| Next changeset 1:1d34936d4497 (2025-06-02) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastplong commit 08a54debca6a5b792e28efaaee1f7d4671556ca1 |
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added:
fastplong.xml test-data/input.fastq test-data/output.fastq test-data/output_failed_out.fastq test-data/output_reads_to_process.fastq |
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| diff -r 000000000000 -r c3e3eecc8fe9 fastplong.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fastplong.xml Tue May 06 08:51:26 2025 +0000 |
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| b'@@ -0,0 +1,170 @@\n+<tool id="fastplong" name="Fastplong" version="@TOOL_VERSION@+galaxy0" profile="23.2" license="MIT">\n+ <description>Filter and trim long reads</description>\n+ <creator>\n+ <organization name="Masaryk University" url="https://www.muni.cz/"/>\n+ <person givenName="Hana" familyName="Resovska" email="499924@mail.muni.cz"/>\n+ </creator>\n+ <macros>\n+ <token name="@TOOL_VERSION@">0.2.2</token>\n+ </macros>\n+ <requirements>\n+ <requirement type="package" version="@TOOL_VERSION@">fastplong</requirement>\n+ </requirements>\n+ <command detect_errors="exit_code">\n+ <![CDATA[\n+ fastplong \n+ --thread \\${GALAXY_SLOTS:-1}\n+ --report_title \'fastplong report for $in\'\n+ --in \'$in\'\n+ --out \'$output\'\n+ #if $reads_to_process: \n+ --reads_to_process \'$reads_to_process\'\n+ #end if\n+ $disable_quality_filtering\n+ $disable_adapter_trimming\n+ #if $start_adapter:\n+ --start_adapter \'$start_adapter\'\n+ #end if\n+ #if $end_adapter:\n+ --end_adapter \'$end_adapter\'\n+ #end if\n+ #if $adapter_fasta:\n+ --adapter_fasta \'$adapter_fasta\'\n+ #end if\n+ #if $distance_threshold:\n+ --distance_threshold \'$distance_threshold\'\n+ #end if\n+ #if $trimming_extension:\n+ --trimming_extension \'$trimming_extension\'\n+ #end if\n+ #if $trim_front:\n+ --trim_front \'$trim_front\'\n+ #end if\n+ #if $trim_tail:\n+ --trim_tail \'$trim_tail\'\n+ #end if\n+ $trim_poly_x\n+ #if $poly_x_min_len:\n+ --poly_x_min_len \'$poly_x_min_len\'\n+ #end if\n+ $cut_front\n+ $cut_tail\n+ #if $cut_window_size:\n+ --cut_window_size \'$cut_window_size\'\n+ #end if\n+ #if $cut_mean_quality:\n+ --cut_mean_quality \'$cut_mean_quality\'\n+ #end if\n+ #if $cut_front_window_size:\n+ --cut_front_window_size \'$cut_front_window_size\'\n+ #end if\n+ #if $cut_front_mean_quality:\n+ --cut_front_mean_quality \'$cut_front_mean_quality\'\n+ #end if\n+ #if $cut_tail_window_size:\n+ --cut_tail_window_size \'$cut_tail_window_size\'\n+ #end if\n+ #if $cut_tail_mean_quality:\n+ --cut_tail_mean_quality \'$cut_tail_mean_quality\'\n+ #end if\n+ #if $qualified_quality_phred:\n+ --qualified_quality_phred \'$qualified_quality_phred\'\n+ #end if\n+ #if $unqualified_percent_limit:\n+ --unqualified_percent_limit \'$unqualified_percent_limit\'\n+ #end if\n+ #if $n_base_limit:\n+ --n_base_limit \'$n_base_limit\'\n+ #end if\n+ #if $mean_qual:\n+ --mean_qual \'$mean_qual\'\n+ #end if\n+ $disable_length_filtering:\n+ #if $length_required:\n+ --length_required \'$length_required\'\n+ #end if\n+ #if $length_limit:\n+ --length_limit \'$length_limit\'\n+ #end if\n+ $low_complexity_filter:\n+ #if $complexity_threshold:\n+ --complexity_threshold \'$complexity_threshold\'\n+ #end if\n+ $failed_out failed_reads.fastq\n+ ]]>\n+ </command>\n+ <inputs>\n+ <param argument="--in" type="data" format="fastq,fastq.gz" label="Input FASTQ file"/>\n+ <param argument="--reads_to_process" type="integer" optional="true" label="Number of reads to process" help="Limit the number of reads to process. Useful for quick QC or creating subsets."/>\n+ <param argument="--disable_quality_filtering" type="boolean" truevalue="--disable_quality_filtering" falsevalue="" checked="false" label="Disable quality filtering?" help="By default, quality filtering is enabled. Enable this option to turn it off."/>\n+ <param argument="--disable_adapter_trimming" type="boolean" truevalue="--disable_adapter_trimming" falsevalue="" checked="false"'..b'bel="Tail mean quality" help="Override quality threshold for cut_tail only. Default: cut_mean_quality"/>\n+ <param argument="--qualified_quality_phred" type="integer" min="0" optional="true" label="Qualified base Phred score" help="Phred quality score that counts as qualified. Default: 15"/>\n+ <param argument="--unqualified_percent_limit" type="integer" min="0" max="100" optional="true" label="Unqualified base percentage limit" help="Percent of bases allowed to be below quality threshold. Default: 40"/>\n+ <param argument="--n_base_limit" type="integer" optional="true" label="N base limit" help="Reads with more than this number of N bases are discarded. Default: 5"/>\n+ <param argument="--mean_qual" type="integer" optional="true" label="Minimum mean quality" help="Reads with mean quality below this are discarded. Default: 0"/>\n+ <param argument="--disable_length_filtering" type="boolean" truevalue="--disable_length_filtering" falsevalue="" checked="false" label="Disable length filtering?" help="Length filtering is enabled by default. Enable this to disable it."/>\n+ <param argument="--length_required" type="integer" optional="true" label="Minimum read length" help="Reads shorter than this will be discarded. Default: 15"/>\n+ <param argument="--length_limit" type="integer" optional="true" label="Maximum read length" help="Reads longer than this will be discarded. Default: 0 (no limit)"/>\n+ <param argument="--low_complexity_filter" type="boolean" truevalue="--low_complexity_filter" falsevalue="" checked="false" label="Enable low complexity filter?" help="Enable low complexity filtering."/>\n+ <param argument="--complexity_threshold" type="integer" min="0" max="100" optional="true" label="Complexity threshold (%)" help="Minimum required sequence complexity (0\xe2\x80\x93100). Default: 30"/>\n+ <param argument="--failed_out" type="boolean" truevalue="--failed_out" falsevalue="" checked="false" label="Save failed reads?" help="Enable this to write failed reads to a separate FASTQ file."/>\n+ </inputs>\n+ <outputs>\n+ <data name="output" format="fastq" label="Filtered Output FASTQ"/>\n+ <data name="failed_out_reads" format="fastq" from_work_dir="failed_reads.fastq" label="Failed Reads FASTQ">\n+ <filter>failed_out</filter>\n+ </data>\n+ <data name="json_output_default" format="json" from_work_dir="fastplong.json" label="JSON Report (default)"/>\n+ <data name="html_output_default" format="html" from_work_dir="fastplong.html" label="HTML Report (default)"/>\n+ </outputs>\n+ <tests>\n+ <test expect_num_outputs="3">\n+ <param name="in" value="input.fastq"/>\n+ <output name="output" file="output.fastq"/>\n+ </test>\n+ <test expect_num_outputs="3">\n+ <param name="in" value="input.fastq"/>\n+ <param name="reads_to_process" value="3"/>\n+ <output name="output" file="output_reads_to_process.fastq"/>\n+ </test>\n+ <test expect_num_outputs="4">\n+ <param name="in" value="input.fastq"/>\n+ <param name="failed_out" value="true"/>\n+ <output name="failed_out_reads" value="output_failed_out.fastq"/>\n+ </test>\n+ </tests>\n+ <help>\n+ **Fastplong: Filter and trim long reads**\n+\n+ This tool wraps the `fastplong` command-line tool to allow filtering and trimming of long reads in FASTQ format.\n+\n+ **Inputs**\n+ - A FASTQ file containing reads and optional parameters to control trimming, quality filtering, adapter detection, and more.\n+\n+ **Outputs**\n+ - A filtered FASTQ file with trimmed reads, HTML and JSON report and an optional FASTQ file of failed reads.\n+\n+ For more information, see https://github.com/OpenGene/fastplong\n+ </help>\n+ <citations>\n+ <citation type="doi">10.1002/imt2.107</citation>\n+ <citation type="doi">10.1093/bioinformatics/bty560</citation>\n+ </citations>\n+</tool>\n' |
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| diff -r 000000000000 -r c3e3eecc8fe9 test-data/input.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input.fastq Tue May 06 08:51:26 2025 +0000 |
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| @@ -0,0 +1,24 @@ +@name +AGGTGCTGCGCATACTTTTCCACGGGGATACTACTGGGTGTTACCGTGGGAATGAATCCTTTTAACCTTAGCAATACGTAAAGGTGCT ++ +///EEEEEEEEEEEEEEEEEEEEEEEEEE////EEEEEEEEEEEEE////E////EEEEEEEEE///EEEEEEEEEEEEEEEEEEEEE + +@name2 +AGGTGCTGCGCATACTTTTCCACGGGGATACTACTGGGTGTTACCGTGGGAATGAATCCTTTTAACCTTAGCAATACGTAAAGGTGCT ++ +///EEEEEEEEEEEEEEEEEEEEEEEEEE////EEEEEEEEEEEEE////E////EEEEEEEEE///EEEEEEEEEEEEEEEEEEEEE + +@name3 +AGGTGCTGCGCATACTTTTCCACGGGGATACTACTGGGTGTTACCGTGGGAATGAATCCTTTTAACCTTAGCAATACGTAAAGGTGCT ++ +///EEEEEEEEEEEEEEEEEEEEEEEEEE////EEEEEEEEEEEEE////E////EEEEEEEEE///EEEEEEEEEEEEEEEEEEEEE + +@name4 +AGGTGCTGCGCATACTTTTCCACGGGGATACTACTGGGTGTTACCGTGGGAATGAATCCTTTTAACCTTAGCAATACGTAAAGGTGCT ++ +///EEEEEEEEEEEEEEEEEEEEEEEEEE////EEEEEEEEEEEEE////E////EEEEEEEEE///EEEEEEEEEEEEEEEEEEEEE + +@name5 +AGGTGCTGCGCATACTTTTCCACGGGGATACTACTGGGTGTTACCGTGGGAATGAATCCTTTTAACCTTAGCAATACGTAAAGGTGCT ++ +)))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))) |
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| diff -r 000000000000 -r c3e3eecc8fe9 test-data/output.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output.fastq Tue May 06 08:51:26 2025 +0000 |
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| @@ -0,0 +1,16 @@ +@name +AGGTGCTGCGCATACTTTTCCACGGGGATACTACTGGGTGTTACCGTGGGAATGAATCCTTTTAACCTTAGCAATACGTAAAGGTGCT ++ +///EEEEEEEEEEEEEEEEEEEEEEEEEE////EEEEEEEEEEEEE////E////EEEEEEEEE///EEEEEEEEEEEEEEEEEEEEE +@name2 +AGGTGCTGCGCATACTTTTCCACGGGGATACTACTGGGTGTTACCGTGGGAATGAATCCTTTTAACCTTAGCAATACGTAAAGGTGCT ++ +///EEEEEEEEEEEEEEEEEEEEEEEEEE////EEEEEEEEEEEEE////E////EEEEEEEEE///EEEEEEEEEEEEEEEEEEEEE +@name3 +AGGTGCTGCGCATACTTTTCCACGGGGATACTACTGGGTGTTACCGTGGGAATGAATCCTTTTAACCTTAGCAATACGTAAAGGTGCT ++ +///EEEEEEEEEEEEEEEEEEEEEEEEEE////EEEEEEEEEEEEE////E////EEEEEEEEE///EEEEEEEEEEEEEEEEEEEEE +@name4 +AGGTGCTGCGCATACTTTTCCACGGGGATACTACTGGGTGTTACCGTGGGAATGAATCCTTTTAACCTTAGCAATACGTAAAGGTGCT ++ +///EEEEEEEEEEEEEEEEEEEEEEEEEE////EEEEEEEEEEEEE////E////EEEEEEEEE///EEEEEEEEEEEEEEEEEEEEE |
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| diff -r 000000000000 -r c3e3eecc8fe9 test-data/output_failed_out.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_failed_out.fastq Tue May 06 08:51:26 2025 +0000 |
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| @@ -0,0 +1,4 @@ +@name5 failed_quality_filter +AGGTGCTGCGCATACTTTTCCACGGGGATACTACTGGGTGTTACCGTGGGAATGAATCCTTTTAACCTTAGCAATACGTAAAGGTGCT ++ +)))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))) |
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| diff -r 000000000000 -r c3e3eecc8fe9 test-data/output_reads_to_process.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_reads_to_process.fastq Tue May 06 08:51:26 2025 +0000 |
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| @@ -0,0 +1,12 @@ +@name +AGGTGCTGCGCATACTTTTCCACGGGGATACTACTGGGTGTTACCGTGGGAATGAATCCTTTTAACCTTAGCAATACGTAAAGGTGCT ++ +///EEEEEEEEEEEEEEEEEEEEEEEEEE////EEEEEEEEEEEEE////E////EEEEEEEEE///EEEEEEEEEEEEEEEEEEEEE +@name2 +AGGTGCTGCGCATACTTTTCCACGGGGATACTACTGGGTGTTACCGTGGGAATGAATCCTTTTAACCTTAGCAATACGTAAAGGTGCT ++ +///EEEEEEEEEEEEEEEEEEEEEEEEEE////EEEEEEEEEEEEE////E////EEEEEEEEE///EEEEEEEEEEEEEEEEEEEEE +@name3 +AGGTGCTGCGCATACTTTTCCACGGGGATACTACTGGGTGTTACCGTGGGAATGAATCCTTTTAACCTTAGCAATACGTAAAGGTGCT ++ +///EEEEEEEEEEEEEEEEEEEEEEEEEE////EEEEEEEEEEEEE////E////EEEEEEEEE///EEEEEEEEEEEEEEEEEEEEE |