# HG changeset patch
# User richard-burhans
# Date 1746226170 0
# Node ID 7cfeba6facd11c2e8e3af2a2482b4e5281e71106
# Parent 7bf95986aaa4da3b81656686a71903b7d6169d39
planemo upload for repository https://github.com/vgl-hub/rdeval commit d55c4b3d6b91d0418950ed6b7806ef779a916099
diff -r 7bf95986aaa4 -r 7cfeba6facd1 macros.xml
--- a/macros.xml Wed Apr 23 19:31:12 2025 +0000
+++ b/macros.xml Fri May 02 22:49:30 2025 +0000
@@ -4,9 +4,8 @@
rdeval
-
- 0.0.5
- 4
+ 0.0.7
+ 0
23.02
diff -r 7bf95986aaa4 -r 7cfeba6facd1 rdeval.xml
--- a/rdeval.xml Wed Apr 23 19:31:12 2025 +0000
+++ b/rdeval.xml Fri May 02 22:49:30 2025 +0000
@@ -15,46 +15,62 @@
#end for
#if $output_options.output_type.type_selector == "combined_reads"
ln -s '$reads_outfile' 'output.${output_type.format_selector}' &&
- #end if
- rdeval --input-reads #echo " ".join([f"'{input}'" for $input in $mangled_inputs])
+ #end if
+ rdeval --input-reads
+ #for $input in $mangled_inputs
+ '$input'
+ #end for
#if $expected_gsize
'$expected_gsize'
#end if
- #if $input_filter.filter_selector == "exclude_file"
- --exclude-list '$exclude_file'
- #else if $input_filter.filter_selector == "include_file"
- --include-list '$include_file'
- #end if
- #if $filter
- --filter '$filter'
+ #if $input_filter.include_list
+ --include-list '$input_filter.include_list'
+ #end if
+ #if $input_filter.exclude_list
+ --exclude-list '$input_filter.exclude_list'
#end if
- --sample '$sample'
- #if $input_subsample.seed_selector == "yes"
- --random-seed '$random_seed'
+ #set $filter_exp_type = $input_filter.filter_expression.filter_selector
+ #if $filter_exp_type != "no_exp"
+ #set $l_exp = "l" + str($input_filter.filter_expression.length_comparison) + str($input_filter.filter_expression.length_value)
+ #set $q_exp = "q" + str($input_filter.filter_expression.quality_comparison) + str($input_filter.filter_expression.quality_value)
+ #if $filter_exp_type == "l_exp"
+ #set $filter_exp = $l_exp
+ #else if $filter_exp_type == "q_exp"
+ #set $filter_exp = $q_exp
+ #else if $filter_exp_type == "lq_exp"
+ #set $filter_exp = $l_exp + str($input_filter.filter_expression.exp_operator) + $q_exp
+ #end if
+ --filter '$filter_exp'
+ #end if
+ #if int($input_subsample.sample) != 1
+ --sample '$input_subsample.sample'
+ #end if
+ #if $input_subsample.random_seed.seed_selector == "yes"
+ --random-seed '$input_subsample.random_seed.random_seed'
#end if
#if $input_compress.compress_selector == "yes"
- --homopolymer-compress '$homopolymer_compress'
+ --homopolymer-compress '$input_compress.homopolymer_compress'
#end if
- #if $stats_flavor.flavor_selector == "stats"
- #if $sequence_report
+ #set $stats_type = $output_options.stats_flavor.flavor_selector
+ #if $stats_type == "stats"
+ #if $output_options.stats_flavor.sequence_report
--sequence-report
#end if
- #else if $stats_flavor.flavor_selector == "quality"
- --quality '$quality'
- #else if $stats_flavor.flavor_selector == "size"
- --out-size '$out_size'
+ #else if $stats_type == "quality"
+ --quality '$output_options.stats_flavor.quality'
+ #else if $stats_type == "size"
+ --out-size '$output_options.stats_flavor.out_size'
#end if
- #if $output_options.output_type.type_selector == "rd_file"
- #if $md5
+ #set $output_type = $output_options.output_type.type_selector
+ #if $output_type == "rd_file"
+ #if $output_options.output_type.md5
--md5
#end if
-o output.rd
- #else if $output_options.output_type.type_selector == "combined_reads"
- -o 'output.${output_type.format_selector}'
+ #else if $output_type == "combined_reads"
+ -o 'output.${output_options.output_type.format_selector}'
#end if
- #if $verbose
--verbose
- #end if
--tabular
--threads \${GALAXY_SLOTS:-2}
> '$stats_outfile'
@@ -63,21 +79,56 @@
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@@ -164,91 +214,103 @@
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| | |
+ * length-expression ::= "l"
+ * quality-expression ::= "q"
+ * combination-operator := "&" | "|"
+ * comparison-operator ::= "<" | "=" | ">"
+ * integer ::= |
+ * digit ::= "0" | "1" | "2" | "3" | "4" | "5" | "6" | "7" | "8" | "9"
-::
+Retain reads longer than 10 base pairs
+
+ l>10
+
+Retain reads with average quality greather than 20
+
+ q>20
- Options:
- --sequence-report generates a per-read report
- -e --exclude-list 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.
+Retain reads longer than 10 base pairs with average quality greather than 20
+
+ l>10 & q>20
+
+.. _sampling-label:
-**Attribution**
+Sub-sampling
+============
+
+4. Retain a subsample of the reads by specifying the fraction to be kept. Use the *random seed* option to keep subsampling reproducible.
-This tool relies on the gfastar suite and the gfalibs toolkit `vgl-hub/gfalibs `_, developed by Giulio Formenti at the Rockefeller University
+Homopolymer Compression
+=======================
+
+5. Runs of repeated nucleotides in each read are collapsed, with any associated quality data discarded. For example, CAGGCTTT would become CAGCT.
]]>
diff -r 7bf95986aaa4 -r 7cfeba6facd1 rdeval_report.xml
--- a/rdeval_report.xml Wed Apr 23 19:31:12 2025 +0000
+++ b/rdeval_report.xml Fri May 02 22:49:30 2025 +0000
@@ -10,23 +10,46 @@
export RDEVAL_SHARE_DIR="\$(dirname \$(dirname \$(type -P rdeval)))/share/rdeval" &&
ln -s "\$RDEVAL_SHARE_DIR/figures.Rmd" &&
ln -s "\$RDEVAL_SHARE_DIR/rdeval_interface.R" &&
- #set $num_files = 0
- #for $input_file in $input_files
- ln -s '$input_file' '${num_files}.rd' &&
- #set $num_files += 1
+ #set $input_file_list = []
+ #for $idx, $input_file in enumerate($input_files)
+ ln -s '$input_file' '${idx}.rd' &&
+ #silent $input_file_list.append(f"'{idx}.rd'")
#end for
- R -e "rmarkdown::render('figures.Rmd', output_file='$html_outfile')" --args #for $idx in range($num_files)# '${idx}.rd' #end for
+ #set $r_vector = "c(" + ",".join(input_file_list) + ")"
+ #set $interactive_value = "FALSE"
+ #if $output_format.format_selector == "html" and $output_format.interactive
+ #set $interactive_value = "TRUE"
+ #end if
+ R -e "rmarkdown::render('figures.Rmd', output_file='$outfile', output_format='${output_format.format_selector}_document', params=list(input_files=$r_vector, interactive='$interactive_value'))"
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