| Previous changeset 17:8ce1e2c7ee72 (2018-06-20) Next changeset 19:f3a5f075498f (2018-07-18) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit b467fdf3fabeed440dcb596108fc792d44e7d8d9 |
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modified:
featurecounts.xml |
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added:
test-data/small.gtf test-data/subset.sorted.bam test-data/subset.sorted.featurecounts.bam |
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| diff -r 8ce1e2c7ee72 -r d60b1c4e0347 featurecounts.xml --- a/featurecounts.xml Wed Jun 20 05:32:55 2018 -0400 +++ b/featurecounts.xml Wed Jul 04 17:32:47 2018 -0400 |
| [ |
| @@ -1,7 +1,7 @@ -<tool id="featurecounts" name="featureCounts" version="1.6.0.7" profile="16.04"> +<tool id="featurecounts" name="featureCounts" version="1.6.1.0" profile="16.04"> <description>Measure gene expression in RNA-Seq experiments from SAM or BAM files.</description> <requirements> - <requirement type="package" version="1.6.0">subread</requirement> + <requirement type="package" version="1.6.1">subread</requirement> <requirement type="package" version="1.7">samtools</requirement> </requirements> @@ -545,6 +545,16 @@ <metadata name="column_names" value="Status,featureCounts_input1.bam"/> </output> </test> + <!-- Ensure BAM output works --> + <test> + <param name="alignment" value="subset.sorted.bam" ftype="bam" /> + <param name="anno_select" value="history" /> + <param name="reference_gene_sets" value="small.gtf" ftype="gtf" /> + <section name="extended_parameters" > + <param name="R" value="true" /> + </section> + <output name="output_bam" value="subset.sorted.featurecounts.bam" /> + </test> </tests> <help><![CDATA[ |
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| diff -r 8ce1e2c7ee72 -r d60b1c4e0347 test-data/small.gtf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/small.gtf Wed Jul 04 17:32:47 2018 -0400 |
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| b'@@ -0,0 +1,3015 @@\n+chr1\tunknown\tCDS\t45515\t45550\t.\t-\t0\tgene_id "ildr1a"; gene_name "ildr1a"; p_id "P8669"; transcript_id "NM_200393"; tss_id "TSS8811";\n+chr1\tunknown\texon\t139486\t139769\t.\t+\t.\tgene_id "f10"; gene_name "f10"; p_id "P339"; transcript_id "NM_201462"; tss_id "TSS4261";\n+chr1\tunknown\tCDS\t183980\t184165\t.\t-\t0\tgene_id "grtp1a"; gene_name "grtp1a"; p_id "P5189"; transcript_id "NM_213402"; tss_id "TSS14313";\n+chr1\tunknown\tCDS\t297366\t297463\t.\t+\t1\tgene_id "cenpe"; gene_name "cenpe"; p_id "P5284"; transcript_id "NM_001076721"; tss_id "TSS5874";\n+chr1\tunknown\texon\t513842\t514315\t.\t-\t.\tgene_id "trmt10c"; gene_name "trmt10c"; p_id "P9514"; transcript_id "NM_001007332"; tss_id "TSS4482";\n+chr1\tunknown\texon\t611175\t611208\t.\t+\t.\tgene_id "jam2a"; gene_name "jam2a"; p_id "P4238"; transcript_id "NM_001098264"; tss_id "TSS13747";\n+chr1\tunknown\tCDS\t1466561\t1466589\t.\t+\t2\tgene_id "urp2"; gene_name "urp2"; p_id "P7393"; transcript_id "NM_001082942"; tss_id "TSS2052";\n+chr1\tunknown\tCDS\t1642135\t1642194\t.\t+\t0\tgene_id "atp1a1a.2"; gene_name "atp1a1a.2"; p_id "P4379"; transcript_id "NM_131687"; tss_id "TSS6001";\n+chr1\tunknown\tCDS\t1693106\t1693223\t.\t+\t0\tgene_id "atp1a1a.5"; gene_name "atp1a1a.5"; p_id "P8241"; transcript_id "NM_178099"; tss_id "TSS245";\n+chr1\tunknown\tCDS\t2057915\t2057967\t.\t+\t2\tgene_id "mbnl2"; gene_name "mbnl2"; p_id "P7443"; transcript_id "NM_001099998"; tss_id "TSS6706";\n+chr1\tunknown\tCDS\t2747373\t2747458\t.\t-\t1\tgene_id "gpc5a"; gene_name "gpc5a"; p_id "P2451"; transcript_id "NM_001302236"; tss_id "TSS4757";\n+chr1\tunknown\tCDS\t4802930\t4803112\t.\t+\t0\tgene_id "atic"; gene_name "atic"; p_id "P12430"; transcript_id "NM_001082796"; tss_id "TSS1401";\n+chr1\tunknown\tCDS\t4878416\t4878474\t.\t+\t0\tgene_id "cpo"; gene_name "cpo"; p_id "P6248"; transcript_id "NM_001145629"; tss_id "TSS8779";\n+chr1\tunknown\texon\t5465109\t5465211\t.\t+\t.\tgene_id "cnppd1"; gene_name "cnppd1"; p_id "P9212"; transcript_id "NM_199928"; tss_id "TSS242";\n+chr1\tunknown\texon\t5731242\t5731824\t.\t-\t.\tgene_id "klf7a"; gene_name "klf7a"; p_id "P4589"; transcript_id "NM_001020643"; tss_id "TSS10652";\n+chr1\tunknown\texon\t6839824\t6840031\t.\t+\t.\tgene_id "lancl1"; gene_name "lancl1"; p_id "P1575"; transcript_id "NM_001009891"; tss_id "TSS12567";\n+chr1\tunknown\tCDS\t6976024\t6976136\t.\t-\t0\tgene_id "efnb2b"; gene_name "efnb2b"; p_id "P1234"; transcript_id "NM_131808"; tss_id "TSS9044";\n+chr1\tunknown\tCDS\t7841073\t7841229\t.\t+\t0\tgene_id "mief2"; gene_name "mief2"; p_id "P3149"; transcript_id "NM_001076648"; tss_id "TSS6025";\n+chr1\tunknown\tCDS\t7995299\t7995388\t.\t-\t1\tgene_id "abcg2b"; gene_name "abcg2b"; p_id "P9804"; transcript_id "NM_001039066"; tss_id "TSS2622";\n+chr1\tunknown\texon\t8472049\t8472271\t.\t+\t.\tgene_id "plk1"; gene_name "plk1"; p_id "P11740"; transcript_id "NM_001003890"; tss_id "TSS12679";\n+chr1\tunknown\tCDS\t8585952\t8586096\t.\t-\t1\tgene_id "ubn1"; gene_name "ubn1"; p_id "P6692"; transcript_id "NM_001105118"; tss_id "TSS9862";\n+chr1\tunknown\tCDS\t9169535\t9169714\t.\t-\t0\tgene_id "mad1l1"; gene_name "mad1l1"; p_id "P9832"; transcript_id "NM_200912"; tss_id "TSS6202";\n+chr1\tunknown\texon\t9252686\t9252896\t.\t-\t.\tgene_id "tmem8a"; gene_name "tmem8a"; p_id "P4268"; transcript_id "NM_001145568"; tss_id "TSS11258";\n+chr1\tunknown\texon\t9615677\t9615814\t.\t+\t.\tgene_id "eif3f"; gene_name "eif3f"; p_id "P3336"; transcript_id "NM_001200009"; tss_id "TSS14015";\n+chr1\tunknown\texon\t9936120\t9936234\t.\t-\t.\tgene_id "trpc5a"; gene_name "trpc5a"; p_id "P8851"; transcript_id "NM_001044827"; tss_id "TSS12700";\n+chr1\tunknown\tCDS\t10429737\t10429811\t.\t+\t0\tgene_id "knstrn"; gene_name "knstrn"; p_id "P2473"; transcript_id "NM_001128774"; tss_id "TSS14568";\n+chr1\tunknown\tCDS\t11189873\t11190025\t.\t-\t2\tgene_id "iqce"; gene_name "iqce"; p_id "P4952"; transcript_id "NM_001287204"; tss_id "TSS10887";\n+chr1\tunknown\tCDS\t11384786\t11384891\t.\t+\t2\tgene_id "xpa"; gene_name "xpa"; p_id "P6569"; transcript_id "NM_200471"; tss_id "TSS14453";\n+chr1\tunknown\tCDS\t11500812\t11500958\t.\t+\t2\tgene_id "stra6l"; gene_name "stra6l"; p_id "P946"; transcript_id "NM_00'..b'3";\n+chr9\tunknown\texon\t53340315\t53340422\t.\t-\t.\tgene_id "trpm2"; gene_name "trpm2"; p_id "P4011"; transcript_id "NM_001288817"; tss_id "TSS13807";\n+chr9\tunknown\tstop_codon\t54203940\t54203942\t.\t+\t.\tgene_id "lect1"; gene_name "lect1"; p_id "P12953"; transcript_id "NM_001126448"; tss_id "TSS8044";\n+chr9\tunknown\tstop_codon\t54918738\t54918740\t.\t+\t.\tgene_id "drd1b"; gene_name "drd1b"; p_id "P3614"; transcript_id "NM_001135976"; tss_id "TSS14250";\n+chr9\tunknown\texon\t55339464\t55339614\t.\t-\t.\tgene_id "glra2"; gene_name "glra2"; p_id "P11067"; transcript_id "NM_001167899"; tss_id "TSS405";\n+chr9\tunknown\texon\t55522098\t55522243\t.\t-\t.\tgene_id "tbl1x"; gene_name "tbl1x"; p_id "P5819"; transcript_id "NM_001082994"; tss_id "TSS10302";\n+chr9\tunknown\tCDS\t56640639\t56640751\t.\t-\t1\tgene_id "rpl31"; gene_name "rpl31"; p_id "P9096"; transcript_id "NM_001040052"; tss_id "TSS2730";\n+chr9\tunknown\tstart_codon\t56792251\t56792253\t.\t-\t.\tgene_id "rab3gap1"; gene_name "rab3gap1"; p_id "P7333"; transcript_id "NM_001077788"; tss_id "TSS8758";\n+chrUn_KN149696v1\tunknown\texon\t166162\t166309\t.\t-\t.\tgene_id "zgc:112970"; gene_name "zgc:112970"; p_id "P13166"; transcript_id "NM_001014357"; tss_id "TSS7314";\n+chrUn_KN149779v1\tunknown\tCDS\t14055\t14134\t.\t-\t2\tgene_id "ift27"; gene_name "ift27"; p_id "P8442"; transcript_id "NM_001008588"; tss_id "TSS13448";\n+chrUn_KN149799v1\tunknown\texon\t2724\t2809\t.\t-\t.\tgene_id "dnaaf2"; gene_name "dnaaf2"; p_id "P14188"; transcript_id "NM_001033100"; tss_id "TSS9714";\n+chrUn_KN149842v1\tunknown\texon\t3126\t3192\t.\t+\t.\tgene_id "ndufaf3"; gene_name "ndufaf3"; p_id "P6163"; transcript_id "NM_001080615"; tss_id "TSS51";\n+chrUn_KN149859v1\tunknown\tCDS\t52763\t52848\t.\t+\t2\tgene_id "zgc:63569"; gene_name "zgc:63569"; p_id "P7566"; transcript_id "NM_198871"; tss_id "TSS6258";\n+chrUn_KN149909v1\tunknown\tCDS\t34467\t34551\t.\t-\t0\tgene_id "wdr77"; gene_name "wdr77"; p_id "P5165"; transcript_id "NM_200534"; tss_id "TSS5125";\n+chrUn_KN149943v1\tunknown\texon\t23472\t23606\t.\t-\t.\tgene_id "slc1a9"; gene_name "slc1a9"; p_id "P8446"; transcript_id "NM_001190759"; tss_id "TSS10209";\n+chrUn_KN149978v1\tunknown\tstart_codon\t15390\t15392\t.\t-\t.\tgene_id "zgc:92045"; gene_name "zgc:92045"; p_id "P13013"; transcript_id "NM_001002390"; tss_id "TSS6046";\n+chrUn_KN150027v1\tunknown\texon\t1941\t1997\t.\t+\t.\tgene_id "arfgap1"; gene_name "arfgap1"; p_id "P10965"; transcript_id "NM_001007303"; tss_id "TSS10946";\n+chrUn_KN150131v1\tunknown\texon\t11069\t11135\t.\t+\t.\tgene_id "papl"; gene_name "papl"; p_id "P147"; transcript_id "NM_001099250"; tss_id "TSS12602";\n+chrUn_KN150178v1\tunknown\tCDS\t12685\t12779\t.\t-\t2\tgene_id "soul3"; gene_name "soul3"; p_id "P9662"; transcript_id "NM_001045401"; tss_id "TSS8205";\n+chrUn_KN150212v1\tunknown\tCDS\t8269\t8422\t.\t-\t1\tgene_id "mpzl3"; gene_name "mpzl3"; p_id "P12137"; transcript_id "NM_213169"; tss_id "TSS11476";\n+chrUn_KN150214v1\tunknown\tCDS\t76979\t77032\t.\t-\t2\tgene_id "prp"; gene_name "prp"; p_id "P11866"; transcript_id "NM_001291376"; tss_id "TSS6705";\n+chrUn_KN150273v1\tunknown\texon\t60953\t61071\t.\t+\t.\tgene_id "fbxw11a"; gene_name "fbxw11a"; p_id "P8078"; transcript_id "NM_201310"; tss_id "TSS14799";\n+chrUn_KN150339v1\tunknown\tCDS\t33173\t33252\t.\t-\t0\tgene_id "trpm6"; gene_name "trpm6"; p_id "P1570"; transcript_id "NM_001251831"; tss_id "TSS1465";\n+chrUn_KN150432v1\tunknown\tCDS\t49171\t49340\t.\t-\t1\tgene_id "zgc:152904"; gene_name "zgc:152904"; p_id "P10215"; transcript_id "NM_001076744"; tss_id "TSS9128";\n+chrUn_KN150506v1\tunknown\tCDS\t8057\t8075\t.\t-\t1\tgene_id "cib1"; gene_name "cib1"; p_id "P13469"; transcript_id "NM_001017681_1"; tss_id "TSS4164";\n+chrUn_KN150550v1\tunknown\tCDS\t10150\t10249\t.\t+\t2\tgene_id "fanca"; gene_name "fanca"; p_id "P11867"; transcript_id "NM_001040635"; tss_id "TSS9959";\n+chrUn_KN150672v1\tunknown\tCDS\t67767\t68126\t.\t+\t0\tgene_id "hsf5"; gene_name "hsf5"; p_id "P8424"; transcript_id "NM_001089476"; tss_id "TSS9299";\n+chrUn_KN150706v1\tunknown\tstop_codon\t880\t882\t.\t-\t.\tgene_id "angptl1b"; gene_name "angptl1b"; p_id "P5887"; transcript_id "NM_001199970"; tss_id "TSS7889";\n' |
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| diff -r 8ce1e2c7ee72 -r d60b1c4e0347 test-data/subset.sorted.bam |
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| diff -r 8ce1e2c7ee72 -r d60b1c4e0347 test-data/subset.sorted.featurecounts.bam |
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| Binary file test-data/subset.sorted.featurecounts.bam has changed |