# HG changeset patch
# User artbio
# Date 1707528768 0
# Node ID ce2d8f611a512adac660850c3e235544128b4f48
# Parent  7883d97fa4794d5548e88269b9aebb57f7e5c6f9
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/mapping_quality_stats commit 2661225fdd0f533d4dc8e2561ea559fcc00b9128

diff -r 7883d97fa479 -r ce2d8f611a51 mapping_quality_stats.r
--- 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)
diff -r 7883d97fa479 -r ce2d8f611a51 mapping_quality_stats.xml
--- 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>
diff -r 7883d97fa479 -r ce2d8f611a51 test-data/distribution.pdf
Binary file test-data/distribution.pdf has changed
diff -r 7883d97fa479 -r ce2d8f611a51 test-data/distribution.tab
--- 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
diff -r 7883d97fa479 -r ce2d8f611a51 test-data/sample.bam
Binary file test-data/sample.bam has changed