# HG changeset patch
# User iuc
# Date 1739027716 0
# Node ID 10678d49d39ecf839357efa0cc6a62bc182bcc6b
# Parent a626e8c0e1bad53f9a863a53625149223fc65999
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
diff -r a626e8c0e1ba -r 10678d49d39e fastp.xml
--- a/fastp.xml Fri Nov 15 15:31:53 2024 +0000
+++ b/fastp.xml Sat Feb 08 15:15:16 2025 +0000
@@ -1,4 +1,4 @@
-
+
fast all-in-one preprocessing for FASTQ files
macros.xml
@@ -23,8 +23,6 @@
#set $in2 = $single_paired.paired_input.reverse
#set $in1_name = re.sub('[^\w\-\s]', '_', str($single_paired.paired_input.name)) + $ext
#set $in2_name = re.sub('[^\w\-\s]', '_', str("%s_%s" % ($single_paired.paired_input.name, "R2"))) + $ext
- #set out1 = $output_paired_coll.forward
- #set out2 = $output_paired_coll.reverse
ln -sf '$in1' '$in1_name' &&
ln -sf '$in2' '$in2_name' &&
#else
@@ -34,11 +32,6 @@
#set $in1_name = re.sub('[^\w\-\s]', '_', str($in1.element_identifier)) + $ext
ln -sf '$in1' '$in1_name' &&
-
- #if str($single_paired.single_paired_selector) == 'paired':
- #set $in2_name = re.sub('[^\w\-\s]', '_', str("%s_R2" % $in2.element_identifier)) + $ext
- ln -sf '$in2' '$in2_name' &&
- #end if
#end if
## Run fastp
@@ -56,14 +49,14 @@
-I '$in2_name'
#if $single_paired.merge_reads.merge
$single_paired.merge_reads.merge
- --merged_out '$merged_reads'
+ --merged_out merged${ext}
#if $single_paired.merge_reads.include_unmerged
$single_paired.merge_reads.include_unmerged
#else
- --out1 '$unmerged_out1'
- --out2 '$unmerged_out2'
- --unpaired1 '$unpaired1'
- --unpaired2 '$unpaired2'
+ --out1 'unmerged_R1${ext}'
+ --out2 'unmerged_R2${ext}'
+ --unpaired1 'unpaired_R1${ext}'
+ --unpaired2 'unpaired_R2${ext}'
#end if
#else
-o first${ext}
@@ -211,21 +204,28 @@
$read_mod_options.base_correction_options.correction
-#if str($single_paired.single_paired_selector).startswith('single')
- &&
- mv first${ext} '${out1}'
-#elif str($single_paired.single_paired_selector).startswith('paired') and not $single_paired.merge_reads.merge:
- &&
- mv first${ext} '${out1}'
- &&
- mv second${ext} '${out2}'
+#if str($single_paired.single_paired_selector) == 'paired_collection'
+ #if $single_paired.merge_reads.merge
+ && mv merged${ext} '$merged_reads'
+ #if not $single_paired.merge_reads.include_unmerged
+ && mv 'unmerged_R1${ext}' '$unmerged_out_coll.forward'
+ && mv 'unmerged_R2${ext}' '$unmerged_out_coll.reverse'
+ && mv 'unpaired_R1${ext}' '$unpaired_out_coll.forward'
+ && mv 'unpaired_R2${ext}' '$unpaired_out_coll.reverse'
+ #end if
+ #else
+ && mv first${ext} '$output_paired_coll.forward'
+ && mv second${ext} '$output_paired_coll.reverse'
+ #end if
+#else
+ && mv first${ext} '${out1}'
#end if
+
]]>
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@@ -281,7 +271,7 @@
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@@ -335,48 +325,37 @@
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- single_paired['single_paired_selector'] in ["single", "paired"] and not single_paired['merge_reads']['merge']
+
+ single_paired['single_paired_selector'] == "single"
-
- single_paired['single_paired_selector'] == "paired" and not single_paired['merge_reads']['merge']
-
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+
single_paired['single_paired_selector'] == "paired_collection" and not single_paired['merge_reads']['merge']
+
output_options['report_html'] is True
output_options['report_json'] is True
-
- single_paired['single_paired_selector'] in ["paired", "paired_collection"] and single_paired['merge_reads']['merge']
-
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- single_paired['single_paired_selector'] in ["paired", "paired_collection"] and single_paired['merge_reads']['merge'] and not single_paired['merge_reads']['include_unmerged']
-
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+ single_paired['single_paired_selector'] == "paired_collection" and single_paired['merge_reads']['merge']
-
- single_paired['single_paired_selector'] in ["paired", "paired_collection"] and single_paired['merge_reads']['merge'] and not single_paired['merge_reads']['include_unmerged']
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- single_paired['single_paired_selector'] in ["paired", "paired_collection"] and single_paired['merge_reads']['merge'] and not single_paired['merge_reads']['include_unmerged']
-
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- single_paired['single_paired_selector'] in ["paired", "paired_collection"] and single_paired['merge_reads']['merge'] and not single_paired['merge_reads']['include_unmerged']
-
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+
+ single_paired['single_paired_selector'] == "paired_collection" and single_paired['merge_reads']['merge'] and not single_paired['merge_reads']['include_unmerged']
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+ single_paired['single_paired_selector'] == "paired_collection" and single_paired['merge_reads']['merge'] and not single_paired['merge_reads']['include_unmerged']
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@@ -633,10 +748,8 @@
* Processed reads
* Merged reads
- * Unmerged filtered reads1, reads that cannot be merged successfully, but both pass all the filters.
- * Unmerged filtered reads2, reads that cannot be merged successfully, but both pass all the filters.
- * Unmerged unfiltered reads1, reads that cannot be merged, **read1** passes filters but **read2** doesn't.
- * Unmerged unfiltered reads2, reads that cannot be merged, **read2** passes filters but **read1** doesn't.
+ * Unmerged filtered reads, reads that cannot be merged successfully, but both pass all the filters.
+ * Unmerged unfiltered reads, reads that cannot be merged, i.e. **forward** passes filters but **reverse** doesn't.
Optionally, under **Output Options** you can choose to output
@@ -649,4 +762,4 @@
10.1101/274100
-
\ No newline at end of file
+
diff -r a626e8c0e1ba -r 10678d49d39e macros.xml
--- a/macros.xml Fri Nov 15 15:31:53 2024 +0000
+++ b/macros.xml Sat Feb 08 15:15:16 2025 +0000
@@ -69,20 +69,4 @@
help="The minimum length to detect polyG in the read tail. 10 by default."/>
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\ No newline at end of file
diff -r a626e8c0e1ba -r 10678d49d39e test-data/bwa-mem-fastq1.fq.gz
Binary file test-data/bwa-mem-fastq1.fq.gz has changed
diff -r a626e8c0e1ba -r 10678d49d39e test-data/bwa-mem-fastq2.fq.gz
Binary file test-data/bwa-mem-fastq2.fq.gz has changed
diff -r a626e8c0e1ba -r 10678d49d39e test-data/bwa-mem-merged-read-include-unmerged.fastqsanger.gz
Binary file test-data/bwa-mem-merged-read-include-unmerged.fastqsanger.gz has changed
diff -r a626e8c0e1ba -r 10678d49d39e test-data/bwa-mem-merged-reads.fastqsanger.gz
Binary file test-data/bwa-mem-merged-reads.fastqsanger.gz has changed
diff -r a626e8c0e1ba -r 10678d49d39e test-data/bwa-mem-unmerged-filtered-reads1.fastqsanger.gz
Binary file test-data/bwa-mem-unmerged-filtered-reads1.fastqsanger.gz has changed
diff -r a626e8c0e1ba -r 10678d49d39e test-data/bwa-mem-unmerged-filtered-reads2.fastqsanger.gz
Binary file test-data/bwa-mem-unmerged-filtered-reads2.fastqsanger.gz has changed
diff -r a626e8c0e1ba -r 10678d49d39e test-data/bwa-mem-unmerged-unfiltered-reads1.fastqsanger.gz
Binary file test-data/bwa-mem-unmerged-unfiltered-reads1.fastqsanger.gz has changed
diff -r a626e8c0e1ba -r 10678d49d39e test-data/out1.fq.gz
Binary file test-data/out1.fq.gz has changed