# HG changeset patch
# User artbio
# Date 1556119104 14400
# Node ID fe1a9cfaf5c3542dce8248868174864c5baf4dc3
# Parent  376fae7c9f32562be1d6e2aa1b8c6d5d5946e6bd
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d234ef45deb84f70c85b3372b8e0137df0be4e29

diff -r 376fae7c9f32 -r fe1a9cfaf5c3 small_rna_maps.py
--- a/small_rna_maps.py	Sun Apr 14 14:43:44 2019 -0400
+++ b/small_rna_maps.py	Wed Apr 24 11:18:24 2019 -0400
@@ -374,14 +374,14 @@
     for method, output in zip(methods, outputs):
         out = open(output, 'w')
         if method == 'Size':
-            header = ["Dataset", "Chromosome", "Polarity", method, "Counts",
+            header = ["# Dataset", "Chromosome", "Polarity", method, "Counts",
                       "Strandness", "z-score"]
         elif cluster:
-            header = ["Dataset", "Chromosome", "Chrom_length", "Coordinate",
+            header = ["# Dataset", "Chromosome", "Chrom_length", "Coordinate",
                       "Polarity", method, "Start-End", "Cluster Size",
                       "density"]
         else:
-            header = ["Dataset", "Chromosome", "Chrom_length", "Coordinate",
+            header = ["# Dataset", "Chromosome", "Chrom_length", "Coordinate",
                       "Polarity", method]
         out.write('\t'.join(header) + '\n')
         for input, sample in zip(inputs, samples):
diff -r 376fae7c9f32 -r fe1a9cfaf5c3 small_rna_maps.r
--- a/small_rna_maps.r	Sun Apr 14 14:43:44 2019 -0400
+++ b/small_rna_maps.r	Wed Apr 24 11:18:24 2019 -0400
@@ -28,6 +28,7 @@
 # data frames implementation
 ## first table
 Table = read.delim(args$first_dataframe, header=T, row.names=NULL)
+colnames(Table)[1] <- "Dataset"
 if (args$first_plot_method == "Counts" | args$first_plot_method == "Size") {
   Table <- within(Table, Counts[Polarity=="R"] <- (Counts[Polarity=="R"]*-1))
 }
@@ -52,6 +53,7 @@
 # second table
 if (args$extra_plot_method != '') {
   ExtraTable=read.delim(args$extra_dataframe, header=T, row.names=NULL)
+  colnames(ExtraTable)[1] <- "Dataset"
   if (args$extra_plot_method == "Counts" | args$extra_plot_method=='Size') {
     ExtraTable <- within(ExtraTable, Counts[Polarity=="R"] <- (Counts[Polarity=="R"]*-1))
   }
diff -r 376fae7c9f32 -r fe1a9cfaf5c3 small_rna_maps.xml
--- a/small_rna_maps.xml	Sun Apr 14 14:43:44 2019 -0400
+++ b/small_rna_maps.xml	Wed Apr 24 11:18:24 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="small_rna_maps" name="small_rna_maps" version="2.13.1">
+<tool id="small_rna_maps" name="small_rna_maps" version="2.13.2">
   <description></description>
   <requirements>
         <requirement type="package" version="1.11.2=py27_0">numpy</requirement>
diff -r 376fae7c9f32 -r fe1a9cfaf5c3 test-data/clustering.tab
--- a/test-data/clustering.tab	Sun Apr 14 14:43:44 2019 -0400
+++ b/test-data/clustering.tab	Wed Apr 24 11:18:24 2019 -0400
@@ -1,4 +1,4 @@
-Dataset	Chromosome	Chrom_length	Coordinate	Polarity	Counts	Start-End	Cluster Size	density
+# Dataset	Chromosome	Chrom_length	Coordinate	Polarity	Counts	Start-End	Cluster Size	density
 input1.bam	FBtr0070001	72	1	F	0	1-1	1	0.0
 input1.bam	FBtr0070001	72	12	F	12	7-39	33	0.363636363636
 input1.bam	FBtr0070001	72	30	F	42	27-53	27	1.55555555556
diff -r 376fae7c9f32 -r fe1a9cfaf5c3 test-data/clustering_unstranded.tab
--- a/test-data/clustering_unstranded.tab	Sun Apr 14 14:43:44 2019 -0400
+++ b/test-data/clustering_unstranded.tab	Wed Apr 24 11:18:24 2019 -0400
@@ -1,4 +1,4 @@
-Dataset	Chromosome	Chrom_length	Coordinate	Polarity	Counts	Start-End	Cluster Size	density
+# Dataset	Chromosome	Chrom_length	Coordinate	Polarity	Counts	Start-End	Cluster Size	density
 input1.bam	FBtr0070001	72	1	F	0	1-1	1	0.0
 input1.bam	FBtr0070001	72	12	F	12	7-39	33	0.363636363636
 input1.bam	FBtr0070001	72	30	F	42	27-53	27	1.55555555556
diff -r 376fae7c9f32 -r fe1a9cfaf5c3 test-data/input1_counts_yminneg5_5.tab
--- a/test-data/input1_counts_yminneg5_5.tab	Sun Apr 14 14:43:44 2019 -0400
+++ b/test-data/input1_counts_yminneg5_5.tab	Wed Apr 24 11:18:24 2019 -0400
@@ -1,4 +1,4 @@
-Dataset	Chromosome	Chrom_length	Coordinate	Polarity	Counts
+# Dataset	Chromosome	Chrom_length	Coordinate	Polarity	Counts
 input1.bam	FBtr0070001	72	1	F	0
 input1.bam	FBtr0070001	72	7	F	5
 input1.bam	FBtr0070001	72	8	F	3
diff -r 376fae7c9f32 -r fe1a9cfaf5c3 test-data/input1_input2_counts.tab
--- a/test-data/input1_input2_counts.tab	Sun Apr 14 14:43:44 2019 -0400
+++ b/test-data/input1_input2_counts.tab	Wed Apr 24 11:18:24 2019 -0400
@@ -1,4 +1,4 @@
-Dataset	Chromosome	Chrom_length	Coordinate	Polarity	Counts
+# Dataset	Chromosome	Chrom_length	Coordinate	Polarity	Counts
 input1.bam	FBtr0070001	72	1	F	0
 input1.bam	FBtr0070001	72	7	F	5
 input1.bam	FBtr0070001	72	8	F	3
diff -r 376fae7c9f32 -r fe1a9cfaf5c3 test-data/input1_input2_norm_1_2_counts.tab
--- a/test-data/input1_input2_norm_1_2_counts.tab	Sun Apr 14 14:43:44 2019 -0400
+++ b/test-data/input1_input2_norm_1_2_counts.tab	Wed Apr 24 11:18:24 2019 -0400
@@ -1,4 +1,4 @@
-Dataset	Chromosome	Chrom_length	Coordinate	Polarity	Counts
+# Dataset	Chromosome	Chrom_length	Coordinate	Polarity	Counts
 input1.bam	FBtr0070001	72	1	F	0
 input1.bam	FBtr0070001	72	7	F	5
 input1.bam	FBtr0070001	72	8	F	3
diff -r 376fae7c9f32 -r fe1a9cfaf5c3 test-data/input1_input2_size.tab
--- a/test-data/input1_input2_size.tab	Sun Apr 14 14:43:44 2019 -0400
+++ b/test-data/input1_input2_size.tab	Wed Apr 24 11:18:24 2019 -0400
@@ -1,4 +1,4 @@
-Dataset	Chromosome	Polarity	Size	Counts	Strandness	z-score
+# Dataset	Chromosome	Polarity	Size	Counts	Strandness	z-score
 input1.bam	FBtr0070001	F	19	1	1.0	-0.448696330732
 input1.bam	FBtr0070001	F	20	4	1.0	-0.104347983891
 input1.bam	FBtr0070001	F	21	4	1.0	-0.104347983891
diff -r 376fae7c9f32 -r fe1a9cfaf5c3 test-data/input1_input2new_norm_1_2_counts.tab
--- a/test-data/input1_input2new_norm_1_2_counts.tab	Sun Apr 14 14:43:44 2019 -0400
+++ b/test-data/input1_input2new_norm_1_2_counts.tab	Wed Apr 24 11:18:24 2019 -0400
@@ -1,4 +1,4 @@
-Dataset	Chromosome	Chrom_length	Coordinate	Polarity	Counts
+# Dataset	Chromosome	Chrom_length	Coordinate	Polarity	Counts
 input1.bam	FBtr0070001	72	1	F	0
 input1.bam	FBtr0070001	72	7	F	5
 input1.bam	FBtr0070001	72	8	F	3
diff -r 376fae7c9f32 -r fe1a9cfaf5c3 test-data/input1_mean.tab
--- a/test-data/input1_mean.tab	Sun Apr 14 14:43:44 2019 -0400
+++ b/test-data/input1_mean.tab	Wed Apr 24 11:18:24 2019 -0400
@@ -1,4 +1,4 @@
-Dataset	Chromosome	Chrom_length	Coordinate	Polarity	Mean
+# Dataset	Chromosome	Chrom_length	Coordinate	Polarity	Mean
 input1.bam	FBtr0070001	72	1	F	0
 input1.bam	FBtr0070001	72	7	F	21.2
 input1.bam	FBtr0070001	72	8	F	21.3
diff -r 376fae7c9f32 -r fe1a9cfaf5c3 test-data/input1_median.tab
--- a/test-data/input1_median.tab	Sun Apr 14 14:43:44 2019 -0400
+++ b/test-data/input1_median.tab	Wed Apr 24 11:18:24 2019 -0400
@@ -1,4 +1,4 @@
-Dataset	Chromosome	Chrom_length	Coordinate	Polarity	Median
+# Dataset	Chromosome	Chrom_length	Coordinate	Polarity	Median
 input1.bam	FBtr0070001	72	1	F	0
 input1.bam	FBtr0070001	72	7	F	21.0
 input1.bam	FBtr0070001	72	8	F	21.0
diff -r 376fae7c9f32 -r fe1a9cfaf5c3 test-data/input1_min20_max30_size.tab
--- a/test-data/input1_min20_max30_size.tab	Sun Apr 14 14:43:44 2019 -0400
+++ b/test-data/input1_min20_max30_size.tab	Wed Apr 24 11:18:24 2019 -0400
@@ -1,4 +1,4 @@
-Dataset	Chromosome	Polarity	Size	Counts	Strandness	z-score
+# Dataset	Chromosome	Polarity	Size	Counts	Strandness	z-score
 input1.bam	FBtr0070001	F	19	1	1.0	-0.448696330732
 input1.bam	FBtr0070001	F	20	4	1.0	-0.104347983891
 input1.bam	FBtr0070001	F	21	4	1.0	-0.104347983891
diff -r 376fae7c9f32 -r fe1a9cfaf5c3 test-data/input_single_chr_x_6_single_plot_coverage.tab
--- a/test-data/input_single_chr_x_6_single_plot_coverage.tab	Sun Apr 14 14:43:44 2019 -0400
+++ b/test-data/input_single_chr_x_6_single_plot_coverage.tab	Wed Apr 24 11:18:24 2019 -0400
@@ -1,4 +1,4 @@
-Dataset	Chromosome	Chrom_length	Coordinate	Polarity	Coverage
+# Dataset	Chromosome	Chrom_length	Coordinate	Polarity	Coverage
 input_single_chr.bam_0	1	80	1	F	0
 input_single_chr.bam_0	1	80	80	F	0
 input_single_chr.bam_1	1	80	1	F	0
diff -r 376fae7c9f32 -r fe1a9cfaf5c3 test-data/size.tab
--- a/test-data/size.tab	Sun Apr 14 14:43:44 2019 -0400
+++ b/test-data/size.tab	Wed Apr 24 11:18:24 2019 -0400
@@ -1,4 +1,4 @@
-Dataset	Chromosome	Polarity	Size	Counts	Strandness	z-score
+# Dataset	Chromosome	Polarity	Size	Counts	Strandness	z-score
 input1.bam	FBtr0070001	F	19	1	1.0	-0.448696330732
 input1.bam	FBtr0070001	F	20	4	1.0	-0.104347983891
 input1.bam	FBtr0070001	F	21	4	1.0	-0.104347983891