| Previous changeset 21:281054a26e41 (2025-06-23) Next changeset 23:1c183b0a6cfd (2025-08-18) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e94b9dd0fba5c4822624687a906f646329d62e8 |
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modified:
fastp.xml |
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added:
test-data/quality_cutting_output.fq.gz |
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| diff -r 281054a26e41 -r 350c736075eb fastp.xml --- a/fastp.xml Mon Jun 23 07:30:30 2025 +0000 +++ b/fastp.xml Thu Aug 14 16:59:43 2025 +0000 |
| [ |
| b'@@ -1,4 +1,4 @@\n-<tool id="fastp" name="fastp" version="@TOOL_VERSION@+galaxy0" profile="23.1">\n+<tool id="fastp" name="fastp" version="@TOOL_VERSION@+galaxy1" profile="23.1">\n <description>fast all-in-one preprocessing for FASTQ files</description>\n <macros>\n <import>macros.xml</import>\n@@ -186,18 +186,22 @@\n \n ## Per read cutting by quality options\n \n-#if $read_mod_options.cutting_by_quality_options.cut_by_quality5 or $read_mod_options.cutting_by_quality_options.cut_by_quality3:\n-\n- $read_mod_options.cutting_by_quality_options.cut_by_quality5\n-\n- $read_mod_options.cutting_by_quality_options.cut_by_quality3\n+#if str($read_mod_options.cutting_by_quality_options.cut_front_select.cut_front) == \'--cut_front\'\n+ $read_mod_options.cutting_by_quality_options.cut_front_select.cut_front\n+ --cut_front_window_size $read_mod_options.cutting_by_quality_options.cut_front_select.cut_front_window_size\n+ --cut_front_mean_quality $read_mod_options.cutting_by_quality_options.cut_front_select.cut_front_mean_quality\n+#end if\n \n- #if str($read_mod_options.cutting_by_quality_options.cut_window_size):\n- -W $read_mod_options.cutting_by_quality_options.cut_window_size\n- #end if\n- #if str($read_mod_options.cutting_by_quality_options.cut_mean_quality):\n- -M $read_mod_options.cutting_by_quality_options.cut_mean_quality\n- #end if\n+#if str($read_mod_options.cutting_by_quality_options.cut_tail_select.cut_tail) == \'--cut_tail\'\n+ $read_mod_options.cutting_by_quality_options.cut_tail_select.cut_tail\n+ --cut_tail_window_size $read_mod_options.cutting_by_quality_options.cut_tail_select.cut_tail_window_size\n+ --cut_tail_mean_quality $read_mod_options.cutting_by_quality_options.cut_tail_select.cut_tail_mean_quality\n+#end if\n+\n+#if str($read_mod_options.cutting_by_quality_options.cut_right_select.cut_right) == \'--cut_right\'\n+ $read_mod_options.cutting_by_quality_options.cut_right_select.cut_right\n+ --cut_right_window_size $read_mod_options.cutting_by_quality_options.cut_right_select.cut_right_window_size\n+ --cut_right_mean_quality $read_mod_options.cutting_by_quality_options.cut_right_select.cut_right_mean_quality\n #end if\n \n ## Base correction by overlap analysis options\n@@ -307,10 +311,42 @@\n </section>\n \n <section name="cutting_by_quality_options" title="Per read cutting by quality options" expanded="True">\n- <param name="cut_by_quality5" argument="-5" type="boolean" truevalue="-5" falsevalue="" checked="false" label="Cut by quality in front (5\')" help="Enable per read cutting by quality in front (5\'), default is disabled (WARNING: this will interfere deduplication for both PE/SE data)."/>\n- <param name="cut_by_quality3" argument="-3" type="boolean" truevalue="-3" falsevalue="" checked="false" label="Cut by quality in tail (3\')" help="Enable per read cutting by quality in tail (3\'), default is disabled (WARNING: this will interfere deduplication for SE data)."/>\n- <param name="cut_window_size" argument="-W" type="integer" optional="true" label="Cutting window size" help="The size of the sliding window for sliding window trimming, default is 4."/>\n- <param name="cut_mean_quality" argument="-M" type="integer" optional="true" label="Cutting mean quality" help="The bases in the sliding window with mean quality below cutting_quality will be cut, default is Q20."/>\n+ <conditional name="cut_front_select">\n+ <param argument="--cut_front" type="select" truevalue="--cut_front" falsevalue="" checked="false" label="Cut by quality in front (5\')" help="Enable per read cutting by quality in front (5\'), default is disabled (WARNING: this will interfere deduplication for both PE/SE data).">\n+ <option value="--cut_front">Yes</option>\n+ <option value="" selected="true">No</option>\n+ </param>\n'..b' </when>\n+ <when value="">\n+ </when>\n+ </conditional>\n+ <conditional name="cut_right_select">\n+ <param argument="--cut_right" type="select" truevalue="--cut_right" falsevalue="" checked="false" label="Cut by quality in tail (3\')" help="Move a sliding window from front to tail, if meet one window with mean quality < threshold, drop the bases in the window and the right part, and then stop.">\n+ <option value="--cut_right">Yes</option>\n+ <option value="" selected="true">No</option>\n+ </param>\n+ <when value="--cut_right">\n+ <param argument="--cut_right_window_size" type="integer" optional="true" value="4" min="1" max="1000" label="Cutting window size for cut right" help="The size of the sliding window for sliding window trimming."/>\n+ <param argument="--cut_right_mean_quality" type="integer" optional="true" value="20" min="1" max="36 " label="Cutting mean quality for cut right" help="The bases in the sliding window with mean quality below cutting_quality will be cut."/>\n+ </when>\n+ <when value="">\n+ </when>\n+ </conditional>\n </section>\n \n <section name="base_correction_options" title="Base correction by overlap analysis options" expanded="True">\n@@ -716,6 +752,46 @@\n <element name="reverse" value="bwa-mem-fastq-paired-collection/output_reverse.fastqsanger.gz" decompress="true" ftype="fastqsanger.gz"/>\n </output_collection>\n </test>\n+ <!-- 17. Ensure quality cutting work -->\n+ <test expect_num_outputs="3">\n+ <conditional name="single_paired">\n+ <param name="single_paired_selector" value="single"/>\n+ <param name="in1" ftype="fastqsanger.gz" value="R1.fq.gz"/>\n+ </conditional>\n+ <section name="read_mod_options">\n+ <section name="cutting_by_quality_options">\n+ <conditional name="cut_front_select">\n+ <param name="cut_front" value="--cut_front"/>\n+ <param name="cut_front_window_size" value="2"/>\n+ <param name="cut_front_mean_quality" value="3"/>\n+ </conditional>\n+ <conditional name="cut_tail_select">\n+ <param name="cut_tail" value="--cut_tail"/>\n+ <param name="cut_tail_window_size" value="4"/>\n+ <param name="cut_tail_mean_quality" value="5"/>\n+ </conditional>\n+ <conditional name="cut_right_select">\n+ <param name="cut_right" value="--cut_right"/>\n+ <param name="cut_right_window_size" value="6"/>\n+ <param name="cut_right_mean_quality" value="7"/>\n+ </conditional>\n+ </section>\n+ </section>\n+ <output name="out1" ftype="fastqsanger.gz" decompress="true" file="quality_cutting_output.fq.gz"/>\n+ <output name="report_json">\n+ <assert_contents>\n+ <has_text text="--cut_front"/>\n+ <has_text text="--cut_tail"/>\n+ <has_text text="--cut_right"/>\n+ <has_text text="--cut_front_window_size 2"/>\n+ <has_text text="--cut_front_mean_quality 3"/>\n+ <has_text text="--cut_tail_window_size 4"/>\n+ <has_text text="--cut_tail_mean_quality 5"/>\n+ <has_text text="--cut_right_window_size 6"/>\n+ <has_text text="--cut_right_mean_quality 7"/>\n+ </assert_contents>\n+ </output>\n+ </test>\n </tests>\n <help><![CDATA[\n .. class:: infomark\n' |
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| diff -r 281054a26e41 -r 350c736075eb test-data/quality_cutting_output.fq.gz |
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| Binary file test-data/quality_cutting_output.fq.gz has changed |