Mercurial > repos > artbio > mapping_quality_stats
changeset 2:ce2d8f611a51 draft default tip
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/mapping_quality_stats commit 2661225fdd0f533d4dc8e2561ea559fcc00b9128
| author | artbio |
|---|---|
| date | Sat, 10 Feb 2024 01:32:48 +0000 |
| parents | 7883d97fa479 |
| children | |
| files | mapping_quality_stats.r mapping_quality_stats.xml test-data/distribution.pdf test-data/distribution.tab test-data/sample.bam |
| diffstat | 5 files changed, 36 insertions(+), 34 deletions(-) [+] |
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--- a/mapping_quality_stats.r Wed Jun 15 15:37:11 2022 +0000 +++ b/mapping_quality_stats.r Sat Feb 10 01:32:48 2024 +0000 @@ -1,9 +1,9 @@ ## Setup R error handling to go to stderr options(show.error.messages = FALSE, - error = function() { - cat(geterrmessage(), file = stderr()) - q("no", 1, FALSE) - } + error = function() { + cat(geterrmessage(), file = stderr()) + q("no", 1, FALSE) + } ) @@ -14,7 +14,7 @@ option_list <- list( make_option(c("-i", "--input"), type = "character", help = "Path to tabular file"), make_option(c("-o", "--output"), type = "character", help = "path to the pdf plot") - ) +) parser <- OptionParser(usage = "%prog [options] file", option_list = option_list) args <- parse_args(parser)
--- a/mapping_quality_stats.xml Wed Jun 15 15:37:11 2022 +0000 +++ b/mapping_quality_stats.xml Sat Feb 10 01:32:48 2024 +0000 @@ -1,10 +1,15 @@ -<tool id="mapqstatistics" name="Mapping Quality Stats" version="0.19.1+galaxy0"> - <description></description> - <requirements> - <requirement type="package" version="1.7.1">r-optparse</requirement> - <requirement type="package" version="3.3.6">r-ggplot2</requirement> - <requirement type="package" version="0.19.1">pysam</requirement> - </requirements> +<tool id="mapqstatistics" name="Mapping Quality Stats" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> + <description></description> + <macros> + <token name="@TOOL_VERSION@">0.22.0</token> + <token name="@VERSION_SUFFIX@">0</token> + <token name="@PROFILE@">23.0</token> + </macros> + <requirements> + <requirement type="package" version="1.7.4">r-optparse</requirement> + <requirement type="package" version="3.4.4">r-ggplot2</requirement> + <requirement type="package" version="@TOOL_VERSION@">pysam</requirement> + </requirements> <stdio> <exit_code range="1:" level="fatal" description="Tool exception" /> </stdio>
--- a/test-data/distribution.tab Wed Jun 15 15:37:11 2022 +0000 +++ b/test-data/distribution.tab Sat Feb 10 01:32:48 2024 +0000 @@ -1,32 +1,29 @@ mapq number_of_alignments -0 54 +0 33 6 1 8 2 -12 1 -14 2 16 1 17 1 21 3 23 1 24 1 25 1 -30 2 -33 6 -40 9 -44 2 -45 9 -46 6 -47 180 -48 196 -49 60 -50 17 -51 7 -52 11 -53 4 -54 6 +33 2 +40 1 +44 1 +45 3 +46 3 +47 105 +48 103 +49 26 +50 14 +51 1 +52 8 +53 2 +54 4 55 1 -56 8 -57 9 -58 10 -59 10 -60 10496 +56 5 +57 2 +58 6 +59 4 +60 5273