| Previous changeset 26:3ea5a2a63fa2 (2023-03-27) Next changeset 28:3e94726bfa9d (2024-02-11) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 65fa34f035934b4e9c1fbeb5dffe00b12e6a0f32 |
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modified:
macros.xml rg_rnaStar.xml |
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added:
test-data/fakexon.Homo_sapiens.GRCh38.100.chr21.gtf test-data/no_exon.gtf test-data/rnastar_test_mapped_reads_fakexon.bam |
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| diff -r 3ea5a2a63fa2 -r 79de45b5069b macros.xml --- a/macros.xml Mon Mar 27 16:37:27 2023 +0000 +++ b/macros.xml Fri Sep 01 13:17:29 2023 +0000 |
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| @@ -5,7 +5,7 @@ the index versions in sync, but you should manually update @IDX_VERSION_SUFFIX@ --> <!-- STAR version to be used --> <token name="@TOOL_VERSION@">2.7.10b</token> - <token name="@VERSION_SUFFIX@">3</token> + <token name="@VERSION_SUFFIX@">4</token> <token name="@PROFILE@">21.01</token> <!-- STAR index version compatible with this version of STAR This is the STAR version that introduced the index structure expected @@ -60,6 +60,7 @@ </xml> <xml name="SJDBOPTIONS"> <param argument="--sjdbGTFfile" type="data" format="gff3,gtf" label="Gene model (gff3,gtf) file for splice junctions" optional="false" help="Exon junction information for mapping splices"/> + <param argument="--sjdbGTFfeatureExon" type="text" value="exon" label="Elements to use from the gene model to use for splice junctions" help="By default and for almost all cases: 'exon', referring to finding junctions at the RNA splice sites. This can optionally be changed to allow splicing at other levels, such as 'gene', 'transcript', 'CDS'."/> <param argument="--sjdbOverhang" type="integer" min="1" value="100" label="Length of the genomic sequence around annotated junctions" help="Used in constructing the splice junctions database. Ideal value is ReadLength-1"/> </xml> <xml name="dbKeyActions"> @@ -103,15 +104,17 @@ #if str($refGenomeSource.GTFconditional.GTFselect) == 'with-gtf': --sjdbOverhang '${refGenomeSource.GTFconditional.sjdbOverhang}' --sjdbGTFfile '${refGenomeSource.GTFconditional.sjdbGTFfile}' + --sjdbGTFfeatureExon '${refGenomeSource.GTFconditional.sjdbGTFfeatureExon}' #if str($refGenomeSource.GTFconditional.sjdbGTFfile.ext) == 'gff3': --sjdbGTFtagExonParentTranscript Parent #end if #end if #else: - ## ref genome selection is less complex for STARsolo cause + ## ref genome selection is less complex for STARsolo because ## with-gtf is mandatory there --sjdbOverhang '${refGenomeSource.sjdbOverhang}' --sjdbGTFfile '${refGenomeSource.sjdbGTFfile}' + --sjdbGTFfeatureExon '${refGenomeSource.sjdbGTFfeatureExon}' #if str($refGenomeSource.sjdbGTFfile.ext) == 'gff3': --sjdbGTFtagExonParentTranscript Parent #end if @@ -137,6 +140,7 @@ #if str($refGenomeSource.GTFconditional.GTFselect) == 'without-gtf-with-gtf': --sjdbOverhang $refGenomeSource.GTFconditional.sjdbOverhang --sjdbGTFfile '${refGenomeSource.GTFconditional.sjdbGTFfile}' + --sjdbGTFfeatureExon '${refGenomeSource.GTFconditional.sjdbGTFfeatureExon}' #if str($refGenomeSource.GTFconditional.sjdbGTFfile.ext) == 'gff3': --sjdbGTFtagExonParentTranscript Parent #end if |
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| diff -r 3ea5a2a63fa2 -r 79de45b5069b rg_rnaStar.xml --- a/rg_rnaStar.xml Mon Mar 27 16:37:27 2023 +0000 +++ b/rg_rnaStar.xml Fri Sep 01 13:17:29 2023 +0000 |
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| @@ -628,6 +628,44 @@ <metadata name="column_names" value="GeneID,Counts_unstrand,Counts_firstStrand,Counts_secondStrand" /> </output> </test> + <!-- Test if an alternative feature can be provided as a splicing unit. + If the splice feature set is not set correctly, + "Fatal INPUT FILE error, no exon lines in the GTF file" is expected --> + <test expect_num_outputs="4"> + <conditional name="singlePaired"> + <param name="sPaired" value="single" /> + <param name="input1" value="tophat_in2.fastqsanger" ftype="fastqsanger" /> + </conditional> + <conditional name="refGenomeSource"> + <param name="geneSource" value="history" /> + <param name="genomeFastaFiles" value="tophat_test.fa" /> + <param name="genomeSAindexNbases" value="5" /> + <conditional name="GTFconditional"> + <param name="GTFselect" value="with-gtf" /> + <param name="sjdbOverhang" value="75"/> + <param name="sjdbGTFfile" value="no_exon.gtf" ftype="gtf"/> + <param name="sjdbGTFfeatureExon" value="fakexon"/> + <conditional name="quantmode_output"> + <param name="quantMode" value="GeneCounts"/> + </conditional> + </conditional> + </conditional> + <section name="oformat"> + <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch" /> + </section> + <section name="algo"> + <conditional name="params"> + <param name="settingsType" value="default" /> + </conditional> + </section> + + <output name="output_log" file="rnastar_test.log" compare="re_match_multiline" /> + <output name="splice_junctions" file="rnastar_test_splicejunctions.bed"/> + <output name="mapped_reads" file="rnastar_test_mapped_reads_fakexon.bam" compare="sim_size" delta="634" /> + <output name="reads_per_gene" file="tophat_test_reads_per_gene.txt"> + <metadata name="column_names" value="GeneID,Counts_unstrand,Counts_firstStrand,Counts_secondStrand" /> + </output> + </test> <!-- test gtf file and TranscriptomeSAM mode --> <test expect_num_outputs="4"> <conditional name="singlePaired"> |
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| diff -r 3ea5a2a63fa2 -r 79de45b5069b test-data/fakexon.Homo_sapiens.GRCh38.100.chr21.gtf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fakexon.Homo_sapiens.GRCh38.100.chr21.gtf Fri Sep 01 13:17:29 2023 +0000 |
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| b'@@ -0,0 +1,461 @@\n+#!genome-build GRCh38.p13\n+#!genome-version GRCh38\n+#!genome-date 2013-12\n+#!genome-build-accession NCBI:GCA_000001405.28\n+#!genebuild-last-updated 2019-06\n+21\thavana\tgene\t1000\t6346\t.\t+\t.\tgene_id "ENSG00000279493"; gene_version "1"; gene_name "FP565260.4"; gene_source "havana"; gene_biotype "protein_coding";\n+21\thavana\ttranscript\t1000\t6346\t.\t+\t.\tgene_id "ENSG00000279493"; gene_version "1"; transcript_id "ENST00000624081"; transcript_version "1"; gene_name "FP565260.4"; gene_source "havana"; gene_biotype "protein_coding"; transcript_name "FP565260.4-201"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "cds_start_NF"; tag "mRNA_start_NF"; tag "basic"; transcript_support_level "5";\n+21\thavana\tfakexon\t1000\t1075\t.\t+\t.\tgene_id "ENSG00000279493"; gene_version "1"; transcript_id "ENST00000624081"; transcript_version "1"; exon_number "1"; gene_name "FP565260.4"; gene_source "havana"; gene_biotype "protein_coding"; transcript_name "FP565260.4-201"; transcript_source "havana"; transcript_biotype "protein_coding"; exon_id "ENSE00003760288"; exon_version "1"; tag "cds_start_NF"; tag "mRNA_start_NF"; tag "basic"; transcript_support_level "5";\n+21\thavana\tCDS\t1000\t1075\t.\t+\t0\tgene_id "ENSG00000279493"; gene_version "1"; transcript_id "ENST00000624081"; transcript_version "1"; exon_number "1"; gene_name "FP565260.4"; gene_source "havana"; gene_biotype "protein_coding"; transcript_name "FP565260.4-201"; transcript_source "havana"; transcript_biotype "protein_coding"; protein_id "ENSP00000485664"; protein_version "1"; tag "cds_start_NF"; tag "mRNA_start_NF"; tag "basic"; transcript_support_level "5";\n+21\thavana\tfakexon\t1749\t1888\t.\t+\t.\tgene_id "ENSG00000279493"; gene_version "1"; transcript_id "ENST00000624081"; transcript_version "1"; exon_number "2"; gene_name "FP565260.4"; gene_source "havana"; gene_biotype "protein_coding"; transcript_name "FP565260.4-201"; transcript_source "havana"; transcript_biotype "protein_coding"; exon_id "ENSE00003758404"; exon_version "1"; tag "cds_start_NF"; tag "mRNA_start_NF"; tag "basic"; transcript_support_level "5";\n+21\thavana\tCDS\t1749\t1888\t.\t+\t2\tgene_id "ENSG00000279493"; gene_version "1"; transcript_id "ENST00000624081"; transcript_version "1"; exon_number "2"; gene_name "FP565260.4"; gene_source "havana"; gene_biotype "protein_coding"; transcript_name "FP565260.4-201"; transcript_source "havana"; transcript_biotype "protein_coding"; protein_id "ENSP00000485664"; protein_version "1"; tag "cds_start_NF"; tag "mRNA_start_NF"; tag "basic"; transcript_support_level "5";\n+21\thavana\tfakexon\t3587\t3672\t.\t+\t.\tgene_id "ENSG00000279493"; gene_version "1"; transcript_id "ENST00000624081"; transcript_version "1"; exon_number "3"; gene_name "FP565260.4"; gene_source "havana"; gene_biotype "protein_coding"; transcript_name "FP565260.4-201"; transcript_source "havana"; transcript_biotype "protein_coding"; exon_id "ENSE00003755466"; exon_version "1"; tag "cds_start_NF"; tag "mRNA_start_NF"; tag "basic"; transcript_support_level "5";\n+21\thavana\tCDS\t3587\t3672\t.\t+\t0\tgene_id "ENSG00000279493"; gene_version "1"; transcript_id "ENST00000624081"; transcript_version "1"; exon_number "3"; gene_name "FP565260.4"; gene_source "havana"; gene_biotype "protein_coding"; transcript_name "FP565260.4-201"; transcript_source "havana"; transcript_biotype "protein_coding"; protein_id "ENSP00000485664"; protein_version "1"; tag "cds_start_NF"; tag "mRNA_start_NF"; tag "basic"; transcript_support_level "5";\n+21\thavana\tfakexon\t6136\t6346\t.\t+\t.\tgene_id "ENSG00000279493"; gene_version "1"; transcript_id "ENST00000624081"; transcript_version "1"; exon_number "4"; gene_name "FP565260.4"; gene_source "havana"; gene_biotype "protein_coding"; transcript_name "FP565260.4-201"; transcript_source "havana"; transcript_biotype "protein_coding"; exon_id "ENSE00003755385"; exon_version "1"; tag "cds_start_NF"; tag "mRNA_start_NF"; tag "basic"; transcript_support_level "5";\n+21\thavana\tCDS\t6136\t6298\t.\t+\t1\tgene_id "ENSG0000027'..b'6691\t.\t+\t.\tgene_id "ENSG00000277777"; gene_version "1"; gene_name "CU633967.2"; gene_source "ensembl"; gene_biotype "misc_RNA";\n+21\tensembl\ttranscript\t586591\t586691\t.\t+\t.\tgene_id "ENSG00000277777"; gene_version "1"; transcript_id "ENST00000610788"; transcript_version "1"; gene_name "CU633967.2"; gene_source "ensembl"; gene_biotype "misc_RNA"; transcript_name "CU633967.2-201"; transcript_source "ensembl"; transcript_biotype "misc_RNA"; tag "basic"; transcript_support_level "NA";\n+21\tensembl\tfakexon\t586591\t586691\t.\t+\t.\tgene_id "ENSG00000277777"; gene_version "1"; transcript_id "ENST00000610788"; transcript_version "1"; exon_number "1"; gene_name "CU633967.2"; gene_source "ensembl"; gene_biotype "misc_RNA"; transcript_name "CU633967.2-201"; transcript_source "ensembl"; transcript_biotype "misc_RNA"; exon_id "ENSE00003748388"; exon_version "1"; tag "basic"; transcript_support_level "NA";\n+21\thavana\tgene\t692383\t694838\t.\t-\t.\tgene_id "ENSG00000279186"; gene_version "1"; gene_name "FP236315.2"; gene_source "havana"; gene_biotype "TEC";\n+21\thavana\ttranscript\t692383\t694838\t.\t-\t.\tgene_id "ENSG00000279186"; gene_version "1"; transcript_id "ENST00000624506"; transcript_version "1"; gene_name "FP236315.2"; gene_source "havana"; gene_biotype "TEC"; transcript_name "FP236315.2-201"; transcript_source "havana"; transcript_biotype "TEC"; tag "basic"; transcript_support_level "NA";\n+21\thavana\tfakexon\t692383\t694838\t.\t-\t.\tgene_id "ENSG00000279186"; gene_version "1"; transcript_id "ENST00000624506"; transcript_version "1"; exon_number "1"; gene_name "FP236315.2"; gene_source "havana"; gene_biotype "TEC"; transcript_name "FP236315.2-201"; transcript_source "havana"; transcript_biotype "TEC"; exon_id "ENSE00003756739"; exon_version "1"; tag "basic"; transcript_support_level "NA";\n+21\thavana\tgene\t694546\t696361\t.\t+\t.\tgene_id "ENSG00000279784"; gene_version "1"; gene_name "FP236315.3"; gene_source "havana"; gene_biotype "lncRNA";\n+21\thavana\ttranscript\t694546\t696361\t.\t+\t.\tgene_id "ENSG00000279784"; gene_version "1"; transcript_id "ENST00000623587"; transcript_version "1"; gene_name "FP236315.3"; gene_source "havana"; gene_biotype "lncRNA"; transcript_name "FP236315.3-201"; transcript_source "havana"; transcript_biotype "lncRNA"; tag "basic"; transcript_support_level "2";\n+21\thavana\tfakexon\t694546\t694654\t.\t+\t.\tgene_id "ENSG00000279784"; gene_version "1"; transcript_id "ENST00000623587"; transcript_version "1"; exon_number "1"; gene_name "FP236315.3"; gene_source "havana"; gene_biotype "lncRNA"; transcript_name "FP236315.3-201"; transcript_source "havana"; transcript_biotype "lncRNA"; exon_id "ENSE00003758868"; exon_version "1"; tag "basic"; transcript_support_level "2";\n+21\thavana\tfakexon\t696164\t696361\t.\t+\t.\tgene_id "ENSG00000279784"; gene_version "1"; transcript_id "ENST00000623587"; transcript_version "1"; exon_number "2"; gene_name "FP236315.3"; gene_source "havana"; gene_biotype "lncRNA"; transcript_name "FP236315.3-201"; transcript_source "havana"; transcript_biotype "lncRNA"; exon_id "ENSE00003757033"; exon_version "1"; tag "basic"; transcript_support_level "2";\n+21\thavana\tgene\t696205\t698657\t.\t-\t.\tgene_id "ENSG00000279064"; gene_version "1"; gene_name "FP236315.1"; gene_source "havana"; gene_biotype "lncRNA";\n+21\thavana\ttranscript\t696205\t698657\t.\t-\t.\tgene_id "ENSG00000279064"; gene_version "1"; transcript_id "ENST00000623723"; transcript_version "1"; gene_name "FP236315.1"; gene_source "havana"; gene_biotype "lncRNA"; transcript_name "FP236315.1-201"; transcript_source "havana"; transcript_biotype "lncRNA"; tag "basic"; transcript_support_level "2";\n+21\thavana\tfakexon\t696205\t696358\t.\t-\t.\tgene_id "ENSG00000279064"; gene_version "1"; transcript_id "ENST00000623723"; transcript_version "1"; exon_number "2"; gene_name "FP236315.1"; gene_source "havana"; gene_biotype "lncRNA"; transcript_name "FP236315.1-201"; transcript_source "havana"; transcript_biotype "lncRNA"; exon_id "ENSE00003756092"; exon_version "1"; tag "basic"; transcript_support_level "2";\n' |
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| diff -r 3ea5a2a63fa2 -r 79de45b5069b test-data/no_exon.gtf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/no_exon.gtf Fri Sep 01 13:17:29 2023 +0000 |
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| @@ -0,0 +1,4 @@ +test_chromosome test gene 1 650 . + . gene_id "GENE1"; gene_name "GENE1"; transcript_id "GENE1_t1"; +test_chromosome test transcript 1 650 . + . gene_id "GENE1"; gene_name "GENE1"; transcript_id "GENE1_t1"; +test_chromosome test fakexon 1 650 . + . gene_id "GENE1"; transcript_id "GENE1_t1"; exon_number "1"; gene_name "GENE1"; +test_chromosome test CDS 100 550 . + . gene_id "GENE1"; transcript_id "GENE1_t1"; exon_number "1"; gene_name "GENE1"; |
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| diff -r 3ea5a2a63fa2 -r 79de45b5069b test-data/rnastar_test_mapped_reads_fakexon.bam |
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| Binary file test-data/rnastar_test_mapped_reads_fakexon.bam has changed |