Upgrade mapping_quality_stats tool (#665)

* Update sample.bam * bump versions and fix tool dev url * update test in mississippi * Update pr.yaml * Update mapping_quality_stats.r
ARTbio · Feb 10, 2024 · 2661225 · 2661225
1 parent 1bcc034
commit 2661225
Show file tree

Hide file tree

Showing 7 changed files with 38 additions and 36 deletions.
diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml
@@ -211,7 +211,7 @@ jobs:
     - name: lintr
       run: |
         library(lintr)
-        linters <- linters_with_defaults(line_length_linter = NULL, cyclocomp_linter = NULL, object_usage_linter = NULL, object_name_linter = NULL)
+        linters <- linters_with_defaults(indentation_linter(indent = 4L), line_length_linter = NULL, cyclocomp_linter = NULL, object_usage_linter = NULL, object_name_linter = NULL)
         con <- file("repository_list.txt", "r")
         status <- 0
         while (TRUE) {

diff --git a/tools/mapping_quality_stats/.shed.yml b/tools/mapping_quality_stats/.shed.yml
@@ -10,7 +10,7 @@ categories:
   - Statistics
 
 homepage_url: http://artbio.fr
-remote_repository_url: https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats
+remote_repository_url: https://github.com/ARTbio/tools-artbio/tree/main/tools/mapping_quality_stats
 toolshed:
   - toolshed
 
diff --git a/tools/mapping_quality_stats/mapping_quality_stats.r b/tools/mapping_quality_stats/mapping_quality_stats.r
@@ -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 @@ library(ggplot2)
 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 --git a/tools/mapping_quality_stats/mapping_quality_stats.xml b/tools/mapping_quality_stats/mapping_quality_stats.xml
@@ -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 --git a/tools/mapping_quality_stats/test-data/distribution.pdf b/tools/mapping_quality_stats/test-data/distribution.pdf
diff --git a/tools/mapping_quality_stats/test-data/distribution.tab b/tools/mapping_quality_stats/test-data/distribution.tab
@@ -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 --git a/tools/mapping_quality_stats/test-data/sample.bam b/tools/mapping_quality_stats/test-data/sample.bam