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comparison nextclade.xml @ 1:495c19a62538 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 8a6f8a1c1cb3fea223e6bf628b930a1182088b0b"
author iuc
date Thu, 20 May 2021 21:10:18 +0000
parents 919cc9dc23f0
children efbf471df058
comparison
equal deleted inserted replaced
0:919cc9dc23f0 1:495c19a62538
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@">0</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
44 #if $outputs and "report_tsv" in $outputs and not $include_header
45 && tail -n+2 report.tsv >'$report_tsv'
46 #end if
40 ]]></command> 47 ]]></command>
41 <inputs> 48 <inputs>
42 <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)" />
43 <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">
44 <option value="report_json">JSON format report</option> 51 <option value="report_json">JSON format report</option>
45 <option value="report_tsv" selected="true">Tabular format report</option> 52 <option value="report_tsv" selected="true">Tabular format report</option>
46 <option value="output_tree">Auspice v2 tree file (JSON format)</option> 53 <option value="output_tree">Auspice v2 tree file (JSON format)</option>
47 </param> 54 </param>
55 <param name="include_header" type="boolean" label="Include header line in output file"
56 truevalue="true" falsevalue="false" />
48 <conditional name="adv"> 57 <conditional name="adv">
49 <param name="advanced_options" type="select" label="Use advanced options" > 58 <param name="advanced_options" type="select" label="Use advanced options" >
50 <option value="yes">Yes</option> 59 <option value="yes">Yes</option>
51 <option value="no" selected="true">No</option> 60 <option value="no" selected="true">No</option>
52 </param> 61 </param>
60 <when value="no"> 69 <when value="no">
61 </when> 70 </when>
62 </conditional> 71 </conditional>
63 </inputs> 72 </inputs>
64 <outputs> 73 <outputs>
65 <data name="report_tsv" format="tabular" label="${tool.name} on ${on_string} (TSV report)"> 74 <data name="report_tsv" format="tabular" label="${tool.name} on ${on_string} (TSV report)">
66 <filter>outputs and "report_tsv" in outputs</filter> 75 <filter>outputs and "report_tsv" in outputs</filter>
76 <actions>
77 <action name="column_names" type="metadata" default="seqName,clade,qc.overallScore,qc.overallStatus,totalGaps,totalInsertions,totalMissing,totalMutations,totalNonACGTNs,totalPcrPrimerChanges,substitutions,deletions,insertionsmissing,nonACGTNs,pcrPrimerChanges,aaSubstitutions,totalAminoacidSubstitutions,aaDeletions,totalAminoacidDeletions,alignmentEnd,alignmentScore,alignmentStart,qc.missingData.miss
78 ingDataThreshold,qc.missingData.score,qc.missingData.status,qc.missingData.totalMissing,qc.mixedSites.mixedSitesThreshold,qc.mixedSites.score,qc.mixedSites.status,qc.mixedSit
79 es.totalMixedSites,qc.privateMutations.cutoff,qc.privateMutations.excess,qc.privateMutations.score,qc.privateMutations.status,qc.privateMutations.total,qc.snpClusters.clus
80 teredSNPs,qc.snpClusters.score,qc.snpClusters.status,qc.snpClusters.totalSNPs,errors" />
81 </actions>
67 </data> 82 </data>
68 <data name="report_json" format="json" label="${tool.name} on ${on_string} (JSON report)"> 83 <data name="report_json" format="json" label="${tool.name} on ${on_string} (JSON report)">
69 <filter>outputs and "report_json" in outputs</filter> 84 <filter>outputs and "report_json" in outputs</filter>
70 </data> 85 </data>
71 <data name="output_tree" format="json" label="${tool.name} on ${on_string} (Auspice v2 tree)"> 86 <data name="output_tree" format="json" label="${tool.name} on ${on_string} (Auspice v2 tree)">
76 <test expect_num_outputs="1"> 91 <test expect_num_outputs="1">
77 <param name="input_fasta" value="sarscov2_1.fasta" ftype="fasta" /> 92 <param name="input_fasta" value="sarscov2_1.fasta" ftype="fasta" />
78 <param name="outputs" value="report_tsv" /> 93 <param name="outputs" value="report_tsv" />
79 <output name="report_tsv"> 94 <output name="report_tsv">
80 <assert_contents> 95 <assert_contents>
96 <has_n_columns n="41" />
81 <has_text text="20A" /> 97 <has_text text="20A" />
82 </assert_contents> 98 </assert_contents>
83 </output> 99 </output>
84 </test> 100 </test>
85 <test expect_num_outputs="3"> 101 <test expect_num_outputs="3">
86 <param name="input_fasta" value="sarscov2_1.fasta" ftype="fasta" /> 102 <param name="input_fasta" value="sarscov2_1.fasta" ftype="fasta" />
87 <param name="outputs" value="report_tsv,report_json,output_tree" /> 103 <param name="outputs" value="report_tsv,report_json,output_tree" />
88 <output name="report_tsv"> 104 <output name="report_tsv">
89 <assert_contents> 105 <assert_contents>
106 <has_n_columns n="41" />
90 <has_text text="20A" /> 107 <has_text text="20A" />
91 </assert_contents> 108 </assert_contents>
92 </output> 109 </output>
93 <output name="report_json"> 110 <output name="report_json">
94 <assert_contents> 111 <assert_contents>
108 <param name="advanced_options" value="yes" /> 125 <param name="advanced_options" value="yes" />
109 <param name="input_qc_config" value="strict_qc.json" ftype="json" /> 126 <param name="input_qc_config" value="strict_qc.json" ftype="json" />
110 </conditional> 127 </conditional>
111 <output name="report_tsv"> 128 <output name="report_tsv">
112 <assert_contents> 129 <assert_contents>
130 <has_n_columns n="41" />
113 <has_text text="mediocre" /> 131 <has_text text="mediocre" />
114 </assert_contents> 132 </assert_contents>
115 </output> 133 </output>
116 </test> 134 </test>
117 </tests> 135 </tests>