# HG changeset patch
# User richard-burhans
# Date 1739819846 0
# Node ID 425a2aa541df755cbd46de0072cdfb8fd41e6cab
planemo upload for repository https://github.com/vgl-hub/rdeval commit bdcd7b1991f872540fb5f87ee945077b5ca68780
diff -r 000000000000 -r 425a2aa541df macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Mon Feb 17 19:17:26 2025 +0000
@@ -0,0 +1,33 @@
+
+
+
+ rdeval
+
+
+ 0.0.5
+ 0
+ 23.02
+ `_, and
+ relies on the gfastar suite and the gfalibs toolkit `vgl-hub/gfalibs
+ `_, developed by Giulio Formenti at the Rockefeller University
+ ]]>
+
+
+
+ @article{formenti2022gfastats,
+ title={Gfastats: conversion, evaluation and manipulation of genome sequences using assembly graphs},
+ author={Formenti, Giulio and Abueg, Linelle and Brajuka, Angelo and Brajuka, Nadolina and Gallardo-Alba, Crist{\'o}bal and Giani, Alice and Fedrigo, Olivier and Jarvis, Erich D},
+ journal={Bioinformatics},
+ volume={38},
+ number={17},
+ pages={4214--4216},
+ year={2022},
+ publisher={Oxford University Press}
+ }
+
+
+
+
diff -r 000000000000 -r 425a2aa541df rdeval.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rdeval.xml Mon Feb 17 19:17:26 2025 +0000
@@ -0,0 +1,248 @@
+
+ Multithreaded read analysis and manipulation tool.
+
+ macros.xml
+
+
+ '$stats_outfile'
+ ]]>
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ output_options["output_type"]["type_selector"] == "rd_file"
+
+
+ output_options["output_type"]["type_selector"] == "combined_reads"
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ generates output on a excluding list of headers.
+ -f --filter filter reads using in quotes, e.g. 'l>10' for longer than 10bp or 'l>10 & q>10' to further exclude reads by quality (default: none).
+ -i --include-list generates output on a subset list of headers.
+ -o --out-format output file (fa*[.gz], bam, cram, rd). Optionally write reads to file or generate rd summary file.
+ -q --quality q|a generates list of average quality for each read (q) or both length and quality (a).
+ -r --input-reads input file (fa*[.gz], bam, cram, rd).
+ -s --out-size u|s|h|c generates size list (unsorted|sorted|histogram|inverse cumulative table).
+ --homopolymer-compress compress all the homopolymers longer than n in the input.
+ --sample fraction of reads to subsample.
+ --random-seed an optional random seed to make subsampling reproducible.
+ --md5 print md5 of .rd files.
+ --tabular tabular output.
+ --verbose verbose output.
+ -j --threads numbers of threads (default:5).
+ -v --version software version.
+ --cmd print $0 to stdout.
+
+@ATTRIBUTION@
+ ]]>
+
+
diff -r 000000000000 -r 425a2aa541df test-data/output1.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output1.tabular Mon Feb 17 19:17:26 2025 +0000
@@ -0,0 +1,10 @@
+# reads 5
+Total read length 50
+Average read length 10.00
+Read N50 15
+Smallest read length 5
+Largest read length 15
+Coverage inf
+GC content % 50.00
+Base composition (A:C:T:G) 9:14:11:6
+Average per base quality 0.00
diff -r 000000000000 -r 425a2aa541df test-data/output2.fastq.gz
Binary file test-data/output2.fastq.gz has changed
diff -r 000000000000 -r 425a2aa541df test-data/output2.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output2.tabular Mon Feb 17 19:17:26 2025 +0000
@@ -0,0 +1,10 @@
+# reads 11
+Total read length 264855
+Average read length 24077.73
+Read N50 24322
+Smallest read length 17465
+Largest read length 36274
+Coverage inf
+GC content % 40.81
+Base composition (A:C:T:G) 79479:54455:77277:53644
+Average per base quality 23.58
diff -r 000000000000 -r 425a2aa541df test-data/test1.fasta.gz
Binary file test-data/test1.fasta.gz has changed
diff -r 000000000000 -r 425a2aa541df test-data/test1.fastq.gz
Binary file test-data/test1.fastq.gz has changed
diff -r 000000000000 -r 425a2aa541df test-data/test2.bam
Binary file test-data/test2.bam has changed