| Previous changeset 21:6f9c0884a3e7 (2018-10-16) Next changeset 23:1cd1cf786389 (2019-05-16) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit b6e11aa8e5fd1da27909207ec4f09cbbac467495 |
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modified:
picard_CollectRnaSeqMetrics.xml read_group_macros.xml test-data/picard_CollectRnaSeqMetrics.gtf test-data/picard_CollectRnaSeqMetrics_test2.tab |
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| diff -r 6f9c0884a3e7 -r f6ced08779c4 picard_CollectRnaSeqMetrics.xml --- a/picard_CollectRnaSeqMetrics.xml Tue Oct 16 11:49:10 2018 -0400 +++ b/picard_CollectRnaSeqMetrics.xml Fri Mar 29 08:34:36 2019 -0400 |
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| @@ -23,7 +23,7 @@ #if str($gene_reference_source.gene_reference_source_selector) == "gtf" #if $gene_reference_source.refFlat.ext != 'gff3' - gtfToGenePred '${gene_reference_source.refFlat}' refFlat.tab.raw && + gtfToGenePred -genePredExt '${gene_reference_source.refFlat}' refFlat.tab.raw && #else gff3ToGenePred '${gene_reference_source.refFlat}' refFlat.tab.raw && #end if |
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| diff -r 6f9c0884a3e7 -r f6ced08779c4 read_group_macros.xml --- a/read_group_macros.xml Tue Oct 16 11:49:10 2018 -0400 +++ b/read_group_macros.xml Fri Mar 29 08:34:36 2019 -0400 |
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| @@ -242,7 +242,7 @@ <param name="PU" type="text" label="Platform unit (PU)" help="Unique identifier (e.g. flowcell-barcode.lane for Illumina or slide for SOLiD)" optional="True" /> </xml> <xml name="read_group_pu_required_param"> - <param name="PU" type="text" label="Platform unit (PU)" help="Unique identifier (e.g. flowcell-barcode.lane for Illumina or slide for SOLiD)" optional="False" /> + <param name="PU" type="text" value="run" label="Platform unit (PU)" help="Unique identifier (e.g. flowcell-barcode.lane for Illumina or slide for SOLiD)" optional="False" /> </xml> <!-- Only ID is required - all groups available --> <xml name="read_group_inputs_spec"> |
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| diff -r 6f9c0884a3e7 -r f6ced08779c4 test-data/picard_CollectRnaSeqMetrics.gtf --- a/test-data/picard_CollectRnaSeqMetrics.gtf Tue Oct 16 11:49:10 2018 -0400 +++ b/test-data/picard_CollectRnaSeqMetrics.gtf Fri Mar 29 08:34:36 2019 -0400 |
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| b'@@ -1,23 +1,144 @@\n-chrM\thg19_knownGene\texon\t236\t368\t0.000000\t-\t.\tgene_id "uc004coq.4"; transcript_id "uc004coq.4"; \n-chrM\thg19_knownGene\texon\t651\t674\t0.000000\t+\t.\tgene_id "uc022bqo.2"; transcript_id "uc022bqo.2"; \n-chrM\thg19_knownGene\texon\t1604\t1634\t0.000000\t+\t.\tgene_id "uc004cor.1"; transcript_id "uc004cor.1"; \n-chrM\thg19_knownGene\texon\t1844\t4264\t0.000000\t+\t.\tgene_id "uc004cos.5"; transcript_id "uc004cos.5"; \n-chrM\thg19_knownGene\texon\t5544\t5566\t0.000000\t-\t.\tgene_id "uc022bqp.1"; transcript_id "uc022bqp.1"; \n-chrM\thg19_knownGene\texon\t5586\t5606\t0.000000\t-\t.\tgene_id "uc022bqq.1"; transcript_id "uc022bqq.1"; \n-chrM\thg19_knownGene\texon\t5691\t5714\t0.000000\t-\t.\tgene_id "uc022bqr.1"; transcript_id "uc022bqr.1"; \n-chrM\thg19_knownGene\texon\t5905\t7439\t0.000000\t+\t.\tgene_id "uc031tga.1"; transcript_id "uc031tga.1"; \n-chrM\thg19_knownGene\texon\t7587\t7982\t0.000000\t-\t.\tgene_id "uc022bqs.1"; transcript_id "uc022bqs.1"; \n-chrM\thg19_knownGene\texon\t15504\t15888\t0.000000\t-\t.\tgene_id "uc022bqs.1"; transcript_id "uc022bqs.1"; \n-chrM\thg19_knownGene\texon\t7587\t9208\t0.000000\t+\t.\tgene_id "uc011mfi.2"; transcript_id "uc011mfi.2"; \n-chrM\thg19_knownGene\texon\t8367\t8472\t0.000000\t-\t.\tgene_id "uc022bqt.1"; transcript_id "uc022bqt.1"; \n-chrM\thg19_knownGene\texon\t13450\t14149\t0.000000\t-\t.\tgene_id "uc022bqt.1"; transcript_id "uc022bqt.1"; \n-chrM\thg19_knownGene\texon\t10060\t10404\t0.000000\t+\t.\tgene_id "uc022bqu.2"; transcript_id "uc022bqu.2"; \n-chrM\thg19_knownGene\texon\t10471\t12138\t0.000000\t+\t.\tgene_id "uc004cov.5"; transcript_id "uc004cov.5"; \n-chrM\thg19_knownGene\texon\t10761\t11231\t0.000000\t-\t.\tgene_id "uc031tgb.1"; transcript_id "uc031tgb.1"; \n-chrM\thg19_knownGene\texon\t13979\t14149\t0.000000\t-\t.\tgene_id "uc031tgb.1"; transcript_id "uc031tgb.1"; \n-chrM\thg19_knownGene\texon\t12208\t12264\t0.000000\t+\t.\tgene_id "uc004cow.2"; transcript_id "uc004cow.2"; \n-chrM\thg19_knownGene\texon\t12908\t14149\t0.000000\t+\t.\tgene_id "uc004cox.4"; transcript_id "uc004cox.4"; \n-chrM\thg19_knownGene\texon\t14675\t14698\t0.000000\t-\t.\tgene_id "uc022bqv.1"; transcript_id "uc022bqv.1"; \n-chrM\thg19_knownGene\texon\t14857\t15888\t0.000000\t+\t.\tgene_id "uc022bqw.1"; transcript_id "uc022bqw.1"; \n-chrM\thg19_knownGene\texon\t15960\t16024\t0.000000\t-\t.\tgene_id "uc022bqx.1"; transcript_id "uc022bqx.1"; \n-chrM\thg19_knownGene\texon\t15999\t16571\t0.000000\t+\t.\tgene_id "uc004coz.1"; transcript_id "uc004coz.1"; \n\\ No newline at end of file\n+chrM\tinsdc\tgene\t577\t647\t.\t+\t.\tgene_id "ENSG00000210049"; gene_version "1"; gene_name "MT-TF"; gene_source "insdc"; gene_biotype "Mt_tRNA";\n+chrM\tinsdc\ttranscript\t577\t647\t.\t+\t.\tgene_id "ENSG00000210049"; gene_version "1"; transcript_id "ENST00000387314"; transcript_version "1"; gene_name "MT-TF"; gene_source "insdc"; gene_biotype "Mt_tRNA"; transcript_name "MT-TF-201"; transcript_source "insdc"; transcript_biotype "Mt_tRNA"; tag "basic";\n+chrM\tinsdc\texon\t577\t647\t.\t+\t.\tgene_id "ENSG00000210049"; gene_version "1"; transcript_id "ENST00000387314"; transcript_version "1"; exon_number "1"; gene_name "MT-TF"; gene_source "insdc"; gene_biotype "Mt_tRNA"; transcript_name "MT-TF-201"; transcript_source "insdc"; transcript_biotype "Mt_tRNA"; exon_id "ENSE00001544501"; exon_version "1"; tag "basic";\n+chrM\tinsdc\tgene\t648\t1601\t.\t+\t.\tgene_id "ENSG00000211459"; gene_version "2"; gene_name "MT-RNR1"; gene_source "insdc"; gene_biotype "Mt_rRNA";\n+chrM\tinsdc\ttranscript\t648\t1601\t.\t+\t.\tgene_id "ENSG00000211459"; gene_version "2"; transcript_id "ENST00000389680"; transcript_version "2"; gene_name "MT-RNR1"; gene_source "insdc"; gene_biotype "Mt_rRNA"; transcript_name "MT-RNR1-201"; transcript_source "insdc"; transcript_biotype "Mt_rRNA"; tag "basic";\n+chrM\tinsdc\texon\t648\t1601\t.\t+\t.\tgene_id "ENSG00000211459"; gene_version "2"; transcript_id "ENST00000389680"; transcript_version "2"; exon_number "1"; gene_name "MT-RNR1"; gene_source "insdc"; gene_biotype "Mt_rRNA"; transcript_name "MT-RNR1-201"; transcript_source "insdc"; transcript_biotype "Mt_rRNA"; exon_id "ENSE00001544499"; exon_version "2"; tag "basic";\n+chrM\tinsdc\tgene\t16'..b'gene\t14674\t14742\t.\t-\t.\tgene_id "ENSG00000210194"; gene_version "1"; gene_name "MT-TE"; gene_source "insdc"; gene_biotype "Mt_tRNA";\n+chrM\tinsdc\ttranscript\t14674\t14742\t.\t-\t.\tgene_id "ENSG00000210194"; gene_version "1"; transcript_id "ENST00000387459"; transcript_version "1"; gene_name "MT-TE"; gene_source "insdc"; gene_biotype "Mt_tRNA"; transcript_name "MT-TE-201"; transcript_source "insdc"; transcript_biotype "Mt_tRNA"; tag "basic";\n+chrM\tinsdc\texon\t14674\t14742\t.\t-\t.\tgene_id "ENSG00000210194"; gene_version "1"; transcript_id "ENST00000387459"; transcript_version "1"; exon_number "1"; gene_name "MT-TE"; gene_source "insdc"; gene_biotype "Mt_tRNA"; transcript_name "MT-TE-201"; transcript_source "insdc"; transcript_biotype "Mt_tRNA"; exon_id "ENSE00001544476"; exon_version "1"; tag "basic";\n+chrM\tinsdc\tgene\t14747\t15887\t.\t+\t.\tgene_id "ENSG00000198727"; gene_version "2"; gene_name "MT-CYB"; gene_source "insdc"; gene_biotype "protein_coding";\n+chrM\tinsdc\ttranscript\t14747\t15887\t.\t+\t.\tgene_id "ENSG00000198727"; gene_version "2"; transcript_id "ENST00000361789"; transcript_version "2"; gene_name "MT-CYB"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-CYB-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; tag "basic";\n+chrM\tinsdc\texon\t14747\t15887\t.\t+\t.\tgene_id "ENSG00000198727"; gene_version "2"; transcript_id "ENST00000361789"; transcript_version "2"; exon_number "1"; gene_name "MT-CYB"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-CYB-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; exon_id "ENSE00001436074"; exon_version "2"; tag "basic";\n+chrM\tinsdc\tCDS\t14747\t15887\t.\t+\t0\tgene_id "ENSG00000198727"; gene_version "2"; transcript_id "ENST00000361789"; transcript_version "2"; exon_number "1"; gene_name "MT-CYB"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-CYB-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; protein_id "ENSP00000354554"; protein_version "2"; tag "basic";\n+chrM\tinsdc\tstart_codon\t14747\t14749\t.\t+\t0\tgene_id "ENSG00000198727"; gene_version "2"; transcript_id "ENST00000361789"; transcript_version "2"; exon_number "1"; gene_name "MT-CYB"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-CYB-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; tag "basic";\n+chrM\tinsdc\tgene\t15888\t15953\t.\t+\t.\tgene_id "ENSG00000210195"; gene_version "2"; gene_name "MT-TT"; gene_source "insdc"; gene_biotype "Mt_tRNA";\n+chrM\tinsdc\ttranscript\t15888\t15953\t.\t+\t.\tgene_id "ENSG00000210195"; gene_version "2"; transcript_id "ENST00000387460"; transcript_version "2"; gene_name "MT-TT"; gene_source "insdc"; gene_biotype "Mt_tRNA"; transcript_name "MT-TT-201"; transcript_source "insdc"; transcript_biotype "Mt_tRNA"; tag "basic";\n+chrM\tinsdc\texon\t15888\t15953\t.\t+\t.\tgene_id "ENSG00000210195"; gene_version "2"; transcript_id "ENST00000387460"; transcript_version "2"; exon_number "1"; gene_name "MT-TT"; gene_source "insdc"; gene_biotype "Mt_tRNA"; transcript_name "MT-TT-201"; transcript_source "insdc"; transcript_biotype "Mt_tRNA"; exon_id "ENSE00001544475"; exon_version "2"; tag "basic";\n+chrM\tinsdc\tgene\t15956\t16023\t.\t-\t.\tgene_id "ENSG00000210196"; gene_version "2"; gene_name "MT-TP"; gene_source "insdc"; gene_biotype "Mt_tRNA";\n+chrM\tinsdc\ttranscript\t15956\t16023\t.\t-\t.\tgene_id "ENSG00000210196"; gene_version "2"; transcript_id "ENST00000387461"; transcript_version "2"; gene_name "MT-TP"; gene_source "insdc"; gene_biotype "Mt_tRNA"; transcript_name "MT-TP-201"; transcript_source "insdc"; transcript_biotype "Mt_tRNA"; tag "basic";\n+chrM\tinsdc\texon\t15956\t16023\t.\t-\t.\tgene_id "ENSG00000210196"; gene_version "2"; transcript_id "ENST00000387461"; transcript_version "2"; exon_number "1"; gene_name "MT-TP"; gene_source "insdc"; gene_biotype "Mt_tRNA"; transcript_name "MT-TP-201"; transcript_source "insdc"; transcript_biotype "Mt_tRNA"; exon_id "ENSE00001544473"; exon_version "2"; tag "basic";\n' |
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| diff -r 6f9c0884a3e7 -r f6ced08779c4 test-data/picard_CollectRnaSeqMetrics_test2.tab --- a/test-data/picard_CollectRnaSeqMetrics_test2.tab Tue Oct 16 11:49:10 2018 -0400 +++ b/test-data/picard_CollectRnaSeqMetrics_test2.tab Fri Mar 29 08:34:36 2019 -0400 |
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| @@ -1,10 +1,113 @@ ## htsjdk.samtools.metrics.StringHeader -# CollectRnaSeqMetrics REF_FLAT=refFlat.tab STRAND_SPECIFICITY=NONE MINIMUM_LENGTH=500 CHART_OUTPUT=/tmp/tmpYRm8q4/files/000/dataset_34.dat RRNA_FRAGMENT_PERCENTAGE=0.8 METRIC_ACCUMULATION_LEVEL=[ALL_READS] INPUT=picard_CollectRnaSeqMetrics_bam OUTPUT=/tmp/tmpYRm8q4/files/000/dataset_35.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 USE_JDK_DEFLATER=false USE_JDK_INFLATER=false +# picard.analysis.CollectRnaSeqMetrics REF_FLAT=refFlat.tab STRAND_SPECIFICITY=NONE MINIMUM_LENGTH=500 CHART_OUTPUT=/opt/galaxy/galaxy/database/files/033/dataset_33778.dat RRNA_FRAGMENT_PERCENTAGE=0.8 METRIC_ACCUMULATION_LEVEL=[ALL_READS] INPUT=picard_CollectRnaSeqMetrics_bam OUTPUT=/opt/galaxy/galaxy/database/files/033/dataset_33779.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: Sat Apr 14 09:30:06 CEST 2018 +# Started on: Thu Jan 31 11:57:28 GMT 2019 ## 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 NUM_R1_TRANSCRIPT_STRAND_READS NUM_R2_TRANSCRIPT_STRAND_READS NUM_UNEXPLAINED_READS PCT_R1_TRANSCRIPT_STRAND_READS PCT_R2_TRANSCRIPT_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 0 0 0 0 0 1 0 0 0 0 0 0 0 +48870 48712 40205 8172 0 335 0 0 0 118 141 5 0.455598 0.544402 0.825361 0.167762 0 0.006877 0.993123 0.989912 0 0.801606 0.364744 0.224119 0.579618 +## HISTOGRAM java.lang.Integer +normalized_position All_Reads.normalized_coverage +0 0.228841 +1 0.251223 +2 0.223738 +3 0.233838 +4 0.256581 +5 0.266966 +6 0.271332 +7 0.265645 +8 0.260346 +9 0.231289 +10 0.269298 +11 0.326408 +12 0.373618 +13 0.473463 +14 0.54793 +15 0.577498 +16 0.542569 +17 0.558467 +18 0.650338 +19 0.635229 +20 0.574853 +21 0.588563 +22 0.650078 +23 0.686162 +24 0.634014 +25 0.644335 +26 0.631052 +27 0.639668 +28 0.705101 +29 0.778048 +30 0.736876 +31 0.70567 +32 0.707551 +33 0.76318 +34 0.852513 +35 0.873038 +36 0.943469 +37 1.040668 +38 1.070803 +39 1.117516 +40 1.166565 +41 1.178104 +42 1.151426 +43 1.209844 +44 1.198299 +45 1.132792 +46 1.149512 +47 1.21306 +48 1.345953 +49 1.32854 +50 1.309067 +51 1.296104 +52 1.346535 +53 1.450902 +54 1.475516 +55 1.548883 +56 1.628424 +57 1.665228 +58 1.612393 +59 1.653451 +60 1.599084 +61 1.674705 +62 1.670767 +63 1.759351 +64 1.771555 +65 1.653379 +66 1.634736 +67 1.642939 +68 1.587437 +69 1.558905 +70 1.571999 +71 1.620224 +72 1.57181 +73 1.545141 +74 1.433348 +75 1.497304 +76 1.693651 +77 1.728257 +78 1.754671 +79 1.731652 +80 1.713865 +81 1.641332 +82 1.515711 +83 1.413569 +84 1.441502 +85 1.330984 +86 1.269559 +87 1.225153 +88 1.133803 +89 0.956795 +90 0.793511 +91 0.692324 +92 0.542889 +93 0.499087 +94 0.422605 +95 0.338219 +96 0.272388 +97 0.207126 +98 0.152439 +99 0.095696 +100 0.069183 |