# HG changeset patch # User iuc # Date 1615816005 0 # Node ID a6fba3d925314b79f6f20b4e54672153f8b77586 # Parent ec9cbd6b9a49b9c0f4c5a3f4fe4ac3bed32d7be6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9" diff -r ec9cbd6b9a49 -r a6fba3d92531 macros.xml --- a/macros.xml Fri Jan 15 17:39:11 2021 +0000 +++ b/macros.xml Mon Mar 15 13:46:45 2021 +0000 @@ -5,7 +5,7 @@ the index versions in sync, but you should manually adjust the +galaxy version number. --> - 2.7.7a + 2.7.8a - + @@ -209,8 +206,9 @@ - - + + + @@ -225,5 +223,26 @@ + + + + + + + + + + + + + + + + + + + + + diff -r ec9cbd6b9a49 -r a6fba3d92531 rg_rnaStarSolo.xml --- a/rg_rnaStarSolo.xml Fri Jan 15 17:39:11 2021 +0000 +++ b/rg_rnaStarSolo.xml Mon Mar 15 13:46:45 2021 +0000 @@ -41,6 +41,17 @@ --soloCBlen $sc.params.soloCBlen --soloUMIstart $sc.params.soloUMIstart --soloUMIlen $sc.params.soloUMIlen + #if $sc.params.bccdna_mate.bc_location == "same_mate": + --soloBarcodeMate $sc.params.bccdna_mate.soloBarcodeMate + #if $sc.params.bccdna_mate.soloBarcodeMate == "1": + --clip5pNbases $sc.params.bccdna_mate.clip_n_bases 0 + #else if $sc.params.bccdna_mate.soloBarcodeMate == "2": + --clip3pNbases 0 $sc.params.bccdna_mate.clip_n_bases + #end if + #end if + --soloAdapterSequence '$sc.params.soloAdapterSequence' + --soloAdapterMismatchesNmax $sc.params.soloAdapterMismatchesNmax + --clipAdapterType $sc.params.clipAdapterType #end if #elif str($sc.solo_type) == "CB_UMI_Complex": @@ -58,8 +69,9 @@ --soloCBposition $cb_pos #set $umi_pos = '_'.join([str($sc.umi_start_anchor), str($sc.umi_start_anchor_pos), str($sc.umi_end_anchor), str($sc.umi_end_anchor_pos)]) --soloUMIposition $umi_pos - --soloAdapterSequence $sc.soloAdapterSequence + --soloAdapterSequence '$sc.soloAdapterSequence' --soloAdapterMismatchesNmax $sc.soloAdapterMismatchesNmax + --clipAdapterType $sc.clipAdapterType #elif str($sc.solo_type) == "SmartSeq": ## Create a manifest file with fastq files and their corresponding cell-ids @@ -87,6 +99,8 @@ #if str($solo.filter.filter_type) == "cellranger2": --soloCellFilter CellRanger2.2 $solo.filter.n_expected $solo.filter.max_perc $solo.filter.max_min_ratio + #else if str($solo.filter.filter_type) == "emptydrops": + --soloCellFilter EmptyDrops_CR $solo.filter.nExpectedCells $solo.filter.maxPercentile $solo.filter.maxMinRatio $solo.filter.indMin $solo.filter.indMax $solo.filter.umiMin $solo.filter.umiMinFracMedian $solo.filter.candMaxN $solo.filter.FDR $solo.filter.simN #else if str($solo.filter.filter_type) == "topcells": --soloCellFilter TopCells $solo.filter.n_cells #else if str($solo.filter.filter_type) == "no_filter": @@ -187,12 +201,28 @@ + + + + + + + + + + + + + + + + @@ -221,11 +251,11 @@ - - + + @@ -234,7 +264,7 @@ - + @@ -254,11 +284,13 @@ - + + + @@ -267,6 +299,18 @@ + + + + + + + + + + + + @@ -420,7 +464,6 @@ -
@@ -577,6 +620,72 @@ + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -612,6 +721,7 @@ + diff -r ec9cbd6b9a49 -r a6fba3d92531 test-data/rnastar_test_genomeSAindexNbases.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rnastar_test_genomeSAindexNbases.bed Mon Mar 15 13:46:45 2021 +0000 @@ -0,0 +1,2 @@ +test_chromosome 251 350 1 1 0 27 0 37 +test_chromosome 401 500 1 1 0 25 0 36 diff -r ec9cbd6b9a49 -r a6fba3d92531 test-data/rnastar_test_genomeSAindexNbases.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rnastar_test_genomeSAindexNbases.log Mon Mar 15 13:46:45 2021 +0000 @@ -0,0 +1,37 @@ + Started job on | Mar 08 19:43:44 + Started mapping on | Mar 08 19:43:45 + Finished on | Mar 08 19:43:45 + Mapping speed, Million of reads per hour | inf + + Number of input reads | 100 + Average input read length | 75 + UNIQUE READS: + Uniquely mapped reads number | 99 + Uniquely mapped reads % | 99.00% + Average mapped length | 74.65 + Number of splices: Total | 52 + Number of splices: Annotated (sjdb) | 0 + Number of splices: GT/AG | 52 + Number of splices: GC/AG | 0 + Number of splices: AT/AC | 0 + Number of splices: Non-canonical | 0 + Mismatch rate per base, % | 2.00% + Deletion rate per base | 0.00% + Deletion average length | 0.00 + Insertion rate per base | 0.00% + Insertion average length | 0.00 + MULTI-MAPPING READS: + Number of reads mapped to multiple loci | 1 + % of reads mapped to multiple loci | 1.00% + Number of reads mapped to too many loci | 0 + % of reads mapped to too many loci | 0.00% + UNMAPPED READS: + Number of reads unmapped: too many mismatches | 0 + % of reads unmapped: too many mismatches | 0.00% + Number of reads unmapped: too short | 0 + % of reads unmapped: too short | 0.00% + Number of reads unmapped: other | 0 + % of reads unmapped: other | 0.00% + CHIMERIC READS: + Number of chimeric reads | 0 + % of chimeric reads | 0.00% diff -r ec9cbd6b9a49 -r a6fba3d92531 test-data/rnastar_test_genomeSAindexNbases_02.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rnastar_test_genomeSAindexNbases_02.bed Mon Mar 15 13:46:45 2021 +0000 @@ -0,0 +1,2 @@ +test_chromosome 251 350 1 1 0 27 0 37 +test_chromosome 401 500 1 1 0 25 0 36 diff -r ec9cbd6b9a49 -r a6fba3d92531 test-data/rnastar_test_genomeSAindexNbases_02.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rnastar_test_genomeSAindexNbases_02.log Mon Mar 15 13:46:45 2021 +0000 @@ -0,0 +1,37 @@ + Started job on | Mar 08 19:43:59 + Started mapping on | Mar 08 19:43:59 + Finished on | Mar 08 19:43:59 + Mapping speed, Million of reads per hour | inf + + Number of input reads | 100 + Average input read length | 75 + UNIQUE READS: + Uniquely mapped reads number | 99 + Uniquely mapped reads % | 99.00% + Average mapped length | 74.65 + Number of splices: Total | 52 + Number of splices: Annotated (sjdb) | 0 + Number of splices: GT/AG | 52 + Number of splices: GC/AG | 0 + Number of splices: AT/AC | 0 + Number of splices: Non-canonical | 0 + Mismatch rate per base, % | 2.00% + Deletion rate per base | 0.00% + Deletion average length | 0.00 + Insertion rate per base | 0.00% + Insertion average length | 0.00 + MULTI-MAPPING READS: + Number of reads mapped to multiple loci | 1 + % of reads mapped to multiple loci | 1.00% + Number of reads mapped to too many loci | 0 + % of reads mapped to too many loci | 0.00% + UNMAPPED READS: + Number of reads unmapped: too many mismatches | 0 + % of reads unmapped: too many mismatches | 0.00% + Number of reads unmapped: too short | 0 + % of reads unmapped: too short | 0.00% + Number of reads unmapped: other | 0 + % of reads unmapped: other | 0.00% + CHIMERIC READS: + Number of chimeric reads | 0 + % of chimeric reads | 0.00% diff -r ec9cbd6b9a49 -r a6fba3d92531 test-data/rnastar_test_mapped_reads_genomeSAindexNbases.bam Binary file test-data/rnastar_test_mapped_reads_genomeSAindexNbases.bam has changed diff -r ec9cbd6b9a49 -r a6fba3d92531 test-data/rnastar_test_mapped_reads_genomeSAindexNbases_02.bam Binary file test-data/rnastar_test_mapped_reads_genomeSAindexNbases_02.bam has changed