Mercurial > repos > iuc > nextclade
comparison nextclade.xml @ 2:6cd62b6d2b5c draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 8a6f8a1c1cb3fea223e6bf628b930a1182088b0b"
author | iuc |
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date | Thu, 20 May 2021 21:12:00 +0000 |
parents | 0f20ed06ed6c |
children | 3b75d5285aff |
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1:0f20ed06ed6c | 2:6cd62b6d2b5c |
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1 <tool id="nextclade" name="Nextclade" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01" license="MIT"> | 1 <tool id="nextclade" name="Nextclade" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01" license="MIT"> |
2 <description></description> | 2 <description></description> |
3 <macros> | 3 <macros> |
4 <import>macros.xml</import> | 4 <import>macros.xml</import> |
5 <token name="@TOOL_VERSION@">0.14.2</token> | 5 <token name="@TOOL_VERSION@">0.14.3</token> |
6 <token name="@VERSION_SUFFIX@">1</token> | 6 <token name="@VERSION_SUFFIX@">1</token> |
7 </macros> | 7 </macros> |
8 <requirements> | 8 <requirements> |
9 <requirement type="package" version="@TOOL_VERSION@">nextclade_js</requirement> | 9 <requirement type="package" version="@TOOL_VERSION@">nextclade_js</requirement> |
10 </requirements> | 10 </requirements> |
11 <command detect_errors="exit_code"><![CDATA[ | 11 <command detect_errors="exit_code"><![CDATA[ |
12 nextclade | 12 nextclade |
13 --input-fasta '${input_fasta}' | 13 --input-fasta '${input_fasta}' |
14 #if $outputs and "report_tsv" in $outputs | 14 #if $outputs and "report_tsv" in $outputs |
15 --output-tsv report.tsv | 15 #if $include_header |
16 --output-tsv '$report_tsv' | |
17 #else | |
18 --output-tsv report.tsv | |
19 #end if | |
16 #end if | 20 #end if |
17 #if $outputs and "report_json" in $outputs | 21 #if $outputs and "report_json" in $outputs |
18 --output-json '${report_json}' | 22 --output-json '${report_json}' |
19 #end if | 23 #end if |
20 #if $outputs and "output_tree" in $outputs | 24 #if $outputs and "output_tree" in $outputs |
35 #end if | 39 #end if |
36 #if $adv.input_pcr_primers | 40 #if $adv.input_pcr_primers |
37 --input-pcr-primers '${adv.input_pcr_primers}' | 41 --input-pcr-primers '${adv.input_pcr_primers}' |
38 #end if | 42 #end if |
39 #end if | 43 #end if |
40 #if $outputs and "report_tsv" in $outputs | 44 #if $outputs and "report_tsv" in $outputs and not $include_header |
41 && tail -n-1 report.tsv >'$report_tsv' | 45 && tail -n+2 report.tsv >'$report_tsv' |
42 #end if | 46 #end if |
43 ]]></command> | 47 ]]></command> |
44 <inputs> | 48 <inputs> |
45 <param argument="--input-fasta" name="input_fasta" type="data" format="fasta" label="SARS-CoV-2 consensus sequences (FASTA)" /> | 49 <param argument="--input-fasta" name="input_fasta" type="data" format="fasta" label="SARS-CoV-2 consensus sequences (FASTA)" /> |
46 <param name="outputs" type="select" label="Output options" help="Output reports and optionally tree" multiple="true"> | 50 <param name="outputs" type="select" label="Output options" help="Output reports and optionally tree" multiple="true"> |
47 <option value="report_json">JSON format report</option> | 51 <option value="report_json">JSON format report</option> |
48 <option value="report_tsv" selected="true">Tabular format report</option> | 52 <option value="report_tsv" selected="true">Tabular format report</option> |
49 <option value="output_tree">Auspice v2 tree file (JSON format)</option> | 53 <option value="output_tree">Auspice v2 tree file (JSON format)</option> |
50 </param> | 54 </param> |
55 <param name="include_header" type="boolean" label="Include header line in output file" | |
56 truevalue="true" falsevalue="false" /> | |
51 <conditional name="adv"> | 57 <conditional name="adv"> |
52 <param name="advanced_options" type="select" label="Use advanced options" > | 58 <param name="advanced_options" type="select" label="Use advanced options" > |
53 <option value="yes">Yes</option> | 59 <option value="yes">Yes</option> |
54 <option value="no" selected="true">No</option> | 60 <option value="no" selected="true">No</option> |
55 </param> | 61 </param> |