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changeset 14:cd75c72e1d75 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 5c55f75e094983228200111277fef7f349507174
author artbio
date Tue, 10 Apr 2018 10:13:04 -0400
parents 458a88317c22
children 82fedc576024
files small_rna_maps.r small_rna_maps.xml test-data/global_merge.pdf test-data/global_merge_20-30.pdf test-data/global_nomerge.pdf test-data/input1__single_plot_mean.pdf test-data/input1_cluster5_single_plot_coverage.pdf test-data/input1_input2_double_plot_counts_size_ylimneg5_5.pdf test-data/input1_input2_norm_1_2_single_plot_counts.pdf test-data/input1_min20_max30_single_plot_size.pdf test-data/input1_single_plot_median.pdf test-data/input1_yminneg5_5_single_plot_counts.pdf test-data/input_single_chr_x_6_single_plot_coverage.pdf test-data/size20-30.tab
diffstat 14 files changed, 3 insertions(+), 266 deletions(-) [+]
line wrap: on
line diff
--- a/small_rna_maps.r	Tue Apr 10 06:12:01 2018 -0400
+++ b/small_rna_maps.r	Tue Apr 10 10:13:04 2018 -0400
@@ -173,8 +173,8 @@
 title_extra_method = list(Counts="Read Counts", Coverage="Coverage depths", Median="Median sizes", Mean="Mean sizes", Size="Size Distributions")
 legend_first_method =list(Counts="Read count", Coverage="Coverage depth", Median="Median size", Mean="Mean size", Size="Read count")
 legend_extra_method =list(Counts="Read count", Coverage="Coverage depth", Median="Median size", Mean="Mean size", Size="Read count")
-bottom_first_method =list(Counts="Coordinates (nbre of bases)",Coverage="Coordinates (nbre of bases)", Median="Coordinates (nbre of bases)", Mean="Coordinates (nbre of bases)", Size="Sizes of reads")
-bottom_extra_method =list(Counts="Coordinates (nbre of bases)",Coverage="Coordinates (nbre of bases)", Median="Coordinates (nbre of bases)", Mean="Coordinates (nbre of bases)", Size="Sizes of reads")
+bottom_first_method =list(Counts="Coordinates (nucleotides)",Coverage="Coordinates (nucleotides)", Median="Coordinates (nucleotides)", Mean="Coordinates (nucleotides)", Size="Sizes of reads")
+bottom_extra_method =list(Counts="Coordinates (nucleotides)",Coverage="Coordinates (nucleotides)", Median="Coordinates (nucleotides)", Mean="Coordinates (nucleotides)", Size="Sizes of reads")
 
 ## Plotting Functions
 
--- a/small_rna_maps.xml	Tue Apr 10 06:12:01 2018 -0400
+++ b/small_rna_maps.xml	Tue Apr 10 10:13:04 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="small_rna_maps" name="small_rna_maps" version="2.5.1">
+<tool id="small_rna_maps" name="small_rna_maps" version="2.5.2">
   <description></description>
   <requirements>
         <requirement type="package" version="1.11.2=py27_0">numpy</requirement>
Binary file test-data/global_merge.pdf has changed
Binary file test-data/global_merge_20-30.pdf has changed
Binary file test-data/global_nomerge.pdf has changed
Binary file test-data/input1__single_plot_mean.pdf has changed
Binary file test-data/input1_cluster5_single_plot_coverage.pdf has changed
Binary file test-data/input1_input2_double_plot_counts_size_ylimneg5_5.pdf has changed
Binary file test-data/input1_input2_norm_1_2_single_plot_counts.pdf has changed
Binary file test-data/input1_min20_max30_single_plot_size.pdf has changed
Binary file test-data/input1_single_plot_median.pdf has changed
Binary file test-data/input1_yminneg5_5_single_plot_counts.pdf has changed
Binary file test-data/input_single_chr_x_6_single_plot_coverage.pdf has changed
--- a/test-data/size20-30.tab	Tue Apr 10 06:12:01 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,263 +0,0 @@
-Dataset	Chromosome	Polarity	Size	Counts
-input1.bam	FBtr0070001	F	20	4
-input1.bam	FBtr0070001	F	21	4
-input1.bam	FBtr0070001	F	22	29
-input1.bam	FBtr0070001	F	23	15
-input1.bam	FBtr0070001	F	24	1
-input1.bam	FBtr0070001	R	20	0
-input1.bam	FBtr0070001	R	21	0
-input1.bam	FBtr0070001	R	22	0
-input1.bam	FBtr0070001	R	23	0
-input1.bam	FBtr0070001	R	24	0
-input1.bam	FBtr0070533	F	20	2
-input1.bam	FBtr0070533	F	21	2
-input1.bam	FBtr0070533	F	22	4
-input1.bam	FBtr0070533	F	23	2
-input1.bam	FBtr0070533	F	24	0
-input1.bam	FBtr0070533	F	25	1
-input1.bam	FBtr0070533	R	20	0
-input1.bam	FBtr0070533	R	21	0
-input1.bam	FBtr0070533	R	22	0
-input1.bam	FBtr0070533	R	23	0
-input1.bam	FBtr0070533	R	24	0
-input1.bam	FBtr0070533	R	25	0
-input1.bam	FBtr0070603	F	20	6
-input1.bam	FBtr0070603	F	21	3
-input1.bam	FBtr0070603	F	22	3
-input1.bam	FBtr0070603	F	23	10
-input1.bam	FBtr0070603	F	24	2
-input1.bam	FBtr0070603	F	25	5
-input1.bam	FBtr0070603	F	26	5
-input1.bam	FBtr0070603	F	27	3
-input1.bam	FBtr0070603	R	20	0
-input1.bam	FBtr0070603	R	21	0
-input1.bam	FBtr0070603	R	22	0
-input1.bam	FBtr0070603	R	23	0
-input1.bam	FBtr0070603	R	24	0
-input1.bam	FBtr0070603	R	25	0
-input1.bam	FBtr0070603	R	26	0
-input1.bam	FBtr0070603	R	27	0
-input1.bam	FBtr0070604	F	21	1
-input1.bam	FBtr0070604	F	22	23
-input1.bam	FBtr0070604	F	23	10
-input1.bam	FBtr0070604	R	21	0
-input1.bam	FBtr0070604	R	22	0
-input1.bam	FBtr0070604	R	23	0
-input1.bam	FBtr0070911	F	21	1
-input1.bam	FBtr0070911	R	21	0
-input1.bam	FBtr0078490	F	23	1
-input1.bam	FBtr0078490	R	23	0
-input1.bam	FBtr0078580	F	20	9
-input1.bam	FBtr0078580	F	21	5
-input1.bam	FBtr0078580	F	22	13
-input1.bam	FBtr0078580	F	23	5
-input1.bam	FBtr0078580	F	24	180
-input1.bam	FBtr0078580	F	25	212
-input1.bam	FBtr0078580	F	26	1
-input1.bam	FBtr0078580	F	27	2
-input1.bam	FBtr0078580	F	28	17
-input1.bam	FBtr0078580	R	20	0
-input1.bam	FBtr0078580	R	21	0
-input1.bam	FBtr0078580	R	22	0
-input1.bam	FBtr0078580	R	23	0
-input1.bam	FBtr0078580	R	24	0
-input1.bam	FBtr0078580	R	25	0
-input1.bam	FBtr0078580	R	26	0
-input1.bam	FBtr0078580	R	27	0
-input1.bam	FBtr0078580	R	28	0
-input1.bam	FBtr0078790	F	20	2
-input1.bam	FBtr0078790	F	21	0
-input1.bam	FBtr0078790	F	22	2
-input1.bam	FBtr0078790	F	23	1
-input1.bam	FBtr0078790	R	20	0
-input1.bam	FBtr0078790	R	21	0
-input1.bam	FBtr0078790	R	22	0
-input1.bam	FBtr0078790	R	23	0
-input1.bam	FBtr0079064	F	21	1
-input1.bam	FBtr0079064	R	21	0
-input1.bam	FBtr0079090	F	21	0
-input1.bam	FBtr0079090	F	22	0
-input1.bam	FBtr0079090	F	23	0
-input1.bam	FBtr0079090	F	24	1
-input1.bam	FBtr0079090	F	25	0
-input1.bam	FBtr0079090	F	26	0
-input1.bam	FBtr0079090	F	27	0
-input1.bam	FBtr0079090	F	28	1
-input1.bam	FBtr0079090	R	21	1
-input1.bam	FBtr0079090	R	22	0
-input1.bam	FBtr0079090	R	23	0
-input1.bam	FBtr0079090	R	24	0
-input1.bam	FBtr0079090	R	25	0
-input1.bam	FBtr0079090	R	26	0
-input1.bam	FBtr0079090	R	27	0
-input1.bam	FBtr0079090	R	28	0
-input1.bam	FBtr0079338	F	21	3
-input1.bam	FBtr0079338	F	22	6
-input1.bam	FBtr0079338	R	21	0
-input1.bam	FBtr0079338	R	22	0
-input1.bam	FBtr0079528	F	20	12
-input1.bam	FBtr0079528	F	21	3
-input1.bam	FBtr0079528	F	22	2
-input1.bam	FBtr0079528	F	23	3
-input1.bam	FBtr0079528	F	24	36
-input1.bam	FBtr0079528	F	25	8
-input1.bam	FBtr0079528	F	26	5
-input1.bam	FBtr0079528	F	27	2
-input1.bam	FBtr0079528	F	28	2
-input1.bam	FBtr0079528	F	29	1
-input1.bam	FBtr0079528	R	20	0
-input1.bam	FBtr0079528	R	21	0
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-input1.bam	FBtr0079528	R	29	0
-input1.bam	FBtr0079596	F	20	13
-input1.bam	FBtr0079596	F	21	3
-input1.bam	FBtr0079596	F	22	16
-input1.bam	FBtr0079596	F	23	8
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-input1.bam	FBtr0079596	F	25	0
-input1.bam	FBtr0079596	F	26	3
-input1.bam	FBtr0079596	F	27	1
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-input1.bam	FBtr0079677	F	23	1
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-input1.bam	FBtr0079690	F	25	1
-input1.bam	FBtr0079690	R	25	0
-input1.bam	FBtr0079692	F	20	1
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-input1.bam	FBtr0079692	R	20	0
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-input1.bam	FBtr0079693	F	23	1
-input1.bam	FBtr0079693	F	24	1
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