Mercurial > repos > artbio > gsc_filter_genes

changeset 1:5d2304b09f58 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_filter_genes commit d9e43e514d5fe7bbc7205a52ccb3e4faef50e856
author artbio
date Mon, 24 Jun 2019 18:07:05 -0400
parents f689c4ea8c43
children afe949d332b3
files filter_genes.R filter_genes.xml test-data/filtered-0.05.tab test-data/filtered-5.tab test-data/filtered-null.tab
diffstat 5 files changed, 6 insertions(+), 5 deletions(-) [+]
line wrap: on
line diff
--- 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
--- 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 @@
-<tool id="filter_genes" name="Filter genes in single cell data" version="0.9.0">
+<tool id="filter_genes" name="Filter genes in single cell data" version="0.9.1">
     <description>which are detected in less that a given fraction of the libraries</description>
     <requirements>
         <requirement type="package" version="1.3.2=r3.3.2_0">r-optparse</requirement>
--- 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 @@
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+Genes	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	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	1001000031.D12	1001000037.D6	1001000250.G2	1001000018.F11	1001000175.F9	1001000254.G1	1001000264.F12	1001000183.B3	1001000241.E6	1001000183.E6	1001000181.F10	1001000176.B1	1001000235.B7	1001000231.D12	1001000230.E7	1001000186.H6	1001000258.H5	1001000237.H10	1001000231.B7	1001000270.H8	1001000240.G1	1001000177.D11	1001000185.D3	1001000238.B5	1001000174.E10
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--- 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 @@
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--- 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 @@
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