| Previous changeset 15:a626e8c0e1ba (2024-11-15) Next changeset 17:25c59c0ceb55 (2025-04-21) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 |
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modified:
fastp.xml macros.xml test-data/out1.fq.gz |
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added:
test-data/bwa-mem-fastq1.fq.gz test-data/bwa-mem-fastq2.fq.gz test-data/bwa-mem-merged-read-include-unmerged.fastqsanger.gz test-data/bwa-mem-merged-reads.fastqsanger.gz test-data/bwa-mem-unmerged-filtered-reads1.fastqsanger.gz test-data/bwa-mem-unmerged-filtered-reads2.fastqsanger.gz test-data/bwa-mem-unmerged-unfiltered-reads1.fastqsanger.gz |
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| 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 |
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| b'@@ -1,4 +1,4 @@\n-<tool id="fastp" name="fastp" version="@TOOL_VERSION@+galaxy3" profile="23.1">\n+<tool id="fastp" name="fastp" version="@TOOL_VERSION@+galaxy4" profile="23.1">\n <description>fast all-in-one preprocessing for FASTQ files</description>\n <macros>\n <import>macros.xml</import>\n@@ -23,8 +23,6 @@\n #set $in2 = $single_paired.paired_input.reverse\n #set $in1_name = re.sub(\'[^\\w\\-\\s]\', \'_\', str($single_paired.paired_input.name)) + $ext\n #set $in2_name = re.sub(\'[^\\w\\-\\s]\', \'_\', str("%s_%s" % ($single_paired.paired_input.name, "R2"))) + $ext\n- #set out1 = $output_paired_coll.forward\n- #set out2 = $output_paired_coll.reverse\n ln -sf \'$in1\' \'$in1_name\' &&\n ln -sf \'$in2\' \'$in2_name\' &&\n #else\n@@ -34,11 +32,6 @@\n \n #set $in1_name = re.sub(\'[^\\w\\-\\s]\', \'_\', str($in1.element_identifier)) + $ext\n ln -sf \'$in1\' \'$in1_name\' &&\n-\n- #if str($single_paired.single_paired_selector) == \'paired\':\n- #set $in2_name = re.sub(\'[^\\w\\-\\s]\', \'_\', str("%s_R2" % $in2.element_identifier)) + $ext\n- ln -sf \'$in2\' \'$in2_name\' &&\n- #end if\n #end if\n \n ## Run fastp\n@@ -56,14 +49,14 @@\n -I \'$in2_name\'\n #if $single_paired.merge_reads.merge\n $single_paired.merge_reads.merge\n- --merged_out \'$merged_reads\'\n+ --merged_out merged${ext}\n #if $single_paired.merge_reads.include_unmerged\n $single_paired.merge_reads.include_unmerged\n #else\n- --out1 \'$unmerged_out1\'\n- --out2 \'$unmerged_out2\'\n- --unpaired1 \'$unpaired1\'\n- --unpaired2 \'$unpaired2\'\n+ --out1 \'unmerged_R1${ext}\'\n+ --out2 \'unmerged_R2${ext}\'\n+ --unpaired1 \'unpaired_R1${ext}\'\n+ --unpaired2 \'unpaired_R2${ext}\'\n #end if\n #else\n -o first${ext}\n@@ -211,21 +204,28 @@\n \n $read_mod_options.base_correction_options.correction\n \n-#if str($single_paired.single_paired_selector).startswith(\'single\')\n- &&\n- mv first${ext} \'${out1}\'\n-#elif str($single_paired.single_paired_selector).startswith(\'paired\') and not $single_paired.merge_reads.merge:\n- &&\n- mv first${ext} \'${out1}\'\n- &&\n- mv second${ext} \'${out2}\'\n+#if str($single_paired.single_paired_selector) == \'paired_collection\'\n+ #if $single_paired.merge_reads.merge\n+ && mv merged${ext} \'$merged_reads\'\n+ #if not $single_paired.merge_reads.include_unmerged\n+ && mv \'unmerged_R1${ext}\' \'$unmerged_out_coll.forward\'\n+ && mv \'unmerged_R2${ext}\' \'$unmerged_out_coll.reverse\'\n+ && mv \'unpaired_R1${ext}\' \'$unpaired_out_coll.forward\'\n+ && mv \'unpaired_R2${ext}\' \'$unpaired_out_coll.reverse\'\n+ #end if\n+ #else\n+ && mv first${ext} \'$output_paired_coll.forward\'\n+ && mv second${ext} \'$output_paired_coll.reverse\'\n+ #end if\n+#else\n+ && mv first${ext} \'${out1}\'\n #end if\n+\n ]]></command>\n <inputs>\n <conditional name="single_paired">\n <param name="single_paired_selector" type="select" label="Single-end or paired reads">\n <option value="single" selected="true">Single-end</option>\n- <option value="paired">Paired</option>\n <option value="paired_collection">Paired Collection</option>\n </param>\n <when value="single">\n@@ -233,16 +233,6 @@\n <expand macro="adapter_trimming_options" />\n <expand macro="global_trimming_options" />\n </when>\n- <when value="paired">\n- <expand macro="in" read_number="1" argument="-i"/>\n- <expand macro="in" read_number="2" argument="-I"/>\n- <expand macro="merge_reads" />\n- <expand macro="adapter_trimming_options">\n- <expand macro="adapter_sequence" read_number="2"/>\n- <expand macro="detect_adapter_for_pe" />\n- </expand>\n- <expand macro="global_trimming_options_pair'..b' <conditional name="merge_reads">\n+ <param name="merge" value="--merge" />\n+ <param name="include_unmerged" value="true" />\n+ </conditional>\n+ </conditional>\n+ <section name="output_options">\n+ <param name="report_html" value="False" />\n+ </section>\n+ <output name="merged_reads" ftype="fastqsanger.gz" decompress="true" file="bwa-mem-merged-read-include-unmerged.fastqsanger.gz" />\n+ <output name="report_json">\n+ <assert_contents>\n+ <has_text text="fastp report"/>\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <!--16. Test paired collection in combination with compressed input-->\n <test expect_num_outputs="4">\n- <param name="single_paired_selector" value="paired_collection"/>\n- <param name="paired_input">\n- <collection type="paired">\n- <element name="forward" value="bwa-mem-fastq-paired-collection/input_forward.fastqsanger.gz" ftype="fastqsanger.gz" />\n- <element name="reverse" value="bwa-mem-fastq-paired-collection/input_reverse.fastqsanger.gz" ftype="fastqsanger.gz" />\n- </collection>\n- </param>\n- <param name="report_json" value="False" />\n+ <conditional name="single_paired">\n+ <param name="single_paired_selector" value="paired_collection"/>\n+ <param name="paired_input">\n+ <collection type="paired">\n+ <element name="forward" value="bwa-mem-fastq-paired-collection/input_forward.fastqsanger.gz" ftype="fastqsanger.gz" />\n+ <element name="reverse" value="bwa-mem-fastq-paired-collection/input_reverse.fastqsanger.gz" ftype="fastqsanger.gz" />\n+ </collection>\n+ </param>\n+ </conditional>\n+ <section name="output_options">\n+ <param name="report_json" value="False" />\n+ </section>\n <output name="report_html">\n <assert_contents>\n <has_text text="fastp report"/>\n </assert_contents>\n </output>\n <output_collection name="output_paired_coll" type="paired">\n- <element name="forward" value="bwa-mem-fastq-paired-collection/output_forward.fastqsanger.gz" decompress="True" ftype="fastqsanger.gz"/>\n- <element name="reverse" value="bwa-mem-fastq-paired-collection/output_reverse.fastqsanger.gz" decompress="True" ftype="fastqsanger.gz"/>\n+ <element name="forward" value="bwa-mem-fastq-paired-collection/output_forward.fastqsanger.gz" decompress="true" ftype="fastqsanger.gz"/>\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 </tests>\n@@ -633,10 +748,8 @@\n \n * Processed reads\n * Merged reads\n- * Unmerged filtered reads1, reads that cannot be merged successfully, but both pass all the filters.\n- * Unmerged filtered reads2, reads that cannot be merged successfully, but both pass all the filters.\n- * Unmerged unfiltered reads1, reads that cannot be merged, **read1** passes filters but **read2** doesn\'t.\n- * Unmerged unfiltered reads2, reads that cannot be merged, **read2** passes filters but **read1** doesn\'t.\n+ * Unmerged filtered reads, reads that cannot be merged successfully, but both pass all the filters.\n+ * Unmerged unfiltered reads, reads that cannot be merged, i.e. **forward** passes filters but **reverse** doesn\'t.\n \n Optionally, under **Output Options** you can choose to output\n \n@@ -649,4 +762,4 @@\n <citations>\n <citation type="doi">10.1101/274100</citation>\n </citations>\n-</tool>\n\\ No newline at end of file\n+</tool>\n' |
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| 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 |
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| @@ -69,20 +69,4 @@ help="The minimum length to detect polyG in the read tail. 10 by default."/> </xml> - <xml name="format_actions" token_read_number="1" token_forward_reverse="forward"> - <actions> - <conditional name="single_paired.single_paired_selector"> - <when value="paired"> - <action type="format"> - <option type="from_param" name="single_paired.in@READ_NUMBER@" param_attribute="ext" /> - </action> - </when> - <when value="paired_collection"> - <action type="format"> - <option type="from_param" name="single_paired.paired_input" param_attribute="@FORWARD_REVERSE@.ext" /> - </action> - </when> - </conditional> - </actions> - </xml> </macros> \ No newline at end of file |
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