Mercurial > repos > iuc > artic_minion
changeset 12:7021ed347f7e draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit 03d00ec10ba919fd8bac8d28f9b2b1e170fb3f55
author | iuc |
---|---|
date | Mon, 23 Jun 2025 07:35:31 +0000 |
parents | 93cfe7df7f8a |
children | |
files | artic_minion.xml macros.xml |
diffstat | 2 files changed, 18 insertions(+), 8 deletions(-) [+] |
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--- a/artic_minion.xml Mon Feb 24 13:54:40 2025 +0000 +++ b/artic_minion.xml Mon Jun 23 07:35:31 2025 +0000 @@ -1,4 +1,4 @@ -<tool id="artic_minion" name="ARTIC minion" version="@TOOL_VERSION@+galaxy1" profile="23.2"> +<tool id="artic_minion" name="ARTIC minion" version="@TOOL_VERSION@+galaxy0" profile="23.2"> <description>Build consensus sequence and call variants from amplicon-based nanopore sequence data</description> <macros> <import>macros.xml</import> @@ -59,6 +59,8 @@ --min-mapq $min_mapq --primer-match-threshold $primer_match_threshold $align_consensus + $linearise_fasta + $allow_mismatched_primers #if $normalise > 0: --normalise ${normalise} @@ -97,6 +99,14 @@ label="Align Consensus to reference" help="Run a MAFFT to align consensus to reference" /> + <param argument="--linearise-fasta" type="boolean" truevalue="--linearise-fasta" falsevalue="" + label="Linearise output fasta" + help="Output linearised (unwrapped) FASTA consensus files" /> + + <param argument="--allow-mismatched-primers" type="boolean" truevalue="--allow-mismatched-primers" falsevalue="" + label="Allow primer mismatch" + help="Reads will not be discarded by align_trim if they appear to have primers from different amplicons." /> + <!-- Primer and Reference fetching --> <conditional name="fetch_primer_scheme"> @@ -224,7 +234,7 @@ </conditional> <output name="consensus_fasta"> <assert_contents> - <has_line line=">test.fastq.gz/MN908947.3/ARTIC/clair3 MN908947.3" /> + <has_text text=">test.fastq.gz MN908947.3_artic-network/fieldbioinformatics_" /> </assert_contents> </output> <output name="alignment_trimmed"> @@ -234,7 +244,7 @@ </output> <output name="variants_merged_vcf"> <assert_contents> - <has_size value="900" delta="200" /> + <has_size value="1800" delta="200" /> </assert_contents> </output> </test> @@ -258,7 +268,7 @@ </conditional> <output name="consensus_fasta"> <assert_contents> - <has_line line=">test.fastq.gz/MN908947.3/ARTIC/clair3 MN908947.3" /> + <has_text text=">test.fastq.gz MN908947.3_artic-network/fieldbioinformatics_" /> </assert_contents> </output> <output name="alignment_trimmed"> @@ -268,7 +278,7 @@ </output> <output name="variants_merged_vcf"> <assert_contents> - <has_size value="3200" delta="200" /> + <has_size value="1800" delta="200" /> </assert_contents> </output> </test> @@ -295,7 +305,7 @@ </conditional> <output name="consensus_fasta"> <assert_contents> - <has_line line=">test.fastq.gz/MN908947.3/ARTIC/clair3 MN908947.3" /> + <has_text text=">test.fastq.gz MN908947.3_artic-network/fieldbioinformatics_" /> </assert_contents> </output> <output name="alignment_trimmed"> @@ -305,7 +315,7 @@ </output> <output name="variants_merged_vcf"> <assert_contents> - <has_size value="3200" delta="200" /> + <has_size value="1800" delta="200" /> </assert_contents> </output> </test>
--- a/macros.xml Mon Feb 24 13:54:40 2025 +0000 +++ b/macros.xml Mon Jun 23 07:35:31 2025 +0000 @@ -1,5 +1,5 @@ <macros> - <token name="@TOOL_VERSION@">1.6.0</token> + <token name="@TOOL_VERSION@">1.7.3</token> <token name="@FASTQ_FORMATS@">fastq,fastq.gz,fastqsanger,fastqsanger.gz</token> <xml name="requirements">