Mercurial > repos > iuc > pimento_std
changeset 0:1ddab994fcee draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento commit 69888afa40f5ac6a42fa9335cf61f0bb6387eb2f
| author | iuc |
|---|---|
| date | Tue, 05 Aug 2025 09:21:07 +0000 |
| parents | |
| children | |
| files | macros.xml std.xml test-data/test.fastq.gz test-data/test_bcv.tsv test-data/test_cutoffs.tsv |
| diffstat | 5 files changed, 92 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Tue Aug 05 09:21:07 2025 +0000 @@ -0,0 +1,20 @@ +<macros> + <token name="@TOOL_VERSION@">1.0.2</token> + <token name="@VERSION_SUFFIX@">0</token> + <token name="@LICENSE@">Apache-2.0</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">mi-pimento</requirement> + </requirements> + </xml> + <xml name="creators"> + <creator> + <person givenName="Rand" familyName="Zoabi" url="https://github.com/RZ9082" identifier="https://orcid.org/0009-0000-2501-8053"/> + </creator> + </xml> + <xml name="citations"> + <citations> + <citation type="doi">10.1101/2025.07.04.663168</citation> + </citations> + </xml> +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/std.xml Tue Aug 05 09:21:07 2025 +0000 @@ -0,0 +1,66 @@ +<tool id="pimento_std" name="PIMENTO Standard primer matching" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="@LICENSE@"> + <description>Finds best-matching primers in reads using a fuzzy search against a standard primer library</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="creators"/> + <expand macro="requirements"/> + <command detect_errors="aggressive"><![CDATA[ + #if $primers: + mkdir primers && + cp '$primers' primers && + pimento std -i '$input_reads' -p primers --minimum_primer_threshold $minimum_primer_threshold $merged -o sample + #else + pimento std -i '$input_reads' --minimum_primer_threshold $minimum_primer_threshold $merged -o sample + #end if + ]]></command> + <inputs> + <param name="input_reads" type="data" label="Input reads" format="fastqsanger.gz"/> + <param name="primers" type="data" label="Input standard primers" format="fasta" optional="true"/> + <param argument="--minimum_primer_threshold" type="float" value="0.6" min="0.1" max="1.0" label="Minimum primer threshold" help="Any primers with a read proportion lower than this threshold are disregarded"/> + <param argument="--merged" type="boolean" truevalue="--merged" falsevalue="" help="Necessary if the input sequence file is made up of merged paired-end or single-end reads"/> + </inputs> + <outputs> + <data name="fasta_output" label="${tool.name} on ${on_string}: FASTA containing best found single or pairs of primers" format="fasta" from_work_dir="sample_std_primers.fasta"/> + <data name="best_found_primers" label="${tool.name} on ${on_string}: Best found primers" format="txt" from_work_dir="sample_std_primer_out.txt"/> + <data name="searched_primers" label="${tool.name} on ${on_string}: Every single searched primer" format="txt" from_work_dir="all_standard_primer_proportions.txt"/> + </outputs> + <tests> + <test expect_num_outputs="3"> + <param name="input_reads" value="test.fastq.gz"/> + <param name="minimum_primer_threshold" value="0.6"/> + <param name="merged" value="true"/> + <output name="fasta_output"> + <assert_contents> + <has_line line=">341F"/> + <has_line line="CCTACGGGNGGCWGCAG"/> + <has_n_lines n="4"/> + </assert_contents> + </output> + <output name="best_found_primers"> + <assert_contents> + <has_line line="V3-V4"/> + <has_line line="341F: 0.984"/> + <has_line line="805R: 0.948"/> + </assert_contents> + </output> + <output name="searched_primers"> + <assert_contents> + <has_line line="V3;341F:0.984"/> + <has_line line="V3;338F:0.0"/> + <has_n_lines n="148"/> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ + Runs the standard primer matching strategy for primer inference. A library + of standard primers will be searched in input reads using fuzzy regex to + identify primers with high degrees of proportions. The best single, or pair, + of primers found will be outputted into a FASTA file (provided any were + indeed found). PIMENTO comes with its own standard primer library which will + be used as a default. Users can however give their own custom input library, + or extend the default library to suit their needs. + ]]></help> + <expand macro="citations"/> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_bcv.tsv Tue Aug 05 09:21:07 2025 +0000 @@ -0,0 +1,3 @@ + 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 +F 0.952 0.9583999999999999 0.96 0.8464 0.8552 0.8343999999999999 0.8112 0.7272 0.828 0.8071999999999999 0.8039999999999999 0.8055999999999999 0.8736 0.8343999999999999 0.8432000000000001 0.8231999999999999 0.8200000000000001 0.836 0.8720000000000001 0.876 0.8168 0.8352 0.8216000000000001 +R 0.9544 0.8472 0.7263999999999999 0.7295999999999999 0.7287999999999999 0.7248 0.8256 0.9408 0.9336 0.9352 0.9328000000000001 0.9359999999999999 0.9368000000000001 0.9384 0.9399999999999998 0.9416 0.8888 0.8880000000000001 0.8928 0.8943999999999999 0.8768 0.9256 0.9199999999999999