# HG changeset patch # User iuc # Date 1661511450 0 # Node ID fe733f05c2f876395e482bc06b1365e15686409b # Parent 09b7b0b2e2c25e4f01693e9c84e45e1e66abb8a0 planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 9142693589056424fb64869b69dbc08b179f57ee diff -r 09b7b0b2e2c2 -r fe733f05c2f8 macro.xml --- a/macro.xml Mon Jun 27 11:03:22 2022 +0000 +++ b/macro.xml Fri Aug 26 10:57:30 2022 +0000 @@ -1,7 +1,7 @@ 1.9.1 - 0 + 1 21.05 @@ -16,6 +16,16 @@ recentrifuge + + + topic_3174 + topic_3697 + + + operation_2238 + operation_3460 + +
diff -r 09b7b0b2e2c2 -r fe733f05c2f8 recentrifuge.xml --- a/recentrifuge.xml Mon Jun 27 11:03:22 2022 +0000 +++ b/recentrifuge.xml Fri Aug 26 10:57:30 2022 +0000 @@ -7,10 +7,28 @@ macro.xml + $logfile + | tee "$logfile" ]]> - + @@ -126,6 +146,7 @@ +
@@ -184,7 +205,9 @@ output_option['nohtml'] == False - + + output_option['no_logfile'] == False + output_option['extra'] == 'CSV' @@ -270,6 +293,29 @@ + +
+ +
+ + + + +
+ + +
+
+ +
+
+ + +
+ + + + +
countunassignedtidrankscoreinput_dir/centrifuge_1_outinput_dir/centrifuge_2_outinput_dir/centrifuge_outSHARED_speciesSHARED_genusSHARED_familySHARED_orderSHARED_classSHARED_phylumSHARED_SUMMARY 757575313567737575751no_rank392.6392.6392.6488.4489.0446.7442.0440.7440.7440.7757575313567737575752superkingdom392.6392.6392.6488.4489.0446.7442.0440.7440.7440.775757531356773757575751224phylum392.6392.6392.6488.4489.0446.7442.0440.7440.7440.77575753135677375752227521236class392.6392.6392.6488.4489.0446.7442.0440.70440.7737373313567737366673691347order390.6390.6390.6488.4489.0446.7442.000442.0676767313567673232326732543family400.3400.3400.3488.4489.0446.7000446.7353535313535444354561genus494.0494.0494.0488.4489.00000489.031313131313131313131562species488.4488.4488.4488.400000488.4
\ No newline at end of file diff -r 09b7b0b2e2c2 -r fe733f05c2f8 test-data/kraken_test/test1_csv.log --- a/test-data/kraken_test/test1_csv.log Mon Jun 27 11:03:22 2022 +0000 +++ b/test-data/kraken_test/test1_csv.log Fri Aug 26 10:57:30 2022 +0000 @@ -1,13 +1,14 @@ -=-= /home/pierre/anaconda3/envs/__recentrifuge@1.8.1/bin/rcf =-= v1.8.1 - Mar 2022 =-= by Jose Manuel Martí =-= +=-= /home/pierre/anaconda3/envs/__recentrifuge@1.9.1/bin/rcf =-= v1.9.1 - Jun 2022 =-= by Jose Manuel Martí =-= +Kraken .krk files to analyze: ['input_dir/kraken_out.krk'] Loading NCBI nodes... OK!  Loading NCBI names... OK!  Building dict of parent to children taxa... OK!   Please, wait, processing files in parallel...  -Loading output file /tmp/tmpz5ieggzi/files/d/5/5/dataset_d55a31f8-0f74-4938-9a4f-dce196b7467b.dat... OK! +Loading output file input_dir/kraken_out.krk... OK!  Seqs read: 99 [52.81 knt]  Seqs clas: 99 (0.00% unclassified)  Seqs pass: 99 (0.00% rejected) @@ -20,8 +21,8 @@ Info: 90 additional seqs discarded (90.909% of accepted)  Warning! 11 orphan taxids (rerun with --debug for details) -/tmp/tmpz5ieggzi/files/d/5/5/dataset_d55a31f8-0f74-4938-9a4f-dce196b7467b sample OK! -Load elapsed time: 0.0028 sec +input_dir/kraken_out sample OK! +Load elapsed time: 0.00392 sec   Building the taxonomy multiple tree... OK! diff -r 09b7b0b2e2c2 -r fe733f05c2f8 test-data/kraken_test/test1_csv.rcf.data.csv --- a/test-data/kraken_test/test1_csv.rcf.data.csv Mon Jun 27 11:03:22 2022 +0000 +++ b/test-data/kraken_test/test1_csv.rcf.data.csv Fri Aug 26 10:57:30 2022 +0000 @@ -1,4 +1,4 @@ -Samples,/tmp/tmpz5ieggzi/files/d/5/5/dataset_d55a31f8-0f74-4938-9a4f-dce196b7467b,/tmp/tmpz5ieggzi/files/d/5/5/dataset_d55a31f8-0f74-4938-9a4f-dce196b7467b,/tmp/tmpz5ieggzi/files/d/5/5/dataset_d55a31f8-0f74-4938-9a4f-dce196b7467b,Details,Details +Samples,input_dir/kraken_out,input_dir/kraken_out,input_dir/kraken_out,Details,Details Stats,count,unassigned,score,Rank,Name Id,,,,, 1,9,0,13.614815253856928,no_rank,root diff -r 09b7b0b2e2c2 -r fe733f05c2f8 test-data/kraken_test/test1_csv.rcf.html --- a/test-data/kraken_test/test1_csv.rcf.html Mon Jun 27 11:03:22 2022 +0000 +++ b/test-data/kraken_test/test1_csv.rcf.html Fri Aug 26 10:57:30 2022 +0000 @@ -6578,4 +6578,4 @@ selectedNodeLast.getDepth() < selectedNode.getDepth()); } */
countunassignedtidrankscore/tmp/tmpz5ieggzi/files/d/5/5/dataset_d55a31f8-0f74-4938-9a4f-dce196b7467b 91no_rank13.692superkingdom13.691224phylum13.691236class13.6991347order13.699543family13.6
\ No newline at end of file +" style="display:none">
countunassignedtidrankscoreinput_dir/kraken_out 91no_rank13.692superkingdom13.691224phylum13.691236class13.6991347order13.699543family13.6
\ No newline at end of file diff -r 09b7b0b2e2c2 -r fe733f05c2f8 test-data/kraken_test/test1_csv.rcf.stat.csv --- a/test-data/kraken_test/test1_csv.rcf.stat.csv Mon Jun 27 11:03:22 2022 +0000 +++ b/test-data/kraken_test/test1_csv.rcf.stat.csv Fri Aug 26 10:57:30 2022 +0000 @@ -1,4 +1,4 @@ -,/tmp/tmpz5ieggzi/files/d/5/5/dataset_d55a31f8-0f74-4938-9a4f-dce196b7467b +,input_dir/kraken_out Seqs. read,99.0 Seqs. unclass.,0.0 Seqs. class.,99.0 diff -r 09b7b0b2e2c2 -r fe733f05c2f8 test-data/kraken_test/test3_rcf.data.tsv --- a/test-data/kraken_test/test3_rcf.data.tsv Mon Jun 27 11:03:22 2022 +0000 +++ b/test-data/kraken_test/test3_rcf.data.tsv Fri Aug 26 10:57:30 2022 +0000 @@ -1,4 +1,4 @@ -Samples /tmp/tmpz5ieggzi/files/f/9/b/dataset_f9b4a772-d0f2-4391-a7bb-7f055b4fce1e /tmp/tmpz5ieggzi/files/f/9/b/dataset_f9b4a772-d0f2-4391-a7bb-7f055b4fce1e /tmp/tmpz5ieggzi/files/f/9/b/dataset_f9b4a772-d0f2-4391-a7bb-7f055b4fce1e Details Details +Samples input_dir/kraken_out input_dir/kraken_out input_dir/kraken_out Details Details Stats count unassigned score Rank Name Id 1 9 0 2.7230463906265316 no_rank root diff -r 09b7b0b2e2c2 -r fe733f05c2f8 test-data/kraken_test/test3_rcf.stat.tsv --- a/test-data/kraken_test/test3_rcf.stat.tsv Mon Jun 27 11:03:22 2022 +0000 +++ b/test-data/kraken_test/test3_rcf.stat.tsv Fri Aug 26 10:57:30 2022 +0000 @@ -1,4 +1,4 @@ - /tmp/tmpz5ieggzi/files/f/9/b/dataset_f9b4a772-d0f2-4391-a7bb-7f055b4fce1e + input_dir/kraken_out Seqs. read 99.0 Seqs. unclass. 0.0 Seqs. class. 99.0 diff -r 09b7b0b2e2c2 -r fe733f05c2f8 test-data/kraken_test/test3_tsv.log --- a/test-data/kraken_test/test3_tsv.log Mon Jun 27 11:03:22 2022 +0000 +++ b/test-data/kraken_test/test3_tsv.log Fri Aug 26 10:57:30 2022 +0000 @@ -1,14 +1,15 @@ -=-= /home/pierre/anaconda3/envs/__recentrifuge@1.8.1/bin/rcf =-= v1.8.1 - Mar 2022 =-= by Jose Manuel Martí =-= +=-= /home/pierre/anaconda3/envs/__recentrifuge@1.9.1/bin/rcf =-= v1.9.1 - Jun 2022 =-= by Jose Manuel Martí =-= CAUTION! --strain experimental mode activated! +Kraken .krk files to analyze: ['input_dir/kraken_out.krk'] Loading NCBI nodes... OK!  Loading NCBI names... OK!  Building dict of parent to children taxa... OK!   Please, wait, processing files in parallel...  -Loading output file /tmp/tmpz5ieggzi/files/f/9/b/dataset_f9b4a772-d0f2-4391-a7bb-7f055b4fce1e.dat... OK! +Loading output file input_dir/kraken_out.krk... OK!  Seqs read: 99 [52.81 knt]  Seqs clas: 99 (0.00% unclassified)  Seqs pass: 99 (0.00% rejected) @@ -21,8 +22,8 @@ Info: 90 additional seqs discarded (90.909% of accepted)  Warning! 11 orphan taxids (rerun with --debug for details) -/tmp/tmpz5ieggzi/files/f/9/b/dataset_f9b4a772-d0f2-4391-a7bb-7f055b4fce1e sample OK! -Load elapsed time: 0.00373 sec +input_dir/kraken_out sample OK! +Load elapsed time: 0.00395 sec   Building the taxonomy multiple tree... OK!