Mercurial > repos > iuc > nextclade

annotate nextclade.xml @ 3:3b75d5285aff draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 7a13866c45dba2337fc37d66c45c77ac73915690"
author iuc
date Mon, 07 Jun 2021 12:39:36 +0000
parents 6cd62b6d2b5c
children b74b9a7b3e3b
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1 <tool id="nextclade" name="Nextclade" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01" license="MIT">
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2 <description></description>
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3 <macros>
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4 <import>macros.xml</import>
3
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5 <token name="@TOOL_VERSION@">0.14.4</token>
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6 <token name="@VERSION_SUFFIX@">0</token>
0
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7 </macros>
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8 <requirements>
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9 <requirement type="package" version="@TOOL_VERSION@">nextclade_js</requirement>
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10 </requirements>
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11 <command detect_errors="exit_code"><![CDATA[
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12 nextclade
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13 --input-fasta '${input_fasta}'
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14 #if $outputs and "report_tsv" in $outputs
2
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15 #if $include_header
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16 --output-tsv '$report_tsv'
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17 #else
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18 --output-tsv report.tsv
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19 #end if
0
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20 #end if
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21 #if $outputs and "report_json" in $outputs
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22 --output-json '${report_json}'
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23 #end if
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24 #if $outputs and "output_tree" in $outputs
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25 --output-tree '${output_tree}'
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26 #end if
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27 #if str($adv.advanced_options) == "yes"
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28 #if $adv.input_qc_config
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29 --input-qc-config '${adv.input_qc_config}'
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30 #end if
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31 #if $adv.input_root_seq
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32 --input-root-seq '${adv.input_root_seq}'
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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33 #end if
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34 #if $adv.input_tree
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35 --input-tree '${adv.input_tree}'
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36 #end if
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37 #if $adv.input_gene_map
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38 --input-gene-map '${adv.input_gene_map}'
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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39 #end if
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40 #if $adv.input_pcr_primers
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41 --input-pcr-primers '${adv.input_pcr_primers}'
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42 #end if
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43 #end if
2
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44 #if $outputs and "report_tsv" in $outputs and not $include_header
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45 && tail -n+2 report.tsv >'$report_tsv'
1
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46 #end if
0
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47 ]]></command>
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48 <inputs>
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49 <param argument="--input-fasta" name="input_fasta" type="data" format="fasta" label="SARS-CoV-2 consensus sequences (FASTA)" />
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50 <param name="outputs" type="select" label="Output options" help="Output reports and optionally tree" multiple="true">
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51 <option value="report_json">JSON format report</option>
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52 <option value="report_tsv" selected="true">Tabular format report</option>
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53 <option value="output_tree">Auspice v2 tree file (JSON format)</option>
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54 </param>
2
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55 <param name="include_header" type="boolean" label="Include header line in output file"
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56 truevalue="true" falsevalue="false" />
0
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57 <conditional name="adv">
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58 <param name="advanced_options" type="select" label="Use advanced options" >
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59 <option value="yes">Yes</option>
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60 <option value="no" selected="true">No</option>
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61 </param>
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62 <when value="yes">
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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" />
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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" />
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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" />
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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" />
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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" />
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68 </when>
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69 <when value="no">
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70 </when>
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71 </conditional>
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72 </inputs>
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73 <outputs>
1
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74 <data name="report_tsv" format="tabular" label="${tool.name} on ${on_string} (TSV report)">
0
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75 <filter>outputs and "report_tsv" in outputs</filter>
1
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76 <actions>
3
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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
1
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78 ingDataThreshold,qc.missingData.score,qc.missingData.status,qc.missingData.totalMissing,qc.mixedSites.mixedSitesThreshold,qc.mixedSites.score,qc.mixedSites.status,qc.mixedSit
0f20ed06ed6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit fd2b9ee5fee733c61c5db0618de96d19261dcb79"
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79 es.totalMixedSites,qc.privateMutations.cutoff,qc.privateMutations.excess,qc.privateMutations.score,qc.privateMutations.status,qc.privateMutations.total,qc.snpClusters.clus
0f20ed06ed6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit fd2b9ee5fee733c61c5db0618de96d19261dcb79"
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80 teredSNPs,qc.snpClusters.score,qc.snpClusters.status,qc.snpClusters.totalSNPs,errors" />
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81 </actions>
0
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
82 </data>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
83 <data name="report_json" format="json" label="${tool.name} on ${on_string} (JSON report)">
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
84 <filter>outputs and "report_json" in outputs</filter>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
85 </data>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
86 <data name="output_tree" format="json" label="${tool.name} on ${on_string} (Auspice v2 tree)">
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
87 <filter>outputs and "output_tree" in outputs</filter>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
88 </data>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
89 </outputs>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
90 <tests>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
91 <test expect_num_outputs="1">
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
92 <param name="input_fasta" value="sarscov2_1.fasta" ftype="fasta" />
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
93 <param name="outputs" value="report_tsv" />
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
94 <output name="report_tsv">
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
95 <assert_contents>
1
0f20ed06ed6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit fd2b9ee5fee733c61c5db0618de96d19261dcb79"
iuc
parents: 0
diff changeset
96 <has_n_columns n="41" />
0
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
97 <has_text text="20A" />
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
98 </assert_contents>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
99 </output>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
100 </test>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
101 <test expect_num_outputs="3">
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
102 <param name="input_fasta" value="sarscov2_1.fasta" ftype="fasta" />
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
103 <param name="outputs" value="report_tsv,report_json,output_tree" />
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
104 <output name="report_tsv">
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
105 <assert_contents>
1
0f20ed06ed6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit fd2b9ee5fee733c61c5db0618de96d19261dcb79"
iuc
parents: 0
diff changeset
106 <has_n_columns n="41" />
0
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
107 <has_text text="20A" />
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
108 </assert_contents>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
109 </output>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
110 <output name="report_json">
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
111 <assert_contents>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
112 <has_text text='"pos": 240,' />
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
113 </assert_contents>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
114 </output>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
115 <output name="output_tree">
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
116 <assert_contents>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
117 <has_text text='"build_url": "https://github.com/nextstrain/nextclade"' />
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
118 </assert_contents>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
119 </output>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
120 </test>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
121 <test expect_num_outputs="1">
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
122 <param name="input_fasta" value="sarscov2_1.fasta" ftype="fasta" />
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
123 <param name="outputs" value="report_tsv" />
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
124 <conditional name="adv">
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
125 <param name="advanced_options" value="yes" />
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
126 <param name="input_qc_config" value="strict_qc.json" ftype="json" />
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
127 </conditional>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
128 <output name="report_tsv">
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
129 <assert_contents>
1
0f20ed06ed6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit fd2b9ee5fee733c61c5db0618de96d19261dcb79"
iuc
parents: 0
diff changeset
130 <has_n_columns n="41" />
0
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
131 <has_text text="mediocre" />
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
132 </assert_contents>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
133 </output>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
134 </test>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
135 </tests>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
136 <help><![CDATA[
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
137
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
138 .. class:: infomark
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
139
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
140 **What it does**
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
141
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
142 Nextclade_ assigns clades, calls mutations and performs sequence quality checks on SARS-CoV-2 genomes.
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
143
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
144 **Input**
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
145
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
146 Input is a FASTA file containing one or more SARS-CoV-2 consensus genomes.
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
147
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
148 **Output**
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
149
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
150 Outputs can include:
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
151
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
152 * A tabular format file with a report, one line per input sequence
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
153
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
154 * A JSON format file with the same information as is present in the tabular report
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
155
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
156 * An Auspice v2 tree file in JSON format
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
157
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
158 .. _Nextclade: https://github.com/nextstrain/nextclade
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
159
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
160 ]]></help>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
161 <expand macro="citations" />
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
162 </tool>