Mercurial > repos > iuc > artic_minion
diff artic_minion.xml @ 0:c411e2205442 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit 41ad91410844b6d399844b253e39fa29955b96d6"
| author | iuc |
|---|---|
| date | Thu, 30 Apr 2020 04:05:09 -0400 |
| parents | |
| children | 20165d3a8fb1 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/artic_minion.xml Thu Apr 30 04:05:09 2020 -0400 @@ -0,0 +1,110 @@ +<tool id="artic_minion" name="ARTIC minion" version="1.1.0_rc2+galaxy0"> + <description></description> + <requirements> + <requirement type="package" version="1.1.0_rc2">artic</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + mkdir -p 'scheme/name/version' && + #if str( $primer_scheme_source.primer_scheme_source_selector ) == "tool_data_table": + ln -s '${primer_scheme_source.primer_scheme_bedfile.fields.path}' 'scheme/name/version/name.scheme.bed' && + #else: + ln -s '${primer_scheme_source.primer_scheme_bedfile}' 'scheme/name/version/name.scheme.bed' && + #end if + #if str( $reference_source.reference_source_selector ) == "history": + ln -s '${reference_source.reference}' 'scheme/name/version/name.reference.fasta' && + samtools faidx 'scheme/name/version/name.reference.fasta' && + #else: + ln -s '${reference_source.reference.fields.path}' 'scheme/name/version/name.reference.fasta' && + samtools faidx 'scheme/name/version/name.reference.fasta' && + #end if + artic minion + --threads \${GALAXY_SLOTS:-1} + --normalise '${normalise}' + --read-file '${read_file}' + --scheme-directory 'scheme' + --medaka + $bwa + 'name/version' + '${read_file.element_identifier}' + ]]></command> + <inputs> + <param argument="--read-file" type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" label="Input Read File"/> + <param argument="--normalise" type="integer" min="1" value="200" max="2000" label="Coverage normalisation depth"/> + <param argument="--bwa" type="boolean" truevalue="--bwa" falsevalue="" label="Use bwa aligner"/> + <conditional name="primer_scheme_source"> + <param name="primer_scheme_source_selector" type="select" label="Select a primer scheme from your history or use one from a tool data table?" + help="Screening files must be stored in the 'primer_scheme_bedfiles' tool data table"> + <option value="tool_data_table">From tool data table</option> + <option value="history">From history</option> + </param> + <when value="tool_data_table"> + <param name="primer_scheme_bedfile" type="select" format="bed" label="Primer Scheme"> + <options from_data_table="primer_scheme_bedfiles"> + <validator type="no_options" message="No primer scheme .bed files are available" /> + </options> + </param> + </when> + <when value="history"> + <param name="primer_scheme_bedfile" type="data" format="bed" label="Primer Scheme" /> + </when> + </conditional> + <conditional name="reference_source"> + <param name="reference_source_selector" type="select" label="Will you select a reference genome from your history or use a built-in reference?" > + <option value="cached">Use a built-in reference</option> + <option value="history">Use a reference from history</option> + </param> + <when value="cached"> + <param name="reference" type="select" label="Using reference genome" help="Select genome from the list"> + <options from_data_table="all_fasta"> + <filter type="sort_by" column="2" /> + <validator type="no_options" message="No references are available" /> + </options> + </param> + </when> + <when value="history"> + <param name="reference" type="data" format="fasta" label="Use the following dataset as the reference sequence" + help="You can upload a FASTA sequence to the history and use it as reference" /> + </when> + </conditional> + </inputs> + <outputs> + <data name="alignment_trimmed" format="bam" from_work_dir="*.trimmed.bam" label="${tool.name} on ${on_string}: trimmed alignment" /> + <data name="variants_tabular" format="tabular" from_work_dir="*.variants.tab" label="${tool.name} on ${on_string}: variants table" /> + <data name="variants_merged_vcf" format="vcf_bgzip" from_work_dir="*.merged.vcf.gz" label="${tool.name} on ${on_string}: variants vcf" /> + <data name="consensus_fasta" format="fasta" from_work_dir="*.consensus.fasta" label="${tool.name} on ${on_string}: consensus sequence" /> + </outputs> + <tests> + <test> + <param name="reference_source_selector" value="history" /> + <param name="read_file" value="SRR11410539_seqtk_sample_250_1.fastq" /> + <param name="reference" value="nCoV-2019.reference.fasta" /> + <param name="primer_scheme_source_selector" value="tool_data_table" /> + <param name="primer_scheme_bedfile" value="test_entry" /> + <output name="consensus_fasta" file="SRR11410539_seqtk_sample_250_1.fastq.consensus.fasta" /> + </test> + <test> + <param name="reference_source_selector" value="history" /> + <param name="read_file" value="SRR11410539_seqtk_sample_250_1.fastq" /> + <param name="reference" value="nCoV-2019.reference.fasta" /> + <param name="primer_scheme_source_selector" value="history" /> + <param name="primer_scheme_bedfile" value="nCoV-2019.V1.bed" /> + <output name="consensus_fasta" file="SRR11410539_seqtk_sample_250_1.fastq.consensus.fasta" /> + </test> + <test> + <param name="reference_source_selector" value="tool_data_table" /> + <param name="read_file" value="SRR11410539_seqtk_sample_250_1.fastq" /> + <param name="reference" value="test_entry" /> + <param name="primer_scheme_source_selector" value="tool_data_table" /> + <param name="primer_scheme_bedfile" value="test_entry" /> + <output name="consensus_fasta" file="SRR11410539_seqtk_sample_250_1.fastq.consensus.fasta" /> + </test> + </tests> + <help><![CDATA[ +This tool aligns MinION reads that were generated from a tiling amplicon library against a viral reference sequence. +It generates a consensus fasta file and a vcf variant file. + +This tool is configured to use the experimental 'medaka' variant caller. + ]]></help> + <citations> + </citations> +</tool>