# HG changeset patch # User artbio # Date 1561414025 14400 # Node ID 5d2304b09f584477de255298776c071e7ed620eb # Parent f689c4ea8c4327059896e8fe168af723977cb8e2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_filter_genes commit d9e43e514d5fe7bbc7205a52ccb3e4faef50e856 diff -r f689c4ea8c43 -r 5d2304b09f58 filter_genes.R --- a/filter_genes.R Mon Jun 24 13:38:10 2019 -0400 +++ b/filter_genes.R Mon Jun 24 18:07:05 2019 -0400 @@ -81,6 +81,7 @@ # Filter matrix data.counts <- data.counts[kept_genes,] +data.counts <- cbind(Genes=rownames(data.counts), data.counts) # Save filtered matrix write.table( @@ -89,5 +90,5 @@ sep = "\t", quote = F, col.names = T, - row.names = T + row.names = F ) \ No newline at end of file diff -r f689c4ea8c43 -r 5d2304b09f58 filter_genes.xml --- a/filter_genes.xml Mon Jun 24 13:38:10 2019 -0400 +++ b/filter_genes.xml Mon Jun 24 18:07:05 2019 -0400 @@ -1,4 +1,4 @@ - + which are detected in less that a given fraction of the libraries r-optparse diff -r f689c4ea8c43 -r 5d2304b09f58 test-data/filtered-0.05.tab --- a/test-data/filtered-0.05.tab Mon Jun 24 13:38:10 2019 -0400 +++ b/test-data/filtered-0.05.tab Mon Jun 24 18:07:05 2019 -0400 @@ -1,4 +1,4 @@ -1001000235.G10 1001000174.B1 1001000177.C5 1001000182.H4 1001000175.A2 1001000230.B11 1001000237.E9 1001000173.E10 1001000241.E7 1001000249.A3 1001000179.A7 1001000247.F11 1001000240.D9 1001000178.G5 1001000249.E3 1001000174.H6 1001000181.F8 1001000177.A10 1001000235.D2 1001000240.G10 1001000248.E7 1001000012.B6 1001000179.H4 1001000230.C1 1001000175.H9 1001000241.G11 1001000174.G2 1001000252.C6 1001000186.D11 1001000239.G7 1001000258.G11 1001000264.A1 1001000174.A10 1001000255.E9 1001000242.B5 1001000179.F3 1001000185.F9 1001000267.F8 1001000183.G10 1001000247.E7 1001000031.A2 1001000271.B1 1001000187.G6 1001000236.C6 1001000238.C12 1001000187.D6 1001000235.E10 1001000036.C1 1001000253.H2 1001000231.C2 1001000178.C10 1001000267.C1 1001000180.E4 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1001000237.H10 1001000231.B7 1001000270.H8 1001000240.G1 1001000177.D11 1001000185.D3 1001000238.B5 1001000174.E10 BAI3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9.97662501806838 0 0 0 0 12.8615775772142 0 0 0 15.9032354384535 0 0 0 0 0 12.2158463533178 9.68026850722175 15.3729581524844 0 0 14.28403727033 0 0 0 0 17.0775051033723 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9.86467441602363 0 0 0 0 0 0 14.2185940019444 0 0 0 0 0 9.4604919129408 0 0 FAM63B 0 14.7268225958904 0 0 0 0 0 14.2095873331695 0 0 0 7.05523661711308 0 0 0 0 10.8662524562421 0 0 0 0 0 0 12.5659445674216 0 0 0 0 0 0 17.508917577493 0 15.2092038075611 0 0 16.3552364080959 0 0 0 0 0 0 0 0 0 0 12.833405122753 0 0 0 0 10.631490277574 0 0 0 0 6.49910345713958 0 0 12.6988507765885 0 17.5291982691478 0 0 0 0 0 0 9.72047933810935 0 0 8.00314342388438 0 0 0 0 0 10.5923353166174 0 13.1956852586776 0 0 0 0 14.4254341461373 0 0 0 0 13.2598797712496 0 0 0 0 0 0 0 6.6653716296684 0 0 TMEM132C 0 0 0 0 0 0 0 0 0 15.6304274760255 0 0 0 0 11.3724171014623 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13.7057920287568 0 0 12.4990036192117 0 0 0 0 0 0 0 0 0 0 0 12.3619870470136 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 16.6895776681193 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 diff -r f689c4ea8c43 -r 5d2304b09f58 test-data/filtered-5.tab --- a/test-data/filtered-5.tab Mon Jun 24 13:38:10 2019 -0400 +++ b/test-data/filtered-5.tab Mon Jun 24 18:07:05 2019 -0400 @@ -1,4 +1,4 @@ -1001000235.G10 1001000174.B1 1001000177.C5 1001000182.H4 1001000175.A2 1001000230.B11 1001000237.E9 1001000173.E10 1001000241.E7 1001000249.A3 1001000179.A7 1001000247.F11 1001000240.D9 1001000178.G5 1001000249.E3 1001000174.H6 1001000181.F8 1001000177.A10 1001000235.D2 1001000240.G10 1001000248.E7 1001000012.B6 1001000179.H4 1001000230.C1 1001000175.H9 1001000241.G11 1001000174.G2 1001000252.C6 1001000186.D11 1001000239.G7 1001000258.G11 1001000264.A1 1001000174.A10 1001000255.E9 1001000242.B5 1001000179.F3 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1001000230.B11 1001000237.E9 1001000173.E10 1001000241.E7 1001000249.A3 1001000179.A7 1001000247.F11 1001000240.D9 1001000178.G5 1001000249.E3 1001000174.H6 1001000181.F8 1001000177.A10 1001000235.D2 1001000240.G10 1001000248.E7 1001000012.B6 1001000179.H4 1001000230.C1 1001000175.H9 1001000241.G11 1001000174.G2 1001000252.C6 1001000186.D11 1001000239.G7 1001000258.G11 1001000264.A1 1001000174.A10 1001000255.E9 1001000242.B5 1001000179.F3 1001000185.F9 1001000267.F8 1001000183.G10 1001000247.E7 1001000031.A2 1001000271.B1 1001000187.G6 1001000236.C6 1001000238.C12 1001000187.D6 1001000235.E10 1001000036.C1 1001000253.H2 1001000231.C2 1001000178.C10 1001000267.C1 1001000180.E4 1001000173.E5 1001000179.F5 1001000245.G11 1001000185.D5 1001000012.A7 1001000010.B4 1001000265.D11 1001000032.F1 1001000036.H9 1001000245.B3 1001000185.A8 1001000178.C6 1001000037.F10 1001000245.H4 1001000012.B10 1001000245.F2 1001000249.G2 1001000187.E11 1001000266.A4 1001000266.G4 1001000179.E3 1001000178.C11 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6.49910345713958 0 0 12.6988507765885 0 17.5291982691478 0 0 0 0 0 0 9.72047933810935 0 0 8.00314342388438 0 0 0 0 0 10.5923353166174 0 13.1956852586776 0 0 0 0 14.4254341461373 0 0 0 0 13.2598797712496 0 0 0 0 0 0 0 6.6653716296684 0 0 TMEM132C 0 0 0 0 0 0 0 0 0 15.6304274760255 0 0 0 0 11.3724171014623 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13.7057920287568 0 0 12.4990036192117 0 0 0 0 0 0 0 0 0 0 0 12.3619870470136 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 16.6895776681193 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 diff -r f689c4ea8c43 -r 5d2304b09f58 test-data/filtered-null.tab --- a/test-data/filtered-null.tab Mon Jun 24 13:38:10 2019 -0400 +++ b/test-data/filtered-null.tab Mon Jun 24 18:07:05 2019 -0400 @@ -1,4 +1,4 @@ -1001000235.G10 1001000174.B1 1001000177.C5 1001000182.H4 1001000175.A2 1001000230.B11 1001000237.E9 1001000173.E10 1001000241.E7 1001000249.A3 1001000179.A7 1001000247.F11 1001000240.D9 1001000178.G5 1001000249.E3 1001000174.H6 1001000181.F8 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