Mercurial > repos > iuc > nextclade
changeset 18:feb40665d7cd draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit e72bef3964ce9d0c52ef2713d177684dfbee4cfb
author | iuc |
---|---|
date | Wed, 31 Aug 2022 16:40:29 +0000 (2022-08-31) |
parents | 07ab9bd68a02 |
children | 128ba8da994f |
files | nextclade.xml |
diffstat | 1 files changed, 9 insertions(+), 9 deletions(-) [+] |
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--- a/nextclade.xml Thu Aug 04 06:58:48 2022 +0000 +++ b/nextclade.xml Wed Aug 31 16:40:29 2022 +0000 @@ -68,7 +68,7 @@ #end if ]]></command> <inputs> - <param argument="--input-fasta" name="input_fasta" type="data" format="fasta,fasta.gz" label="FASTA file with input sequences" /> + <param argument="--input-fasta" type="data" format="fasta,fasta.gz" label="FASTA file with input sequences" /> <param name="organism" type="select" label="Organism"> <option value="sars-cov-2" selected="true">SARS-CoV-2</option> <option value="sars-cov-2-no-recomb">SARS-CoV-2 without recombinants</option> @@ -114,13 +114,13 @@ <option value="no" selected="true">No</option> </param> <when value="yes"> - <param argument="--input-qc-config" name="input_qc_config" type="data" label="Quality Control (QC) Config file" format="json" optional="true" help="QC config json file containing custom QC configuration" /> - <param argument="--input-root-seq" name="input_root_seq" type="data" label="Custom root sequence" format="txt" optional="true" help="Text file containing custom root sequence" /> - <param argument="--input-tree" name="input_tree" type="data" label="Custom reference tree" format="json" optional="true" help="Auspice JSON v2 file containing custom reference tree" /> - <param argument="--input-gene-map" name="input_gene_map" type="data" label="Custom gene map" format="json" optional="true" help="JSON file containing custom gene map. Gene map (sometimes also called 'gene annotations') is used to resolve aminoacid changes in genes" /> - <param argument="--input-pcr-primers" name="input_pcr_primers" type="data" label="Custom PCR primer sites" format="json" optional="true" help="CSV file containing a list of custom PCR primer sites. These are used to report mutations in these sites" /> - <param argument="--input-virus-properties" name="input_virus_properties" type="data" label="Configuration and data specific to a pathogen" format="json" optional="true" help="For more info on the virus properties JSON file, see the Nextclade documentation." /> - <param argument="--include-reference" name="include_reference" truevalue="--include-reference" falsevalue="" type="boolean" label="Include reference sequence in FASTA alignment output" help="The FASTA alignment is an optional output of nextclade. Select this option to include the reference sequence in that alignment file" /> + <param argument="--input-qc-config" type="data" label="Quality Control (QC) Config file" format="json" optional="true" help="QC config json file containing custom QC configuration" /> + <param argument="--input-root-seq" type="data" label="Custom root sequence" format="txt" optional="true" help="Text file containing custom root sequence" /> + <param argument="--input-tree" type="data" label="Custom reference tree" format="json" optional="true" help="Auspice JSON v2 file containing custom reference tree" /> + <param argument="--input-gene-map" type="data" label="Custom gene map" format="json" optional="true" help="JSON file containing custom gene map. Gene map (sometimes also called 'gene annotations') is used to resolve aminoacid changes in genes" /> + <param argument="--input-pcr-primers" type="data" label="Custom PCR primer sites" format="json" optional="true" help="CSV file containing a list of custom PCR primer sites. These are used to report mutations in these sites" /> + <param argument="--input-virus-properties" type="data" label="Configuration and data specific to a pathogen" format="json" optional="true" help="For more info on the virus properties JSON file, see the Nextclade documentation." /> + <param argument="--include-reference" truevalue="--include-reference" falsevalue="" type="boolean" label="Include reference sequence in FASTA alignment output" help="The FASTA alignment is an optional output of nextclade. Select this option to include the reference sequence in that alignment file" /> </when> <when value="no"> </when> @@ -228,7 +228,7 @@ <param name="organism" value="MPXV" /> <output name="report_tsv"> <assert_contents> - <has_n_columns n="66" /> + <has_n_columns n="67" /> <has_text text="hMPXV-1" /> </assert_contents> </output>