Mercurial > repos > iuc > nextclade
comparison nextclade.xml @ 4:b74b9a7b3e3b draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit e6c24a9360cd88f87804b6e7648295d6f300eac9"
author | iuc |
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date | Mon, 23 Aug 2021 12:26:05 +0000 |
parents | 3b75d5285aff |
children | 0c46b95d60c3 |
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3:3b75d5285aff | 4:b74b9a7b3e3b |
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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@">0.14.4</token> | 5 <token name="@TOOL_VERSION@">1.2.3</token> |
6 <token name="@VERSION_SUFFIX@">0</token> | 6 <token name="@VERSION_SUFFIX@">0</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</requirement> |
10 <requirement type="package">coreutils</requirement> | |
10 </requirements> | 11 </requirements> |
11 <command detect_errors="exit_code"><![CDATA[ | 12 <command detect_errors="exit_code"><![CDATA[ |
13 export DB_PATH="\$(dirname "\$(dirname "\$(which nextclade)")")/share/nextclade" && | |
14 ln -s "\$DB_PATH" db && | |
15 #set $input_qc_config = "db/qc.json" | |
16 #set $input_root_seq = "db/reference.fasta" | |
17 #set $input_tree = "db/tree.json" | |
18 #set $input_gene_map = "db/genemap.gff" | |
19 #set $input_pcr_primers = "db/primers.csv" | |
20 #if str($adv.advanced_options) == "yes" | |
21 #if $adv.input_qc_config | |
22 #set $input_qc_config = $adv.input_qc_config | |
23 #end if | |
24 #if $adv.input_root_seq | |
25 #set $input_root_seq = $adv.input_root_seq | |
26 #end if | |
27 #if $adv.input_tree | |
28 #set $input_tree = $adv.input_tree | |
29 #end if | |
30 #if $adv.input_gene_map | |
31 #set $input_gene_map = $adv.input_gene_map | |
32 #end if | |
33 #if $adv.input_pcr_primers | |
34 #set $input_pcr_primers = $adv.input_pcr_primers | |
35 #end if | |
36 #end if | |
12 nextclade | 37 nextclade |
13 --input-fasta '${input_fasta}' | 38 --input-fasta '${input_fasta}' |
39 --input-qc-config '${input_qc_config}' | |
40 --input-root-seq '${input_root_seq}' | |
41 --input-tree '${input_tree}' | |
42 --input-gene-map '${input_gene_map}' | |
43 --input-pcr-primers '${input_pcr_primers}' | |
14 #if $outputs and "report_tsv" in $outputs | 44 #if $outputs and "report_tsv" in $outputs |
15 #if $include_header | 45 #if $include_header |
16 --output-tsv '$report_tsv' | 46 --output-tsv '$report_tsv' |
17 #else | 47 #else |
18 --output-tsv report.tsv | 48 --output-tsv report.tsv |
22 --output-json '${report_json}' | 52 --output-json '${report_json}' |
23 #end if | 53 #end if |
24 #if $outputs and "output_tree" in $outputs | 54 #if $outputs and "output_tree" in $outputs |
25 --output-tree '${output_tree}' | 55 --output-tree '${output_tree}' |
26 #end if | 56 #end if |
27 #if str($adv.advanced_options) == "yes" | 57 #if $outputs and "output_fasta" in $outputs |
28 #if $adv.input_qc_config | 58 --output-fasta "${output_fasta}" |
29 --input-qc-config '${adv.input_qc_config}' | 59 #if str($adv.advanced_options) == "yes" |
30 #end if | 60 $adv.include_reference |
31 #if $adv.input_root_seq | |
32 --input-root-seq '${adv.input_root_seq}' | |
33 #end if | |
34 #if $adv.input_tree | |
35 --input-tree '${adv.input_tree}' | |
36 #end if | |
37 #if $adv.input_gene_map | |
38 --input-gene-map '${adv.input_gene_map}' | |
39 #end if | |
40 #if $adv.input_pcr_primers | |
41 --input-pcr-primers '${adv.input_pcr_primers}' | |
42 #end if | 61 #end if |
43 #end if | 62 #end if |
44 #if $outputs and "report_tsv" in $outputs and not $include_header | 63 #if $outputs and "report_tsv" in $outputs and not $include_header |
45 && tail -n+2 report.tsv >'$report_tsv' | 64 && tail -n+2 report.tsv >'$report_tsv' |
46 #end if | 65 #end if |
49 <param argument="--input-fasta" name="input_fasta" type="data" format="fasta" label="SARS-CoV-2 consensus sequences (FASTA)" /> | 68 <param argument="--input-fasta" name="input_fasta" type="data" format="fasta" label="SARS-CoV-2 consensus sequences (FASTA)" /> |
50 <param name="outputs" type="select" label="Output options" help="Output reports and optionally tree" multiple="true"> | 69 <param name="outputs" type="select" label="Output options" help="Output reports and optionally tree" multiple="true"> |
51 <option value="report_json">JSON format report</option> | 70 <option value="report_json">JSON format report</option> |
52 <option value="report_tsv" selected="true">Tabular format report</option> | 71 <option value="report_tsv" selected="true">Tabular format report</option> |
53 <option value="output_tree">Auspice v2 tree file (JSON format)</option> | 72 <option value="output_tree">Auspice v2 tree file (JSON format)</option> |
73 <option value="output_fasta">Aligned sequences (FASTA format)</option> | |
54 </param> | 74 </param> |
55 <param name="include_header" type="boolean" label="Include header line in output file" | 75 <param name="include_header" type="boolean" label="Include header line in output file" |
56 truevalue="true" falsevalue="false" /> | 76 truevalue="true" falsevalue="false" /> |
57 <conditional name="adv"> | 77 <conditional name="adv"> |
58 <param name="advanced_options" type="select" label="Use advanced options" > | 78 <param name="advanced_options" type="select" label="Use advanced options" > |
63 <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" /> | 83 <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" /> |
64 <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" /> | 84 <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" /> |
65 <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" /> | 85 <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" /> |
66 <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" /> | 86 <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" /> |
67 <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" /> | 87 <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" /> |
88 <param argument="--include-reference" name="include_reference" 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" /> | |
68 </when> | 89 </when> |
69 <when value="no"> | 90 <when value="no"> |
70 </when> | 91 </when> |
71 </conditional> | 92 </conditional> |
72 </inputs> | 93 </inputs> |
73 <outputs> | 94 <outputs> |
74 <data name="report_tsv" format="tabular" label="${tool.name} on ${on_string} (TSV report)"> | 95 <data name="report_tsv" format="tabular" label="${tool.name} on ${on_string} (TSV report)"> |
75 <filter>outputs and "report_tsv" in outputs</filter> | 96 <filter>outputs and "report_tsv" in outputs</filter> |
76 <actions> | 97 <actions> |
77 <action name="column_names" type="metadata" default="seqName,clade,qc.overallScore,qc.overallStatus,totalGaps,totalInsertions,totalMissing,totalMutations,totalNonACGTNs,totalPcrPrimerChanges,substitutions,deletions,insertions,missing,nonACGTNs,pcrPrimerChanges,aaSubstitutions,totalAminoacidSubstitutions,aaDeletions,totalAminoacidDeletions,alignmentEnd,alignmentScore,alignmentStart,qc.missingData.miss | 98 <action name="column_names" type="metadata" default="seqName,clade,qc.overallScore,qc.overallStatus,totalSubstitutions,totalDeletions,totalInsertions,totalAminoacidSubstitutions,totalAminoacidDeletions,totalMissing,totalNonACGTNs,totalPcrPrimerChanges,substitutions,deletions,insertions,aaSubstitutions,aaDeletions,missing,nonACGTNs,pcrPrimerChanges,alignmentScore,alignmentStart,alignmentEnd,qc.missingData.missingDataThreshold,qc.missingData.score,qc.missingData.status,qc.missingData.totalMissing,qc.mixedSites.mixedSitesThreshold,qc.mixedSites.score,qc.mixedSites.status,qc.mixedSites.totalMixedSites,qc.privateMutations.cutoff,qc.privateMutations.excess,qc.privateMutations.score,qc.privateMutations.status,qc.privateMutations.total,qc.snpClusters.clusteredSNPs,qc.snpClusters.score,qc.snpClusters.status,qc.snpClusters.totalSNPs,qc.frameShifts.frameShifts,qc.frameShifts.totalFrameShifts,qc.frameShifts.score,qc.frameShifts.status,qc.stopCodons.stopCodons,qc.stopCodons.totalStopCodons,qc.stopCodons.score,qc.stopCodons.status,errors" /> |
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> | 99 </actions> |
82 </data> | 100 </data> |
83 <data name="report_json" format="json" label="${tool.name} on ${on_string} (JSON report)"> | 101 <data name="report_json" format="json" label="${tool.name} on ${on_string} (JSON report)"> |
84 <filter>outputs and "report_json" in outputs</filter> | 102 <filter>outputs and "report_json" in outputs</filter> |
85 </data> | 103 </data> |
86 <data name="output_tree" format="json" label="${tool.name} on ${on_string} (Auspice v2 tree)"> | 104 <data name="output_tree" format="json" label="${tool.name} on ${on_string} (Auspice v2 tree)"> |
87 <filter>outputs and "output_tree" in outputs</filter> | 105 <filter>outputs and "output_tree" in outputs</filter> |
88 </data> | 106 </data> |
107 <data name="output_fasta" format="fasta" label="${tool.name} on ${on_string} (FASTA alignment)"> | |
108 <filter>outputs and "output_fasta" in outputs</filter> | |
109 </data> | |
89 </outputs> | 110 </outputs> |
90 <tests> | 111 <tests> |
91 <test expect_num_outputs="1"> | 112 <test expect_num_outputs="1"> |
92 <param name="input_fasta" value="sarscov2_1.fasta" ftype="fasta" /> | 113 <param name="input_fasta" value="sarscov2_1.fasta" ftype="fasta" /> |
93 <param name="outputs" value="report_tsv" /> | 114 <param name="outputs" value="report_tsv" /> |
94 <output name="report_tsv"> | 115 <output name="report_tsv"> |
95 <assert_contents> | 116 <assert_contents> |
96 <has_n_columns n="41" /> | 117 <has_n_columns n="48" /> |
97 <has_text text="20A" /> | 118 <has_text text="20A" /> |
98 </assert_contents> | 119 </assert_contents> |
99 </output> | 120 </output> |
100 </test> | 121 </test> |
101 <test expect_num_outputs="3"> | 122 <test expect_num_outputs="3"> |
102 <param name="input_fasta" value="sarscov2_1.fasta" ftype="fasta" /> | 123 <param name="input_fasta" value="sarscov2_1.fasta" ftype="fasta" /> |
103 <param name="outputs" value="report_tsv,report_json,output_tree" /> | 124 <param name="outputs" value="report_tsv,report_json,output_tree" /> |
104 <output name="report_tsv"> | 125 <output name="report_tsv"> |
105 <assert_contents> | 126 <assert_contents> |
106 <has_n_columns n="41" /> | 127 <has_n_columns n="48" /> |
107 <has_text text="20A" /> | 128 <has_text text="20A" /> |
108 </assert_contents> | 129 </assert_contents> |
109 </output> | 130 </output> |
110 <output name="report_json"> | 131 <output name="report_json"> |
111 <assert_contents> | 132 <assert_contents> |
125 <param name="advanced_options" value="yes" /> | 146 <param name="advanced_options" value="yes" /> |
126 <param name="input_qc_config" value="strict_qc.json" ftype="json" /> | 147 <param name="input_qc_config" value="strict_qc.json" ftype="json" /> |
127 </conditional> | 148 </conditional> |
128 <output name="report_tsv"> | 149 <output name="report_tsv"> |
129 <assert_contents> | 150 <assert_contents> |
130 <has_n_columns n="41" /> | 151 <has_n_columns n="48" /> |
131 <has_text text="mediocre" /> | 152 <has_text text="mediocre" /> |
132 </assert_contents> | 153 </assert_contents> |
133 </output> | 154 </output> |
134 </test> | 155 </test> |
135 </tests> | 156 </tests> |