annotate pangolin.xml @ 17:5f8727ff21e7 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit f5ffd712c1a38f3876eb69b6fa0384683c8fc171"
author iuc
date Mon, 31 Jan 2022 21:04:40 +0000
parents ca0d8cf80567
children 2fa9d4f1b48f
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1 <tool id="pangolin" name="Pangolin" version="@TOOL_VERSION@+galaxy0" profile="20.01">
0
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2 <description>Phylogenetic Assignment of Outbreak Lineages</description>
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3 <macros>
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4 <token name="@TOOL_VERSION@">3.1.19</token>
0
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5 </macros>
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6 <requirements>
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7 <requirement type="package" version="@TOOL_VERSION@">pangolin</requirement>
16
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8 <requirement type="package" version="0.3.16">scorpio</requirement>
7
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9 <requirement type="package" version="0.23.0">csvtk</requirement>
0
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10 </requirements>
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11 <command detect_errors="exit_code"><![CDATA[
1
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12 #if str($db.source) == "download"
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13 pangolin --update-data --datadir datadir &&
1
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14 #else if str($db.source) == "builtin"
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15 ln -s $db.db_release.fields.path datadir &&
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16 #end if
0
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17 pangolin
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18 --threads \${GALAXY_SLOTS:-1}
1
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19 #if str($db.source) == "download" or str($db.source) == "builtin"
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20 --datadir 'datadir'
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21 #end if
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22 $usher
0
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23 $alignment
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24 --outfile report.csv
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25 --max-ambig $max_ambig
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26 --min-length $min_length
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27 '$input1'
3
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28 && csvtk csv2tab report.csv
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29 #if not $include_header:
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30 | tail -n+2
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31 #end if
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32 > '$output1'
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33 #if $alignment
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34 && mv sequences.aln.fasta '$align1'
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35 #end if
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36 ]]></command>
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37 <inputs>
3
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38 <param type="data" name="input1" format="fasta" label="Input FASTA File(s)" />
4
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39 <param argument="--usher" type="boolean" label="Use UShER model" truevalue="--usher" falsevalue="" help="Use UShER model instead of default pangoLEARN model" />
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40 <param argument="--alignment" type="boolean" label="Generate output alignment"
0
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41 truevalue="--alignment" falsevalue="" />
3
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42 <param argument="--max-ambig" type="float" label="Maximum proportion of Ns allowed"
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43 value="0.5" min="0" max="1" help="Maximum proportion of Ns allowed for pangolin to attempt assignment" />
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44 <param argument="--min-length" type="integer" label="Minimum query length allowed"
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45 value="10000" min="0" help="Minimum query length allowed for pangolin to attempt assignment"/>
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46 <param name="include_header" type="boolean" label="Include header line in output file"
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47 truevalue="true" falsevalue="false" />
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48 <conditional name="db">
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49 <param type="select" name="source" label="pangoLEARN source" help="Where to find the pangoLEARN database. While 'Download latest from web' is recommended, if errors occur see the warning in the main help text below.">
1
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50 <option value="download">Download latest from web</option>
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51 <option value="builtin">Use database from Galaxy server</option>
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52 <option value="default">Use default database built in to pangolin (not recommended)</option>
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53 </param>
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54 <when value="download">
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55 <!-- these are currently not supported by the pangolin downloader -->
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56 <!-- <param name="max_retries" label="Max download retries" help="How many times to retry downloading the pangoLEARN database" type="integer" value="5" /> -->
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57 <!-- <param name="timeout" label="Download timeout" help="How many seconds to wait when downloading the pangoLEARN database" type="float" value="60.0" /> -->
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58 </when>
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59 <when value="builtin">
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60 <param name="db_release" label="pangoLEARN release" type="select">
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61 <options from_data_table="pangolearn">
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62 <column name="value" index="0" />
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63 <column name="name" index="1" />
3
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64 <column name="path" index="3" />
4
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65 <filter type="sort_by" column="0" />
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66 <filter type="static_value" column="2" value="3.0" />
1
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67 </options>
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68 </param>
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69 </when>
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70 <when value="default">
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71 </when>
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72 </conditional>
0
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73 </inputs>
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74 <outputs>
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75 <data name="output1" format="tabular" label="pangolin on ${on_string}">
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76 <actions>
4
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77 <action name="column_names" type="metadata" default="taxon,lineage,conflict,ambiguity_score,scorpio_call,scorpio_support,scorpio_conflict,version,pangolin_version,pangoLEARN_version,pango_version,status,note" />
0
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78 </actions>
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79 </data>
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80 <data name="align1" format="fasta" label="pangolin alignment on ${on_string}">
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81 <filter>alignment</filter>
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82 </data>
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83 </outputs>
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84 <tests>
3
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
85 <test expect_num_outputs="1">
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
86 <param name="input1" value="test1.fasta"/>
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
87 <conditional name="db">
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
88 <param name="source" value="download" />
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
89 </conditional>
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
90 <output name="output1" ftype="tabular">
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
91 <assert_contents>
14
83a69484cb87 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 402a11a20ec3f724dfe0b1a4bc60d806e77c1b3d"
iuc
parents: 13
diff changeset
92 <has_text_matching expression="B\.1\.1\t\d\.\d" />
4
42126b414951 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit ab174c9f8cbfc741501068dfa4f6ccf229a54489"
iuc
parents: 3
diff changeset
93 <has_text text="passed_qc" />
42126b414951 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit ab174c9f8cbfc741501068dfa4f6ccf229a54489"
iuc
parents: 3
diff changeset
94 <has_n_lines n="1" />
42126b414951 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit ab174c9f8cbfc741501068dfa4f6ccf229a54489"
iuc
parents: 3
diff changeset
95 </assert_contents>
42126b414951 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit ab174c9f8cbfc741501068dfa4f6ccf229a54489"
iuc
parents: 3
diff changeset
96 </output>
42126b414951 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit ab174c9f8cbfc741501068dfa4f6ccf229a54489"
iuc
parents: 3
diff changeset
97 </test>
42126b414951 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit ab174c9f8cbfc741501068dfa4f6ccf229a54489"
iuc
parents: 3
diff changeset
98 <!-- test UShER mode -->
42126b414951 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit ab174c9f8cbfc741501068dfa4f6ccf229a54489"
iuc
parents: 3
diff changeset
99 <test expect_num_outputs="1">
42126b414951 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit ab174c9f8cbfc741501068dfa4f6ccf229a54489"
iuc
parents: 3
diff changeset
100 <param name="input1" value="test1.fasta"/>
42126b414951 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit ab174c9f8cbfc741501068dfa4f6ccf229a54489"
iuc
parents: 3
diff changeset
101 <param name="usher" value="true" />
42126b414951 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit ab174c9f8cbfc741501068dfa4f6ccf229a54489"
iuc
parents: 3
diff changeset
102 <conditional name="db">
42126b414951 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit ab174c9f8cbfc741501068dfa4f6ccf229a54489"
iuc
parents: 3
diff changeset
103 <param name="source" value="download" />
42126b414951 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit ab174c9f8cbfc741501068dfa4f6ccf229a54489"
iuc
parents: 3
diff changeset
104 </conditional>
42126b414951 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit ab174c9f8cbfc741501068dfa4f6ccf229a54489"
iuc
parents: 3
diff changeset
105 <output name="output1" ftype="tabular">
42126b414951 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit ab174c9f8cbfc741501068dfa4f6ccf229a54489"
iuc
parents: 3
diff changeset
106 <assert_contents>
14
83a69484cb87 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 402a11a20ec3f724dfe0b1a4bc60d806e77c1b3d"
iuc
parents: 13
diff changeset
107 <has_text_matching expression="B\.1\.1.*\t\d\.\d\t*PUSHER" />
3
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
108 <has_text text="passed_qc" />
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
109 <has_n_lines n="1" />
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
110 </assert_contents>
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
111 </output>
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
112 </test>
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
113 <test expect_num_outputs="2">
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
114 <param name="alignment" value="--alignment" />
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
115 <param name="input1" value="test1.fasta" />
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
116 <conditional name="db">
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
117 <param name="source" value="download" />
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
118 </conditional>
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
119 <output name="output1" ftype="tabular">
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
120 <assert_contents>
14
83a69484cb87 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 402a11a20ec3f724dfe0b1a4bc60d806e77c1b3d"
iuc
parents: 13
diff changeset
121 <has_text_matching expression="B\.1\.1\t\d\.\d" />
3
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
122 <has_text text="passed_qc" />
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
123 <has_n_lines n="1" />
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
124 </assert_contents>
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
125 </output>
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
126 <output name="align1" file="aln1.fasta" ftype="fasta">
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
127 <assert_contents>
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
128 <has_text text="Consensus_EB232-crude-prep_S297" />
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
129 <has_n_lines n="2" />
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
130 </assert_contents>
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
131 </output>
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
132 </test>
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
133 <!-- test include-header option -->
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
134 <test expect_num_outputs="1">
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
135 <param name="input1" value="multiple_alignment.fasta.gz"/>
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
136 <param name="include_header" value="true" />
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
137 <conditional name="db">
4
42126b414951 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit ab174c9f8cbfc741501068dfa4f6ccf229a54489"
iuc
parents: 3
diff changeset
138 <param name="source" value="download" />
3
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
139 </conditional>
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
140 <output name="output1" ftype="tabular">
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
141 <assert_contents>
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
142 <has_text text="pangoLEARN_version" />
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
143 <has_text text="lineage" />
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
144 <has_text text="Serbia" />
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
145 <has_text text="Poland" />
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
146 <has_text text="USA" />
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
147 <has_n_lines n="35" />
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
148 </assert_contents>
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
149 </output>
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
150 </test>
0
0ec813ad2910 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit aca98a23e13f05dd076a203e73f43ca90e349e21"
iuc
parents:
diff changeset
151 </tests>
0ec813ad2910 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit aca98a23e13f05dd076a203e73f43ca90e349e21"
iuc
parents:
diff changeset
152 <help><![CDATA[
0ec813ad2910 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit aca98a23e13f05dd076a203e73f43ca90e349e21"
iuc
parents:
diff changeset
153
0ec813ad2910 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit aca98a23e13f05dd076a203e73f43ca90e349e21"
iuc
parents:
diff changeset
154 .. class:: infomark
0ec813ad2910 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit aca98a23e13f05dd076a203e73f43ca90e349e21"
iuc
parents:
diff changeset
155
0ec813ad2910 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit aca98a23e13f05dd076a203e73f43ca90e349e21"
iuc
parents:
diff changeset
156 `Pangolin <https://cov-lineages.org/pangolin.html>`_ (Phylogenetic Assignment of Named Global Outbreak LINeages)
0ec813ad2910 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit aca98a23e13f05dd076a203e73f43ca90e349e21"
iuc
parents:
diff changeset
157 is used to assign a SARS-CoV-2 genome sequence the most likely lineage based on the PANGO nomenclature system.
0ec813ad2910 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit aca98a23e13f05dd076a203e73f43ca90e349e21"
iuc
parents:
diff changeset
158
1
f557122d379e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 1522bdb834ffab157d1ca25e6e74db21f62e3aae"
iuc
parents: 0
diff changeset
159 Pangolin uses the `pangoLEARN <https://github.com/cov-lineages/pangoLEARN>`_ stored model for lineage assignment. This
f557122d379e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 1522bdb834ffab157d1ca25e6e74db21f62e3aae"
iuc
parents: 0
diff changeset
160 model is updated more frequently than the pangolin tool is. In general one should use the most recent model for lineage
f557122d379e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 1522bdb834ffab157d1ca25e6e74db21f62e3aae"
iuc
parents: 0
diff changeset
161 assignment, and the default option for this tool is to download the latest version of the model before the pangolin
f557122d379e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 1522bdb834ffab157d1ca25e6e74db21f62e3aae"
iuc
parents: 0
diff changeset
162 tool runs. A pangoLEARN data manager exists so that the Galaxy admin can download specific versions of the pangoLEARN
f557122d379e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 1522bdb834ffab157d1ca25e6e74db21f62e3aae"
iuc
parents: 0
diff changeset
163 model as required. Finally the pangolin tool can use its default built-in model, but this is **not recommended** as the
f557122d379e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 1522bdb834ffab157d1ca25e6e74db21f62e3aae"
iuc
parents: 0
diff changeset
164 default model rapidly becomes out of date.
f557122d379e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 1522bdb834ffab157d1ca25e6e74db21f62e3aae"
iuc
parents: 0
diff changeset
165
16
ca0d8cf80567 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit c180ed8ecef5956fb7dec68b947464b805fcea0b"
iuc
parents: 15
diff changeset
166 .. class:: warningmark
ca0d8cf80567 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit c180ed8ecef5956fb7dec68b947464b805fcea0b"
iuc
parents: 15
diff changeset
167
ca0d8cf80567 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit c180ed8ecef5956fb7dec68b947464b805fcea0b"
iuc
parents: 15
diff changeset
168 The "Download latest from web" updates the pangolin database but not the pangolin (and scorpio) software. If
ca0d8cf80567 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit c180ed8ecef5956fb7dec68b947464b805fcea0b"
iuc
parents: 15
diff changeset
169 the database format changes this can cause the pangolin job and the tool to fail. The solution to this kind of
ca0d8cf80567 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit c180ed8ecef5956fb7dec68b947464b805fcea0b"
iuc
parents: 15
diff changeset
170 failure is to update the pangolin tool installed in the Galaxy server.
0
0ec813ad2910 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit aca98a23e13f05dd076a203e73f43ca90e349e21"
iuc
parents:
diff changeset
171 ]]></help>
0ec813ad2910 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit aca98a23e13f05dd076a203e73f43ca90e349e21"
iuc
parents:
diff changeset
172 <citations>
8
3a656a4a43ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 5a3f70ab430c70b260dd6e0f5b6c53aed2ca5520"
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parents: 7
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173 <citation type="doi">10.1093/ve/veab064</citation>
0
0ec813ad2910 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit aca98a23e13f05dd076a203e73f43ca90e349e21"
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parents:
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174 </citations>
0ec813ad2910 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit aca98a23e13f05dd076a203e73f43ca90e349e21"
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parents:
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175 </tool>