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comparison nextclade.xml @ 17:f09378dd39b0 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit e72bef3964ce9d0c52ef2713d177684dfbee4cfb
author iuc
date Wed, 31 Aug 2022 16:38:48 +0000
parents ae29ea21e448
children 6f40b91cd1ac
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16:ae29ea21e448 17:f09378dd39b0
66 #if $outputs and "report_tsv" in $outputs and not $include_header 66 #if $outputs and "report_tsv" in $outputs and not $include_header
67 && tail -n+2 report.tsv >'$report_tsv' 67 && tail -n+2 report.tsv >'$report_tsv'
68 #end if 68 #end if
69 ]]></command> 69 ]]></command>
70 <inputs> 70 <inputs>
71 <param argument="--input-fasta" name="input_fasta" type="data" format="fasta,fasta.gz" label="FASTA file with input sequences" /> 71 <param argument="--input-fasta" type="data" format="fasta,fasta.gz" label="FASTA file with input sequences" />
72 <param name="organism" type="select" label="Organism"> 72 <param name="organism" type="select" label="Organism">
73 <option value="sars-cov-2" selected="true">SARS-CoV-2</option> 73 <option value="sars-cov-2" selected="true">SARS-CoV-2</option>
74 <option value="sars-cov-2-no-recomb">SARS-CoV-2 without recombinants</option> 74 <option value="sars-cov-2-no-recomb">SARS-CoV-2 without recombinants</option>
75 <option value="flu_h1n1pdm_ha">Influenza A H1N1pdm HA</option> 75 <option value="flu_h1n1pdm_ha">Influenza A H1N1pdm HA</option>
76 <option value="flu_h3n2_ha">Influenza A H3N2 HA</option> 76 <option value="flu_h3n2_ha">Influenza A H3N2 HA</option>
112 <param name="advanced_options" type="select" label="Use advanced options" > 112 <param name="advanced_options" type="select" label="Use advanced options" >
113 <option value="yes">Yes</option> 113 <option value="yes">Yes</option>
114 <option value="no" selected="true">No</option> 114 <option value="no" selected="true">No</option>
115 </param> 115 </param>
116 <when value="yes"> 116 <when value="yes">
117 <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" /> 117 <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" />
118 <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" /> 118 <param argument="--input-root-seq" type="data" label="Custom root sequence" format="txt" optional="true" help="Text file containing custom root sequence" />
119 <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" /> 119 <param argument="--input-tree" type="data" label="Custom reference tree" format="json" optional="true" help="Auspice JSON v2 file containing custom reference tree" />
120 <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" /> 120 <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" />
121 <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" /> 121 <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" />
122 <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." /> 122 <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." />
123 <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" /> 123 <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" />
124 </when> 124 </when>
125 <when value="no"> 125 <when value="no">
126 </when> 126 </when>
127 </conditional> 127 </conditional>
128 </inputs> 128 </inputs>
226 </conditional> 226 </conditional>
227 <param name="outputs" value="report_tsv" /> 227 <param name="outputs" value="report_tsv" />
228 <param name="organism" value="MPXV" /> 228 <param name="organism" value="MPXV" />
229 <output name="report_tsv"> 229 <output name="report_tsv">
230 <assert_contents> 230 <assert_contents>
231 <has_n_columns n="66" /> 231 <has_n_columns n="67" />
232 <has_text text="hMPXV-1" /> 232 <has_text text="hMPXV-1" />
233 </assert_contents> 233 </assert_contents>
234 </output> 234 </output>
235 </test> 235 </test>
236 </tests> 236 </tests>