# HG changeset patch
# User richard-burhans
# Date 1746467470 0
# Node ID 24b05d3958d734b8a93fa99cbd2beff3d9fd5921
# Parent 7cfeba6facd11c2e8e3af2a2482b4e5281e71106
planemo upload for repository https://github.com/vgl-hub/rdeval commit 344add351131179b6c41777e7574823ef678e7a7
diff -r 7cfeba6facd1 -r 24b05d3958d7 macros.xml
--- a/macros.xml Fri May 02 22:49:30 2025 +0000
+++ b/macros.xml Mon May 05 17:51:10 2025 +0000
@@ -5,7 +5,7 @@
0.0.7
- 0
+ 1
23.02
diff -r 7cfeba6facd1 -r 24b05d3958d7 rdeval.xml
--- a/rdeval.xml Fri May 02 22:49:30 2025 +0000
+++ b/rdeval.xml Mon May 05 17:51:10 2025 +0000
@@ -9,7 +9,12 @@
#set $mangled_inputs = []
#for $input in $input_reads
#set $mangled_base = re.sub(r"[^\w\-\s]", "_", str($input.element_identifier))
- #set $mangled_input = $mangled_base + "." + str($input.ext)
+ #if str($input.ext).lower().startswith("fastq")
+ #set $mangled_ext = "fastq"
+ #else
+ #set $mangled_ext = str($input.ext)
+ #end if
+ #set $mangled_input = $mangled_base + "." + $mangled_ext
#silent $mangled_inputs.append($mangled_input)
ln -s '$input' '$mangled_input' &&
#end for
@@ -82,7 +87,7 @@
-
+
@@ -268,6 +273,8 @@
**rdeval** accepts an arbitrary number of sequencing files and optionally **filters**, **subsamples**, and/or **compresses homopolymers** within the reads. The retained reads can be saved in multiple formats, and metrics on these reads can be stored in a '*sketch*' file. Statistics can then be efficiently retrieved from these sketch files for further processing.
.. image:: pipeline.svg
+ :alt: pipeline diagram
+ :align: left
Filtering
=========
diff -r 7cfeba6facd1 -r 24b05d3958d7 static/images/pipeline.svg
--- a/static/images/pipeline.svg Fri May 02 22:49:30 2025 +0000
+++ b/static/images/pipeline.svg Mon May 05 17:51:10 2025 +0000
@@ -2,9 +2,9 @@