| Previous changeset 0:b36afbb04e1c (2018-03-28) Next changeset 2:75427ceb32d1 (2019-12-18) |
|
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit 1b1520d42f96f78662e75bce1e899a57b052ec1e |
|
modified:
feelnc_wrapper.xml |
|
added:
test-data/candidate_lncRNA.classifier.txt |
| b |
| diff -r b36afbb04e1c -r 17a77824c8e4 feelnc_wrapper.xml --- a/feelnc_wrapper.xml Wed Mar 28 13:14:02 2018 -0400 +++ b/feelnc_wrapper.xml Wed Apr 25 15:55:19 2018 -0400 |
| [ |
| @@ -1,16 +1,20 @@ <?xml version="1.0" encoding="utf-8"?> -<tool id="feelnc" name="FEELnc" profile="17.01" version="0.1.1"> +<tool id="feelnc" name="FEELnc" profile="17.01" version="0.1.1.1"> <description>FlExible Extraction of LncRNA</description> <requirements> <requirement type="package" version="0.1.1">feelnc</requirement> </requirements> <command detect_errors="aggressive"><![CDATA[ -FEELnc_pipeline.sh +FEELnc_pipeline.sh --candidate='${transcripts}' --reference='${annotation}' ---genome='${genome}' +--genome='${genome}' --outname='candidate_lncRNA' --outdir='out_feelnc' + +&& + +cat out_feelnc/codpot/candidate_lncRNA.codpot_RF_summary.txt out_feelnc/classifier/candidate_lncRNA.classifier.log ]]></command> <inputs> <param name="transcripts" argument="--candidate" type="data" format="gtf" label="Transcripts assembly" help="Stringtie or Cufflinks output" /> @@ -20,6 +24,7 @@ <outputs> <data format="gtf" name="candidate_lncRNA" from_work_dir="out_feelnc/codpot/candidate_lncRNA.codpot.lncRNA.gtf" label="lncRNA annotation with ${tool.name} on ${on_string}" /> <data format="gtf" name="candidate_mRNA" from_work_dir="out_feelnc/codpot/candidate_lncRNA.codpot.mRNA.gtf" label="mRNA annotation with ${tool.name} on ${on_string}" /> + <data format="txt" name="classifier" from_work_dir="out_feelnc/classifier/candidate_lncRNA.classifier.txt" label="Classifier output with ${tool.name} on ${on_string}" /> </outputs> <tests> <test> @@ -28,12 +33,13 @@ <param name="genome" value="genome_chr38.fa" /> <output name="candidate_lncRNA" file="candidate_lncRNA.gtf.lncRNA-sort.gtf" sort="True" /> <output name="candidate_mRNA" file="candidate_lncRNA.gtf.mRNA-sort.gtf" sort="True" /> + <output name="classifier" file="candidate_lncRNA.classifier.txt" compare="sim_size" /> </test> </tests> <help><![CDATA[ **What it does** -FEELnc pipeline is used to annotate long non-coding RNAs (lncRNAs) based on reconstructed transcripts from RNA-seq data (either with or without a reference genome). +FEELnc pipeline is used to annotate long non-coding RNAs (lncRNAs) based on reconstructed transcripts from RNA-seq data (either with or without a reference genome). -------- |
| b |
| diff -r b36afbb04e1c -r 17a77824c8e4 test-data/candidate_lncRNA.classifier.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/candidate_lncRNA.classifier.txt Wed Apr 25 15:55:19 2018 -0400 |
| b |
| b'@@ -0,0 +1,406 @@\n+isBest\tlncRNA_gene\tlncRNA_transcript\tpartnerRNA_gene\tpartnerRNA_transcript\tdirection\ttype\tdistance\tsubtype\tlocation\n+1\tXLOC_090599\tTCONS_00231415\tENSCAFG00000009602\tENSCAFT00000049169\tsense\tintergenic\t8145\tsame_strand\tdownstream\n+1\tXLOC_090738\tTCONS_00232020\tENSCAFG00000013491\tENSCAFT00000021392\tsense\tintergenic\t6860\tsame_strand\tdownstream\n+1\tXLOC_090744\tTCONS_00232064\tENSCAFG00000013336\tENSCAFT00000021179\tsense\tintergenic\t28636\tsame_strand\tupstream\n+1\tXLOC_090744\tTCONS_00232060\tENSCAFG00000013346\tENSCAFT00000021186\tantisense\tintergenic\t32820\tdivergent\tupstream\n+0\tXLOC_090744\tTCONS_00232060\tENSCAFG00000013336\tENSCAFT00000021179\tsense\tintergenic\t35060\tsame_strand\tupstream\n+1\tXLOC_090795\tTCONS_00232275\tENSCAFG00000012566\tENSCAFT00000019952\tantisense\tintergenic\t24437\tconvergent\tdownstream\n+0\tXLOC_090795\tTCONS_00232275\tENSCAFG00000023704\tENSCAFT00000036617\tsense\tintergenic\t26617\tsame_strand\tdownstream\n+1\tXLOC_090752\tTCONS_00232087\tENSCAFG00000013259\tENSCAFT00000021052\tantisense\tintergenic\t3325\tdivergent\tupstream\n+1\tXLOC_090831\tTCONS_00232408\tENSCAFG00000011692\tENSCAFT00000018544\tsense\tintergenic\t12346\tsame_strand\tupstream\n+0\tXLOC_090831\tTCONS_00232408\tENSCAFG00000011706\tENSCAFT00000018594\tantisense\tintergenic\t14517\tdivergent\tupstream\n+1\tXLOC_090599\tTCONS_00231412\tENSCAFG00000009602\tENSCAFT00000049169\tsense\tintergenic\t7295\tsame_strand\tdownstream\n+1\tXLOC_090849\tTCONS_00232436\tENSCAFG00000030554\tENSCAFT00000018156\tantisense\tintergenic\t6167\tdivergent\tupstream\n+0\tXLOC_090849\tTCONS_00232436\tENSCAFG00000030554\tENSCAFT00000018170\tantisense\tintergenic\t7092\tdivergent\tupstream\n+1\tXLOC_091057\tTCONS_00233513\tENSCAFG00000023704\tENSCAFT00000036617\tantisense\tintergenic\t24758\tconvergent\tdownstream\n+0\tXLOC_091057\tTCONS_00233513\tENSCAFG00000012566\tENSCAFT00000019952\tsense\tintergenic\t26122\tsame_strand\tdownstream\n+1\tXLOC_090599\tTCONS_00231416\tENSCAFG00000009602\tENSCAFT00000049169\tsense\tintergenic\t8242\tsame_strand\tdownstream\n+1\tXLOC_090878\tTCONS_00232600\tENSCAFG00000009675\tENSCAFT00000015370\tsense\tintergenic\t19181\tsame_strand\tupstream\n+1\tXLOC_090628\tTCONS_00231554\tENSCAFG00000025208\tENSCAFT00000039078\tantisense\tintergenic\t1622\tdivergent\tupstream\n+0\tXLOC_090628\tTCONS_00231554\tENSCAFG00000010051\tENSCAFT00000015981\tsense\tintergenic\t4505\tsame_strand\tupstream\n+1\tXLOC_090726\tTCONS_00231956\tENSCAFG00000013637\tENSCAFT00000021622\tsense\tintergenic\t74091\tsame_strand\tupstream\n+1\tXLOC_090743\tTCONS_00232054\tENSCAFG00000013346\tENSCAFT00000021186\tantisense\tgenic\t0\toverlapping\tintronic\n+1\tXLOC_090727\tTCONS_00231958\tENSCAFG00000013637\tENSCAFT00000021622\tsense\tgenic\t0\tcontaining\tintronic\n+1\tXLOC_090743\tTCONS_00232058\tENSCAFG00000013346\tENSCAFT00000021186\tantisense\tintergenic\t377\tdivergent\tupstream\n+1\tXLOC_090660\tTCONS_00231733\tENSCAFG00000010552\tENSCAFT00000016789\tantisense\tgenic\t0\toverlapping\tintronic\n+0\tXLOC_090660\tTCONS_00231733\tENSCAFG00000010573\tENSCAFT00000016817\tsense\tintergenic\t4547\tsame_strand\tupstream\n+1\tXLOC_090599\tTCONS_00231410\tENSCAFG00000009602\tENSCAFT00000049169\tsense\tintergenic\t7295\tsame_strand\tdownstream\n+1\tXLOC_090744\tTCONS_00232061\tENSCAFG00000013336\tENSCAFT00000021179\tsense\tintergenic\t28636\tsame_strand\tupstream\n+1\tXLOC_090599\tTCONS_00231402\tENSCAFG00000009602\tENSCAFT00000049169\tsense\tintergenic\t7295\tsame_strand\tdownstream\n+1\tXLOC_091060\tTCONS_00233538\tENSCAFG00000023513\tENSCAFT00000036175\tsense\tintergenic\t369\tsame_strand\tdownstream\n+1\tXLOC_090894\tTCONS_00232667\tENSCAFG00000010137\tENSCAFT00000016099\tantisense\tintergenic\t2168\tdivergent\tupstream\n+0\tXLOC_090894\tTCONS_00232667\tENSCAFG00000010109\tENSCAFT00000016064\tantisense\tintergenic\t3957\tconvergent\tdownstream\n+1\tXLOC_091083\tTCONS_00233600\tENSCAFG00000031934\tENSCAFT00000048683\tsense\tintergenic\t4985\tsame_strand\tupstream\n+1\tXLOC_090801\tTCONS_00232316\tENSCAFG00000012174\tENSCAFT00000019707\tantisense\tgenic\t0\tnested\texonic\n+1\tXLOC_090970\tTCONS_00232964\tENSCAFG00000021604\tENSCAFT00000033711\tsense\tintergenic\t5524\tsame_strand\tupstream\n+1\tXLOC_091031\tTCONS_00233349\tENSCAFG00000013035\tENSCAFT000'..b'se\tintergenic\t40976\tconvergent\tdownstream\n+1\tXLOC_090737\tTCONS_00232010\tENSCAFG00000013502\tENSCAFT00000021419\tantisense\tgenic\t0\tnested\texonic\n+1\tXLOC_091073\tTCONS_00233580\tENSCAFG00000011857\tENSCAFT00000018829\tantisense\tgenic\t0\toverlapping\texonic\n+0\tXLOC_091073\tTCONS_00233580\tENSCAFG00000011835\tENSCAFT00000018806\tantisense\tintergenic\t6095\tdivergent\tupstream\n+1\tXLOC_091111\tTCONS_00233707\tENSCAFG00000030554\tENSCAFT00000018156\tsense\tintergenic\t3652\tsame_strand\tupstream\n+0\tXLOC_091111\tTCONS_00233707\tENSCAFG00000030554\tENSCAFT00000018170\tsense\tintergenic\t4577\tsame_strand\tupstream\n+1\tXLOC_090937\tTCONS_00232868\tENSCAFG00000032530\tENSCAFT00000043356\tsense\tintergenic\t23510\tsame_strand\tupstream\n+1\tXLOC_090675\tTCONS_00231790\tENSCAFG00000010731\tENSCAFT00000017072\tantisense\tgenic\t0\tnested\texonic\n+1\tXLOC_090989\tTCONS_00233037\tENSCAFG00000011340\tENSCAFT00000018023\tantisense\tintergenic\t5988\tconvergent\tdownstream\n+1\tXLOC_090947\tTCONS_00232887\tENSCAFG00000029859\tENSCAFT00000048330\tsense\tgenic\t0\tcontaining\tintronic\n+0\tXLOC_090947\tTCONS_00232887\tENSCAFG00000028763\tENSCAFT00000050209\tsense\tgenic\t0\tcontaining\tintronic\n+0\tXLOC_090947\tTCONS_00232887\tENSCAFG00000002103\tENSCAFT00000013152\tantisense\tgenic\t0\tcontaining\tintronic\n+1\tXLOC_090991\tTCONS_00233053\tENSCAFG00000013637\tENSCAFT00000021622\tantisense\tintergenic\t27440\tconvergent\tdownstream\n+1\tXLOC_090628\tTCONS_00231553\tENSCAFG00000025208\tENSCAFT00000039078\tantisense\tintergenic\t1622\tdivergent\tupstream\n+0\tXLOC_090628\tTCONS_00231553\tENSCAFG00000010051\tENSCAFT00000015981\tsense\tintergenic\t4505\tsame_strand\tupstream\n+1\tXLOC_090991\tTCONS_00233054\tENSCAFG00000013637\tENSCAFT00000021622\tantisense\tintergenic\t27440\tconvergent\tdownstream\n+1\tXLOC_090599\tTCONS_00231404\tENSCAFG00000009602\tENSCAFT00000049169\tsense\tintergenic\t7295\tsame_strand\tdownstream\n+1\tXLOC_090599\tTCONS_00231408\tENSCAFG00000009602\tENSCAFT00000049169\tsense\tintergenic\t7295\tsame_strand\tdownstream\n+1\tXLOC_090627\tTCONS_00231552\tENSCAFG00000010038\tENSCAFT00000015965\tantisense\tintergenic\t1824\tconvergent\tdownstream\n+1\tXLOC_090974\tTCONS_00232974\tENSCAFG00000010842\tENSCAFT00000017240\tsense\tintergenic\t44952\tsame_strand\tdownstream\n+1\tXLOC_090878\tTCONS_00232598\tENSCAFG00000009675\tENSCAFT00000015370\tsense\tintergenic\t19181\tsame_strand\tupstream\n+1\tXLOC_090802\tTCONS_00232320\tENSCAFG00000012174\tENSCAFT00000019707\tantisense\tintergenic\t692\tdivergent\tupstream\n+0\tXLOC_090802\tTCONS_00232320\tENSCAFG00000028933\tENSCAFT00000048290\tsense\tintergenic\t3788\tsame_strand\tupstream\n+0\tXLOC_090802\tTCONS_00232320\tENSCAFG00000032332\tENSCAFT00000047817\tantisense\tintergenic\t8255\tconvergent\tdownstream\n+0\tXLOC_090802\tTCONS_00232320\tENSCAFG00000028933\tENSCAFT00000050050\tsense\tintergenic\t779\tsame_strand\tupstream\n+1\tXLOC_090675\tTCONS_00231789\tENSCAFG00000010731\tENSCAFT00000017072\tantisense\tgenic\t0\tnested\texonic\n+1\tXLOC_090652\tTCONS_00231714\tENSCAFG00000021533\tENSCAFT00000033640\tantisense\tgenic\t0\tcontaining\tintronic\n+1\tXLOC_090690\tTCONS_00231846\tENSCAFG00000021604\tENSCAFT00000033711\tantisense\tgenic\t0\tcontaining\tintronic\n+1\tXLOC_090606\tTCONS_00231448\tENSCAFG00000009623\tENSCAFT00000015286\tantisense\tgenic\t0\tnested\texonic\n+0\tXLOC_090606\tTCONS_00231448\tENSCAFG00000009619\tENSCAFT00000015284\tantisense\tintergenic\t2139\tdivergent\tupstream\n+1\tXLOC_090700\tTCONS_00231871\tENSCAFG00000011125\tENSCAFT00000017715\tantisense\tgenic\t0\toverlapping\texonic\n+1\tXLOC_090707\tTCONS_00231909\tENSCAFG00000011325\tENSCAFT00000018005\tantisense\tintergenic\t6195\tdivergent\tupstream\n+0\tXLOC_090707\tTCONS_00231909\tENSCAFG00000031609\tENSCAFT00000047625\tsense\tintergenic\t9383\tsame_strand\tdownstream\n+1\tXLOC_091056\tTCONS_00233512\tENSCAFG00000023704\tENSCAFT00000036617\tantisense\tgenic\t0\toverlapping\texonic\n+1\tXLOC_090634\tTCONS_00231602\tENSCAFG00000010148\tENSCAFT00000016118\tantisense\tintergenic\t9337\tdivergent\tupstream\n+1\tXLOC_091009\tTCONS_00233127\tENSCAFG00000013336\tENSCAFT00000021179\tantisense\tintergenic\t6186\tconvergent\tdownstream\n+1\tXLOC_091058\tTCONS_00233516\tENSCAFG00000012566\tENSCAFT00000019952\tsense\tintergenic\t14665\tsame_strand\tdownstream\n' |