Mercurial > repos > artbio > small_rna_maps
changeset 27:fe1a9cfaf5c3 draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d234ef45deb84f70c85b3372b8e0137df0be4e29
| author | artbio |
|---|---|
| date | Wed, 24 Apr 2019 11:18:24 -0400 |
| parents | 376fae7c9f32 |
| children | 14adf24603b6 |
| files | small_rna_maps.py small_rna_maps.r small_rna_maps.xml test-data/clustering.tab test-data/clustering_unstranded.tab test-data/input1_counts_yminneg5_5.tab test-data/input1_input2_counts.tab test-data/input1_input2_norm_1_2_counts.tab test-data/input1_input2_size.tab test-data/input1_input2new_norm_1_2_counts.tab test-data/input1_mean.tab test-data/input1_median.tab test-data/input1_min20_max30_size.tab test-data/input_single_chr_x_6_single_plot_coverage.tab test-data/size.tab |
| diffstat | 15 files changed, 18 insertions(+), 16 deletions(-) [+] |
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--- 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):
--- 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)) }
--- 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>
--- 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
--- 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
--- 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
--- 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
--- 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
--- 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
--- 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
--- 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
--- 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
--- 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
--- 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
--- 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