| Previous changeset 14:465cbb0cf2eb (2016-12-07) Next changeset 16:6741a8ace658 (2017-02-08) |
|
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit f65b40f4eb3c3431b8d9213f86238deebfd6bc29 |
|
modified:
picard_AddOrReplaceReadGroups.xml picard_CollectRnaSeqMetrics.xml test-data/picard_ARRG_test1.bam test-data/picard_CollectRnaSeqMetrics_test1.tab |
|
added:
test-data/picard_CollectRnaSeqMetrics.gff3 test-data/picard_CollectRnaSeqMetrics.gtf test-data/picard_CollectRnaSeqMetrics_test2.tab test-data/picard_CollectRnaSeqMetrics_test3.tab |
| b |
| diff -r 465cbb0cf2eb -r 00fe2ff64467 picard_AddOrReplaceReadGroups.xml --- a/picard_AddOrReplaceReadGroups.xml Wed Dec 07 14:56:30 2016 -0500 +++ b/picard_AddOrReplaceReadGroups.xml Thu Dec 08 06:43:38 2016 -0500 |
| b |
| @@ -107,17 +107,3 @@ @more_info@ </help> </tool> - - - - - - - - - - - - - - |
| b |
| diff -r 465cbb0cf2eb -r 00fe2ff64467 picard_CollectRnaSeqMetrics.xml --- a/picard_CollectRnaSeqMetrics.xml Wed Dec 07 14:56:30 2016 -0500 +++ b/picard_CollectRnaSeqMetrics.xml Thu Dec 08 06:43:38 2016 -0500 |
| [ |
| b'@@ -1,13 +1,14 @@\n-<tool name="CollectRnaSeqMetrics" id="picard_CollectRnaSeqMetrics" version="@TOOL_VERSION@.0">\n+<tool name="CollectRnaSeqMetrics" id="picard_CollectRnaSeqMetrics" version="@TOOL_VERSION@.1">\n <description> collect metrics about the alignment of RNA to various functional classes of loci in the genome</description>\n <macros>\n <import>picard_macros.xml</import>\n </macros>\n <expand macro="requirements">\n <requirement type="package" version="3.3.1">r</requirement>\n+ <requirement type="package" version="324">ucsc-gff3togenepred</requirement>\n+ <requirement type="package" version="324">ucsc-gtftogenepred</requirement>\n </expand>\n <command detect_errors="exit_code"><![CDATA[\n-\n ## Set up input files\n @symlink_element_identifier@\n ## Reference sequences\n@@ -23,7 +24,18 @@\n ## refFlat data\n ## The awk line below converts a file obtained from UCSC as specified in the tool help to refFlat format\n \n- grep -v \'^#\' ${refFlat} | awk \'{print $11"\\t"$1"\\t"$2"\\t"$3"\\t"$4"\\t"$5"\\t"$6"\\t"$7"\\t"$8"\\t"$9"\\t"$10}\' > refFlat.tab &&\n+ #if str($gene_reference_source.gene_reference_source_selector) == "gtf"\n+ #if $gene_reference_source.refFlat.ext != \'gff3\'\n+ gtfToGenePred \'${gene_reference_source.refFlat}\' refFlat.tab.raw &&\n+ #else\n+ gff3ToGenePred \'${gene_reference_source.refFlat}\' refFlat.tab.raw &&\n+ #end if\n+\n+ grep -v \'^#\' refFlat.tab.raw | awk \'{print $12"\\t"$1"\\t"$2"\\t"$3"\\t"$4"\\t"$5"\\t"$6"\\t"$7"\\t"$8"\\t"$9"\\t"$10}\' > refFlat.tab &&\n+ #else\n+ grep -v \'^#\' ${refFlat} | awk \'{print $11"\\t"$1"\\t"$2"\\t"$3"\\t"$4"\\t"$5"\\t"$6"\\t"$7"\\t"$8"\\t"$9"\\t"$10}\' > refFlat.tab &&\n+ #end if\n+\n \n ## Start picard command\n \n@@ -33,7 +45,7 @@\n REF_FLAT=refFlat.tab\n \n #if str( $ribosomal_intervals ) != "None":\n-\t RIBOSOMAL_INTERVALS="${ribosomal_intervals}"\n+ RIBOSOMAL_INTERVALS="${ribosomal_intervals}"\n #end if\n \n STRAND_SPECIFICITY="${strand_specificity}"\n@@ -41,7 +53,7 @@\n CHART_OUTPUT="${pdfFile}"\n \n #for $sequence_to_ignore in $ignore_list:\n-\t IGNORE_SEQUENCE="${sequence_to_ignore.sequence}"\n+ IGNORE_SEQUENCE="${sequence_to_ignore.sequence}"\n #end for\n \n RRNA_FRAGMENT_PERCENTAGE="${rrna_fragment_percentage}"\n@@ -50,9 +62,7 @@\n OUTPUT="${outFile}"\n REFERENCE_SEQUENCE="${reference_fasta_filename}"\n ASSUME_SORTED="${assume_sorted}"\n-\n- QUIET=true\n- VERBOSITY=ERROR\n+ \n VALIDATION_STRINGENCY=${validation_stringency}\n \n ]]></command>\n@@ -60,21 +70,42 @@\n <inputs>\n <param format="sam,bam" type="data" name="inputFile" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset" />\n <conditional name="reference_source">\n-\t <param name="reference_source_selector" type="select" label="Load reference genome from">\n-\t <option value="cached">Local cache</option>\n-\t <option value="history">History</option>\n-\t </param>\n-\t <when value="cached">\n-\t <param name="ref_file" type="select" label="Using reference genome" help="REFERENCE_SEQUENCE">\n-\t <options from_data_table="all_fasta"></options>\n-\t <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>\n-\t </param>\n-\t </when>\n-\t <when value="history">\n-\t <param name="ref_file" type="data" format="fasta" label="Use the folloing dataset as the reference sequence" help="REFERENCE_SEQUENCE; You can upload a FASTA sequence to the history and use it as reference" />\n-\t </when>\n+ <param name="reference_source_selector" type="select" label="Load reference genome from">\n+ <option value="cached">Local cache</option>\n+ <option value="history">History</option>\n+ </param>\n+ <when value="cached">\n+ <param name="ref_file" type="select" label="'..b'" type="data" label="Gene annotations in refFlat form" help="See "Obtaining gene annotations in refFlat format" below for help" />\n+\n+ <conditional name="gene_reference_source">\n+ <param name="gene_reference_source_selector" type="select" label="Load gene annotation from">\n+ <option value="gtf">GTF/GFF3</option>\n+ <option value="refflat">refFlat</option>\n+ </param>\n+ <when value="gtf">\n+ <param name="refFlat"\n+ format="gtf,gff3"\n+ type="data"\n+ label="Gene annotation (GTF/GFF3)"/>\n+ </when>\n+ <when value="refflat">\n+ <param name="refFlat"\n+ format="tabular"\n+ type="data"\n+ label="Gene annotations in refFlat form"\n+ help="See "Obtaining gene annotations in refFlat format" below for help"/>\n+ </when>\n+ </conditional>\n+\n+\n <param name="ribosomal_intervals" format="picard_interval_list" type="data" optional="True" label="Location of rRNA sequences in genome, in interval_list format" help="RIBOSOMAL_INTERVALS; If not specified no bases will be identified as being ribosomal. The list of intervals can be geberated from BED or Interval datasets using Galaxy BedToIntervalList tool"/>\n <param name="strand_specificity" type="select" label="What is the RNA-seq library strand specificity" help="STRAND_SPECIFICITY; For unpaired reads, use FIRST_READ_TRANSCRIPTION_STRAND if the reads are expected to be on the transcription strand.">\n \t <option value="NONE" selected="True">None</option>\n@@ -108,6 +139,8 @@\n <param name="ref_file" value="picard_CollectRnaSeqMetrics_ref.fa" ftype="fasta"/>\n <param name="inputFile" value="picard_CollectRnaSeqMetrics.bam" ftype="bam"/>\n <param name="assume_sorted" value="true" />\n+ \n+ <param name="gene_reference_source_selector" value="refflat" />\n <param name="refFlat" value="picard_CollectRnaSeqMetrics.refFlat" />\n <param name="metric_accumulation_level" value="ALL_READS" />\n <param name="minimum_length" value="500" />\n@@ -116,6 +149,35 @@\n <output name="outFile" file="picard_CollectRnaSeqMetrics_test1.tab" ftype="tabular" lines_diff="4"/>\n </test>\n \n+ <test>\n+ <param name="reference_source_selector" value="history"/>\n+ <param name="ref_file" value="picard_CollectRnaSeqMetrics_ref.fa" ftype="fasta"/>\n+ <param name="inputFile" value="picard_CollectRnaSeqMetrics.bam" ftype="bam"/>\n+ <param name="assume_sorted" value="true" />\n+ \n+ <param name="gene_reference_source_selector" value="gtf" />\n+ <param name="refFlat" value="picard_CollectRnaSeqMetrics.gtf" ftype="gtf" />\n+ <param name="metric_accumulation_level" value="ALL_READS" />\n+ <param name="minimum_length" value="500" />\n+ <param name="strand_specificity" value="NONE" />\n+ <param name="rrna_fragment_percentage" value="0.8" />\n+ <output name="outFile" file="picard_CollectRnaSeqMetrics_test2.tab" ftype="tabular" lines_diff="4"/>\n+ </test>\n+\n+ <test>\n+ <param name="reference_source_selector" value="history"/>\n+ <param name="ref_file" value="picard_CollectRnaSeqMetrics_ref.fa" ftype="fasta"/>\n+ <param name="inputFile" value="picard_CollectRnaSeqMetrics.bam" ftype="bam"/>\n+ <param name="assume_sorted" value="true" />\n+ \n+ <param name="gene_reference_source_selector" value="gtf" />\n+ <param name="refFlat" value="picard_CollectRnaSeqMetrics.gff3" ftype="gff3" />\n+ <param name="metric_accumulation_level" value="ALL_READS" />\n+ <param name="minimum_length" value="500" />\n+ <param name="strand_specificity" value="NONE" />\n+ <param name="rrna_fragment_percentage" value="0.8" />\n+ <output name="outFile" file="picard_CollectRnaSeqMetrics_test3.tab" ftype="tabular" lines_diff="4"/>\n+ </test>\n </tests>\n <help>\n \n' |
| b |
| diff -r 465cbb0cf2eb -r 00fe2ff64467 test-data/picard_ARRG_test1.bam |
| b |
| Binary file test-data/picard_ARRG_test1.bam has changed |
| b |
| diff -r 465cbb0cf2eb -r 00fe2ff64467 test-data/picard_CollectRnaSeqMetrics.gff3 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/picard_CollectRnaSeqMetrics.gff3 Thu Dec 08 06:43:38 2016 -0500 |
| b |
| @@ -0,0 +1,70 @@ +##gff-version 3 +chrM hg19_knownGene gene 236 368 0.000000 - . ID=uc004coq.4; +chrM hg19_knownGene mRNA 236 368 0.000000 - . ID=uc004coq.4.m;Parent=uc004coq.4; +chrM hg19_knownGene exon 236 368 0.000000 - . ID=uc004coq.4.e;Parent=uc004coq.4.m; +chrM hg19_knownGene gene 651 674 0.000000 + . ID=uc022bqo.2; +chrM hg19_knownGene mRNA 651 674 0.000000 + . ID=uc022bqo.2.m;Parent=uc022bqo.2; +chrM hg19_knownGene exon 651 674 0.000000 + . ID=uc022bqo.2.e;Parent=uc022bqo.2.m; +chrM hg19_knownGene gene 1604 1634 0.000000 + . ID=uc004cor.1; +chrM hg19_knownGene mRNA 1604 1634 0.000000 + . ID=uc004cor.1.m;Parent=uc004cor.1; +chrM hg19_knownGene exon 1604 1634 0.000000 + . ID=uc004cor.1.e;Parent=uc004cor.1.m; +chrM hg19_knownGene gene 1844 4264 0.000000 + . ID=uc004cos.5; +chrM hg19_knownGene mRNA 1844 4264 0.000000 + . ID=uc004cos.5.m;Parent=uc004cos.5; +chrM hg19_knownGene exon 1844 4264 0.000000 + . ID=uc004cos.5.e;Parent=uc004cos.5.m; +chrM hg19_knownGene gene 5544 5566 0.000000 - . ID=uc022bqp.1; +chrM hg19_knownGene mRNA 5544 5566 0.000000 - . ID=uc022bqp.1.m;Parent=uc022bqp.1; +chrM hg19_knownGene exon 5544 5566 0.000000 - . ID=uc022bqp.1.e;Parent=uc022bqp.1.m; +chrM hg19_knownGene gene 5586 5606 0.000000 - . ID=uc022bqq.1; +chrM hg19_knownGene mRNA 5586 5606 0.000000 - . ID=uc022bqq.1.m;Parent=uc022bqq.1; +chrM hg19_knownGene exon 5586 5606 0.000000 - . ID=uc022bqq.1.e;Parent=uc022bqq.1.m; +chrM hg19_knownGene gene 5691 5714 0.000000 - . ID=uc022bqr.1; +chrM hg19_knownGene mRNA 5691 5714 0.000000 - . ID=uc022bqr.1.m;Parent=uc022bqr.1; +chrM hg19_knownGene exon 5691 5714 0.000000 - . ID=uc022bqr.1.e;Parent=uc022bqr.1.m; +chrM hg19_knownGene gene 5905 7439 0.000000 + . ID=uc031tga.1; +chrM hg19_knownGene mRNA 5905 7439 0.000000 + . ID=uc031tga.1.m;Parent=uc031tga.1; +chrM hg19_knownGene exon 5905 7439 0.000000 + . ID=uc031tga.1.e;Parent=uc031tga.1.m; +chrM hg19_knownGene gene 7587 7982 0.000000 - . ID=uc022bqs.1; +chrM hg19_knownGene mRNA 7587 7982 0.000000 - . ID=uc022bqs.1.m;Parent=uc022bqs.1; +chrM hg19_knownGene exon 7587 7982 0.000000 - . ID=uc022bqs.1.e;Parent=uc022bqs.1.m; +chrM hg19_knownGene gene 15504 15888 0.000000 - . ID=uc022bqs.1; +chrM hg19_knownGene mRNA 15504 15888 0.000000 - . ID=uc022bqs.1.m;Parent=uc022bqs.1; +chrM hg19_knownGene exon 15504 15888 0.000000 - . ID=uc022bqs.1.e;Parent=uc022bqs.1.m; +chrM hg19_knownGene gene 7587 9208 0.000000 + . ID=uc011mfi.2; +chrM hg19_knownGene mRNA 7587 9208 0.000000 + . ID=uc011mfi.2.m;Parent=uc011mfi.2; +chrM hg19_knownGene exon 7587 9208 0.000000 + . ID=uc011mfi.2.e;Parent=uc011mfi.2.m; +chrM hg19_knownGene gene 8367 8472 0.000000 - . ID=uc022bqt.1; +chrM hg19_knownGene mRNA 8367 8472 0.000000 - . ID=uc022bqt.1.m;Parent=uc022bqt.1; +chrM hg19_knownGene exon 8367 8472 0.000000 - . ID=uc022bqt.1.e;Parent=uc022bqt.1.m; +chrM hg19_knownGene gene 13450 14149 0.000000 - . ID=uc022bqt.1; +chrM hg19_knownGene mRNA 13450 14149 0.000000 - . ID=uc022bqt.1.m;Parent=uc022bqt.1; +chrM hg19_knownGene exon 13450 14149 0.000000 - . ID=uc022bqt.1.e;Parent=uc022bqt.1.m; +chrM hg19_knownGene gene 10060 10404 0.000000 + . ID=uc022bqu.2; +chrM hg19_knownGene mRNA 10060 10404 0.000000 + . ID=uc022bqu.2.m;Parent=uc022bqu.2; +chrM hg19_knownGene exon 10060 10404 0.000000 + . ID=uc022bqu.2.e;Parent=uc022bqu.2.m; +chrM hg19_knownGene gene 10471 12138 0.000000 + . ID=uc004cov.5; +chrM hg19_knownGene mRNA 10471 12138 0.000000 + . ID=uc004cov.5.m;Parent=uc004cov.5; +chrM hg19_knownGene exon 10471 12138 0.000000 + . ID=uc004cov.5.e;Parent=uc004cov.5.m; +chrM hg19_knownGene gene 10761 11231 0.000000 - . ID=uc031tgb.1; +chrM hg19_knownGene mRNA 10761 11231 0.000000 - . ID=uc031tgb.1.m;Parent=uc031tgb.1; +chrM hg19_knownGene exon 10761 11231 0.000000 - . ID=uc031tgb.1.e;Parent=uc031tgb.1.m; +chrM hg19_knownGene gene 13979 14149 0.000000 - . ID=uc031tgb.1; +chrM hg19_knownGene mRNA 13979 14149 0.000000 - . ID=uc031tgb.1.m;Parent=uc031tgb.1; +chrM hg19_knownGene exon 13979 14149 0.000000 - . ID=uc031tgb.1.e;Parent=uc031tgb.1.m; +chrM hg19_knownGene gene 12208 12264 0.000000 + . ID=uc004cow.2; +chrM hg19_knownGene mRNA 12208 12264 0.000000 + . ID=uc004cow.2.m;Parent=uc004cow.2; +chrM hg19_knownGene exon 12208 12264 0.000000 + . ID=uc004cow.2.e;Parent=uc004cow.2.m; +chrM hg19_knownGene gene 12908 14149 0.000000 + . ID=uc004cox.4; +chrM hg19_knownGene mRNA 12908 14149 0.000000 + . ID=uc004cox.4.m;Parent=uc004cox.4; +chrM hg19_knownGene exon 12908 14149 0.000000 + . ID=uc004cox.4.e;Parent=uc004cox.4.m; +chrM hg19_knownGene gene 14675 14698 0.000000 - . ID=uc022bqv.1; +chrM hg19_knownGene mRNA 14675 14698 0.000000 - . ID=uc022bqv.1.m;Parent=uc022bqv.1; +chrM hg19_knownGene exon 14675 14698 0.000000 - . ID=uc022bqv.1.e;Parent=uc022bqv.1.m; +chrM hg19_knownGene gene 14857 15888 0.000000 + . ID=uc022bqw.1; +chrM hg19_knownGene mRNA 14857 15888 0.000000 + . ID=uc022bqw.1.m;Parent=uc022bqw.1; +chrM hg19_knownGene exon 14857 15888 0.000000 + . ID=uc022bqw.1.e;Parent=uc022bqw.1.m; +chrM hg19_knownGene gene 15960 16024 0.000000 - . ID=uc022bqx.1; +chrM hg19_knownGene mRNA 15960 16024 0.000000 - . ID=uc022bqx.1.m;Parent=uc022bqx.1; +chrM hg19_knownGene exon 15960 16024 0.000000 - . ID=uc022bqx.1.e;Parent=uc022bqx.1.m; +chrM hg19_knownGene gene 15999 16571 0.000000 + . ID=uc004coz.1; +chrM hg19_knownGene mRNA 15999 16571 0.000000 + . ID=uc004coz.1.m;Parent=uc004coz.1; +chrM hg19_knownGene exon 15999 16571 0.000000 + . ID=uc004coz.1.e;Parent=uc004coz.1.m; |
| b |
| diff -r 465cbb0cf2eb -r 00fe2ff64467 test-data/picard_CollectRnaSeqMetrics.gtf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/picard_CollectRnaSeqMetrics.gtf Thu Dec 08 06:43:38 2016 -0500 |
| b |
| @@ -0,0 +1,23 @@ +chrM hg19_knownGene exon 236 368 0.000000 - . gene_id "uc004coq.4"; transcript_id "uc004coq.4"; +chrM hg19_knownGene exon 651 674 0.000000 + . gene_id "uc022bqo.2"; transcript_id "uc022bqo.2"; +chrM hg19_knownGene exon 1604 1634 0.000000 + . gene_id "uc004cor.1"; transcript_id "uc004cor.1"; +chrM hg19_knownGene exon 1844 4264 0.000000 + . gene_id "uc004cos.5"; transcript_id "uc004cos.5"; +chrM hg19_knownGene exon 5544 5566 0.000000 - . gene_id "uc022bqp.1"; transcript_id "uc022bqp.1"; +chrM hg19_knownGene exon 5586 5606 0.000000 - . gene_id "uc022bqq.1"; transcript_id "uc022bqq.1"; +chrM hg19_knownGene exon 5691 5714 0.000000 - . gene_id "uc022bqr.1"; transcript_id "uc022bqr.1"; +chrM hg19_knownGene exon 5905 7439 0.000000 + . gene_id "uc031tga.1"; transcript_id "uc031tga.1"; +chrM hg19_knownGene exon 7587 7982 0.000000 - . gene_id "uc022bqs.1"; transcript_id "uc022bqs.1"; +chrM hg19_knownGene exon 15504 15888 0.000000 - . gene_id "uc022bqs.1"; transcript_id "uc022bqs.1"; +chrM hg19_knownGene exon 7587 9208 0.000000 + . gene_id "uc011mfi.2"; transcript_id "uc011mfi.2"; +chrM hg19_knownGene exon 8367 8472 0.000000 - . gene_id "uc022bqt.1"; transcript_id "uc022bqt.1"; +chrM hg19_knownGene exon 13450 14149 0.000000 - . gene_id "uc022bqt.1"; transcript_id "uc022bqt.1"; +chrM hg19_knownGene exon 10060 10404 0.000000 + . gene_id "uc022bqu.2"; transcript_id "uc022bqu.2"; +chrM hg19_knownGene exon 10471 12138 0.000000 + . gene_id "uc004cov.5"; transcript_id "uc004cov.5"; +chrM hg19_knownGene exon 10761 11231 0.000000 - . gene_id "uc031tgb.1"; transcript_id "uc031tgb.1"; +chrM hg19_knownGene exon 13979 14149 0.000000 - . gene_id "uc031tgb.1"; transcript_id "uc031tgb.1"; +chrM hg19_knownGene exon 12208 12264 0.000000 + . gene_id "uc004cow.2"; transcript_id "uc004cow.2"; +chrM hg19_knownGene exon 12908 14149 0.000000 + . gene_id "uc004cox.4"; transcript_id "uc004cox.4"; +chrM hg19_knownGene exon 14675 14698 0.000000 - . gene_id "uc022bqv.1"; transcript_id "uc022bqv.1"; +chrM hg19_knownGene exon 14857 15888 0.000000 + . gene_id "uc022bqw.1"; transcript_id "uc022bqw.1"; +chrM hg19_knownGene exon 15960 16024 0.000000 - . gene_id "uc022bqx.1"; transcript_id "uc022bqx.1"; +chrM hg19_knownGene exon 15999 16571 0.000000 + . gene_id "uc004coz.1"; transcript_id "uc004coz.1"; \ No newline at end of file |
| b |
| diff -r 465cbb0cf2eb -r 00fe2ff64467 test-data/picard_CollectRnaSeqMetrics_test1.tab --- a/test-data/picard_CollectRnaSeqMetrics_test1.tab Wed Dec 07 14:56:30 2016 -0500 +++ b/test-data/picard_CollectRnaSeqMetrics_test1.tab Thu Dec 08 06:43:38 2016 -0500 |
| [ |
| @@ -1,7 +1,7 @@ ## htsjdk.samtools.metrics.StringHeader -# picard.analysis.CollectRnaSeqMetrics REF_FLAT=refFlat.tab STRAND_SPECIFICITY=NONE MINIMUM_LENGTH=500 CHART_OUTPUT=/Users/anton/galaxy-central/database/files/000/dataset_792.dat RRNA_FRAGMENT_PERCENTAGE=0.8 METRIC_ACCUMULATION_LEVEL=[ALL_READS] INPUT=/Users/anton/galaxy-central/database/files/000/dataset_773.dat OUTPUT=/Users/anton/galaxy-central/database/files/000/dataset_793.dat REFERENCE_SEQUENCE=localref.fa ASSUME_SORTED=true VERBOSITY=ERROR QUIET=true VALIDATION_STRINGENCY=LENIENT STOP_AFTER=0 COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false +# picard.analysis.CollectRnaSeqMetrics REF_FLAT=refFlat.tab STRAND_SPECIFICITY=NONE MINIMUM_LENGTH=500 CHART_OUTPUT=/tmp/tmpRJquSu/files/000/dataset_4.dat RRNA_FRAGMENT_PERCENTAGE=0.8 METRIC_ACCUMULATION_LEVEL=[ALL_READS] INPUT=picard_CollectRnaSeqMetrics_bam OUTPUT=/tmp/tmpRJquSu/files/000/dataset_5.dat ASSUME_SORTED=true VALIDATION_STRINGENCY=LENIENT REFERENCE_SEQUENCE=localref.fa STOP_AFTER=0 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json ## htsjdk.samtools.metrics.StringHeader -# Started on: Mon Oct 06 22:24:48 EDT 2014 +# Started on: Thu Dec 08 10:54:07 CET 2016 ## METRICS CLASS picard.analysis.RnaSeqMetrics PF_BASES PF_ALIGNED_BASES RIBOSOMAL_BASES CODING_BASES UTR_BASES INTRONIC_BASES INTERGENIC_BASES IGNORED_READS CORRECT_STRAND_READS INCORRECT_STRAND_READS PCT_RIBOSOMAL_BASES PCT_CODING_BASES PCT_UTR_BASES PCT_INTRONIC_BASES PCT_INTERGENIC_BASES PCT_MRNA_BASES PCT_USABLE_BASES PCT_CORRECT_STRAND_READS MEDIAN_CV_COVERAGE MEDIAN_5PRIME_BIAS MEDIAN_3PRIME_BIAS MEDIAN_5PRIME_TO_3PRIME_BIAS SAMPLE LIBRARY READ_GROUP |
| b |
| diff -r 465cbb0cf2eb -r 00fe2ff64467 test-data/picard_CollectRnaSeqMetrics_test2.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/picard_CollectRnaSeqMetrics_test2.tab Thu Dec 08 06:43:38 2016 -0500 |
| [ |
| @@ -0,0 +1,10 @@ +## htsjdk.samtools.metrics.StringHeader +# picard.analysis.CollectRnaSeqMetrics REF_FLAT=refFlat.tab STRAND_SPECIFICITY=NONE MINIMUM_LENGTH=500 CHART_OUTPUT=/tmp/tmpRJquSu/files/000/dataset_9.dat RRNA_FRAGMENT_PERCENTAGE=0.8 METRIC_ACCUMULATION_LEVEL=[ALL_READS] INPUT=picard_CollectRnaSeqMetrics_bam OUTPUT=/tmp/tmpRJquSu/files/000/dataset_10.dat ASSUME_SORTED=true VALIDATION_STRINGENCY=LENIENT REFERENCE_SEQUENCE=localref.fa STOP_AFTER=0 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json +## htsjdk.samtools.metrics.StringHeader +# Started on: Thu Dec 08 10:54:36 CET 2016 + +## METRICS CLASS picard.analysis.RnaSeqMetrics +PF_BASES PF_ALIGNED_BASES RIBOSOMAL_BASES CODING_BASES UTR_BASES INTRONIC_BASES INTERGENIC_BASES IGNORED_READS CORRECT_STRAND_READS INCORRECT_STRAND_READS PCT_RIBOSOMAL_BASES PCT_CODING_BASES PCT_UTR_BASES PCT_INTRONIC_BASES PCT_INTERGENIC_BASES PCT_MRNA_BASES PCT_USABLE_BASES PCT_CORRECT_STRAND_READS MEDIAN_CV_COVERAGE MEDIAN_5PRIME_BIAS MEDIAN_3PRIME_BIAS MEDIAN_5PRIME_TO_3PRIME_BIAS SAMPLE LIBRARY READ_GROUP +48870 48712 0 0 0 48712 0 0 0 0 0 0 1 0 0 0 0 0 0 0 + + |
| b |
| diff -r 465cbb0cf2eb -r 00fe2ff64467 test-data/picard_CollectRnaSeqMetrics_test3.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/picard_CollectRnaSeqMetrics_test3.tab Thu Dec 08 06:43:38 2016 -0500 |
| [ |
| @@ -0,0 +1,113 @@ +## htsjdk.samtools.metrics.StringHeader +# picard.analysis.CollectRnaSeqMetrics REF_FLAT=refFlat.tab STRAND_SPECIFICITY=NONE MINIMUM_LENGTH=500 CHART_OUTPUT=/tmp/tmpRJquSu/files/000/dataset_14.dat RRNA_FRAGMENT_PERCENTAGE=0.8 METRIC_ACCUMULATION_LEVEL=[ALL_READS] INPUT=picard_CollectRnaSeqMetrics_bam OUTPUT=/tmp/tmpRJquSu/files/000/dataset_15.dat ASSUME_SORTED=true VALIDATION_STRINGENCY=LENIENT REFERENCE_SEQUENCE=localref.fa STOP_AFTER=0 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json +## htsjdk.samtools.metrics.StringHeader +# Started on: Thu Dec 08 10:55:06 CET 2016 + +## METRICS CLASS picard.analysis.RnaSeqMetrics +PF_BASES PF_ALIGNED_BASES RIBOSOMAL_BASES CODING_BASES UTR_BASES INTRONIC_BASES INTERGENIC_BASES IGNORED_READS CORRECT_STRAND_READS INCORRECT_STRAND_READS PCT_RIBOSOMAL_BASES PCT_CODING_BASES PCT_UTR_BASES PCT_INTRONIC_BASES PCT_INTERGENIC_BASES PCT_MRNA_BASES PCT_USABLE_BASES PCT_CORRECT_STRAND_READS MEDIAN_CV_COVERAGE MEDIAN_5PRIME_BIAS MEDIAN_3PRIME_BIAS MEDIAN_5PRIME_TO_3PRIME_BIAS SAMPLE LIBRARY READ_GROUP +48870 48712 0 38786 0 9926 0 0 0 0 0.796231 0 0.203769 0.796231 0.793657 0 0.91593 0.430026 0.235755 1.402829 + +## HISTOGRAM java.lang.Integer +normalized_position All_Reads.normalized_coverage +0 0.313906 +1 0.333933 +2 0.365536 +3 0.344525 +4 0.371353 +5 0.378606 +6 0.518015 +7 0.51266 +8 0.500497 +9 0.690539 +10 0.829611 +11 0.784227 +12 0.825037 +13 0.730533 +14 0.73133 +15 0.693057 +16 0.873759 +17 0.774195 +18 0.721989 +19 0.791727 +20 0.697702 +21 0.698451 +22 0.568885 +23 0.689955 +24 0.580475 +25 0.602348 +26 0.657286 +27 0.600594 +28 0.48185 +29 0.478605 +30 0.646053 +31 0.689366 +32 0.740073 +33 0.695415 +34 0.708419 +35 0.714707 +36 0.707421 +37 0.793703 +38 0.84384 +39 0.819497 +40 0.982412 +41 1.172387 +42 1.28116 +43 1.379184 +44 1.416285 +45 1.32892 +46 1.248258 +47 1.308676 +48 1.085518 +49 1.006687 +50 0.851309 +51 0.693805 +52 0.672921 +53 0.684999 +54 0.62579 +55 0.529832 +56 0.546564 +57 0.566014 +58 0.615824 +59 0.565042 +60 0.547677 +61 0.642067 +62 0.83636 +63 0.937071 +64 1.057465 +65 1.168829 +66 1.375228 +67 1.489487 +68 1.530099 +69 1.287542 +70 1.442585 +71 1.347823 +72 1.424913 +73 1.468345 +74 1.796846 +75 1.79639 +76 1.747908 +77 1.76867 +78 1.773528 +79 1.670178 +80 1.740083 +81 1.809632 +82 2.019967 +83 2.201517 +84 2.150455 +85 2.327367 +86 2.261259 +87 1.929731 +88 1.936627 +89 1.80697 +90 1.789004 +91 1.642341 +92 1.408203 +93 1.159737 +94 0.990047 +95 0.697842 +96 0.377809 +97 0.243433 +98 0.218816 +99 0.223665 +100 0.225079 + |