100|35.211287|0.000000|85.007567|2.000000|-\n+TCONS_00000098\tXLOC_000082\tXkr4|Xkr4\ti\t-\tq2:CUFF.99|CUFF.99.1|100|19.602160|0.000000|39.204320|1.113402|-\n' |
| b |
| diff -r 67695d7ff787 -r 8e534225baa9 test-data/cuffcompare_out7.txt --- a/test-data/cuffcompare_out7.txt Thu Jan 09 14:27:37 2014 -0500 +++ b/test-data/cuffcompare_out7.txt Fri Dec 19 11:55:55 2014 -0500 |
| b |
| @@ -1,22 +1,22 @@ -# Cuffcompare v2.0.2 | Command line was: -#cuffcompare -o cc_output -r /Users/jeremy/projects/galaxy-central/database/files/002/dataset_2770.dat -R ./input1 ./input2 +# Cuffcompare v2.2.1 | Command line was: +#cuffcompare -o cc_output -r /tmp/tmpZ9KXPVfiles/000/dataset_3.dat -R -e 100 -d 100 ./input1 ./input2 # #= Summary for dataset: ./input1 : # Query mRNAs : 50 in 50 loci (0 multi-exon transcripts) # (0 multi-transcript loci, ~1.0 transcripts per locus) # Reference mRNAs : 1 in 1 loci (1 multi-exon) -# Corresponding super-loci: 1 +# Super-loci w/ reference transcripts: 1 #--------------------| Sn | Sp | fSn | fSp Base level: 2.2 2.3 - - Exon level: 0.0 0.0 0.0 0.0 - Intron level: 0.0 nan 0.0 nan -Intron chain level: 0.0 nan 0.0 nan + Intron level: 0.0 -nan 0.0 -nan +Intron chain level: 0.0 -nan 0.0 -nan Transcript level: 0.0 0.0 0.0 0.0 Locus level: 0.0 0.0 0.0 0.0 -Matching intron chains: 0 - Matching loci: 0 + Matching intron chains: 0 + Matching loci: 0 Missed exons: 2/3 ( 66.7%) Novel exons: 49/50 ( 98.0%) |
| b |
| diff -r 67695d7ff787 -r 8e534225baa9 tool_dependencies.xml --- a/tool_dependencies.xml Thu Jan 09 14:27:37 2014 -0500 +++ b/tool_dependencies.xml Fri Dec 19 11:55:55 2014 -0500 |
| b |
| @@ -1,6 +1,6 @@ <?xml version="1.0"?> <tool_dependency> - <package name="cufflinks" version="2.1.1"> - <repository changeset_revision="394b13717223" name="package_cufflinks_2_1_1" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" /> + <package name="cufflinks" version="2.2.1"> + <repository changeset_revision="899067a260d1" name="package_cufflinks_2_2_1" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> </tool_dependency> |