annotate pangolin.xml @ 7:7bb8726be37c draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit a5dacfed40bb73aabd9a9a6d1e1076e0e9890a0e"
author iuc
date Tue, 20 Jul 2021 12:23:51 +0000
parents 437e28791761
children 3a656a4a43ed
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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@">3.1.7</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>
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8 <requirement type="package" version="0.23.0">csvtk</requirement>
0
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9 </requirements>
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10 <command detect_errors="exit_code"><![CDATA[
1
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11 #if str($db.source) == "download"
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12 python '$__tool_directory__/fetch_latest_pangolearn.py' --max_retries=$db.max_retries --timeout=$db.timeout &&
1
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13 #else if str($db.source) == "builtin"
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14 ln -s $db.db_release.fields.path datadir &&
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15 #end if
0
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16 pangolin
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17 --threads \${GALAXY_SLOTS:-1}
1
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18 #if str($db.source) == "download" or str($db.source) == "builtin"
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19 --datadir 'datadir'
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20 #end if
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21 $usher
0
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22 $alignment
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23 --outfile report.csv
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24 --max-ambig $max_ambig
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25 --min-length $min_length
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26 '$input1'
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27 && csvtk csv2tab report.csv
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28 #if not $include_header:
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29 | tail -n+2
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30 #end if
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31 > '$output1'
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32 #if $alignment
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33 && mv sequences.aln.fasta '$align1'
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34 #end if
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35 ]]></command>
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36 <inputs>
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37 <param type="data" name="input1" format="fasta" label="Input FASTA File(s)" />
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38 <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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39 <param argument="--alignment" type="boolean" label="Generate output alignment"
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40 truevalue="--alignment" falsevalue="" />
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41 <param argument="--max-ambig" type="float" label="Maximum proportion of Ns allowed"
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42 value="0.5" min="0" max="1" help="Maximum proportion of Ns allowed for pangolin to attempt assignment" />
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43 <param argument="--min-length" type="integer" label="Minimum query length allowed"
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44 value="10000" min="0" help="Minimum query length allowed for pangolin to attempt assignment"/>
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45 <param name="include_header" type="boolean" label="Include header line in output file"
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46 truevalue="true" falsevalue="false" />
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47 <conditional name="db">
1
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48 <param type="select" name="source" label="pangoLEARN source" help="Where to find the pangoLEARN database">
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49 <option value="download">Download latest from web</option>
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50 <option value="builtin">Use database from Galaxy server</option>
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51 <option value="default">Use default database built in to pangolin (not recommended)</option>
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52 </param>
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53 <when value="download">
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54 <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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55 <param name="timeout" label="Download timeout" help="How many seconds to wait when downloading the pangoLEARN database" type="float" value="60.0" />
1
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56 </when>
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57 <when value="builtin">
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58 <param name="db_release" label="pangoLEARN release" type="select">
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59 <options from_data_table="pangolearn">
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60 <column name="value" index="0" />
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61 <column name="name" index="1" />
3
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62 <column name="path" index="3" />
4
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63 <filter type="sort_by" column="0" />
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64 <filter type="static_value" column="2" value="3.0" />
1
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65 </options>
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66 </param>
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67 </when>
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68 <when value="default">
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69 </when>
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70 </conditional>
0
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71 </inputs>
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72 <outputs>
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73 <data name="output1" format="tabular" label="pangolin on ${on_string}">
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74 <actions>
4
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75 <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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76 </actions>
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77 </data>
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78 <data name="align1" format="fasta" label="pangolin alignment on ${on_string}">
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79 <filter>alignment</filter>
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80 </data>
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81 </outputs>
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82 <tests>
3
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83 <test expect_num_outputs="1">
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84 <param name="input1" value="test1.fasta"/>
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diff changeset
85 <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
86 <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
87 </conditional>
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
88 <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
89 <assert_contents>
4
42126b414951 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit ab174c9f8cbfc741501068dfa4f6ccf229a54489"
iuc
parents: 3
diff changeset
90 <has_text_matching expression="B.1.1\t0.0" />
42126b414951 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit ab174c9f8cbfc741501068dfa4f6ccf229a54489"
iuc
parents: 3
diff changeset
91 <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
92 <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
93 </assert_contents>
42126b414951 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit ab174c9f8cbfc741501068dfa4f6ccf229a54489"
iuc
parents: 3
diff changeset
94 </output>
42126b414951 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit ab174c9f8cbfc741501068dfa4f6ccf229a54489"
iuc
parents: 3
diff changeset
95 </test>
42126b414951 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit ab174c9f8cbfc741501068dfa4f6ccf229a54489"
iuc
parents: 3
diff changeset
96 <!-- 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
97 <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
98 <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
99 <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
100 <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
101 <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
102 </conditional>
42126b414951 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit ab174c9f8cbfc741501068dfa4f6ccf229a54489"
iuc
parents: 3
diff changeset
103 <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
104 <assert_contents>
5
42a174224817 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 93a8521684d03889f607b8c43db5539d9a0de8d0"
iuc
parents: 4
diff changeset
105 <has_text_matching expression="B.1.1\t0.0\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
106 <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
107 <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
108 </assert_contents>
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
109 </output>
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
110 </test>
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
111 <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
112 <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
113 <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
114 <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
115 <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
116 </conditional>
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
117 <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
118 <assert_contents>
4
42126b414951 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit ab174c9f8cbfc741501068dfa4f6ccf229a54489"
iuc
parents: 3
diff changeset
119 <has_text_matching expression="B.1.1\t0.0" />
3
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
120 <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
121 <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
122 </assert_contents>
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
123 </output>
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
124 <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
125 <assert_contents>
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
126 <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
127 <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
128 </assert_contents>
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
129 </output>
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
130 </test>
4
42126b414951 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit ab174c9f8cbfc741501068dfa4f6ccf229a54489"
iuc
parents: 3
diff changeset
131 <!-- testing with builtin data is too large -->
42126b414951 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit ab174c9f8cbfc741501068dfa4f6ccf229a54489"
iuc
parents: 3
diff changeset
132 <!-- <test expect_num_outputs="1">
3
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
133 <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
134 <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
135 <param name="source" value="builtin" />
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
136 </conditional>
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
137 <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
138 <assert_contents>
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
139 <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
140 <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
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 </output>
4
42126b414951 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit ab174c9f8cbfc741501068dfa4f6ccf229a54489"
iuc
parents: 3
diff changeset
143 </test>
3
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
144 <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
145 <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
146 <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
147 <param name="source" value="builtin" />
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
148 </conditional>
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
149 <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
150 <assert_contents>
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
151 <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
152 <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
153 <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
154 <has_n_lines n="34" />
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
155 </assert_contents>
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
156 </output>
4
42126b414951 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit ab174c9f8cbfc741501068dfa4f6ccf229a54489"
iuc
parents: 3
diff changeset
157 </test> -->
3
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
158 <!-- 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
159 <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
160 <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
161 <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
162 <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
163 <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
164 </conditional>
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
165 <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
166 <assert_contents>
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
167 <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
168 <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
169 <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
170 <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
171 <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
172 <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
173 </assert_contents>
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
174 </output>
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175 </test>
6
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176 <test expect_failure="true">
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177 <param name="input1" value="test1.fasta" />
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178 <conditional name="db">
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179 <param name="source" value="download" />
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180 <param name="timeout" value="0.00001" />
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181 <param name="max_retries" value="1" />
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182 </conditional>
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183 <assert_stderr>
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184 <has_text text="timed out" />
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185 </assert_stderr>
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186 </test>
0
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187 </tests>
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188 <help><![CDATA[
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189
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190 .. class:: infomark
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191
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192 `Pangolin <https://cov-lineages.org/pangolin.html>`_ (Phylogenetic Assignment of Named Global Outbreak LINeages)
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193 is used to assign a SARS-CoV-2 genome sequence the most likely lineage based on the PANGO nomenclature system.
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194
1
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195 Pangolin uses the `pangoLEARN <https://github.com/cov-lineages/pangoLEARN>`_ stored model for lineage assignment. This
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196 model is updated more frequently than the pangolin tool is. In general one should use the most recent model for lineage
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197 assignment, and the default option for this tool is to download the latest version of the model before the pangolin
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198 tool runs. A pangoLEARN data manager exists so that the Galaxy admin can download specific versions of the pangoLEARN
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199 model as required. Finally the pangolin tool can use its default built-in model, but this is **not recommended** as the
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200 default model rapidly becomes out of date.
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201
0
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202 ]]></help>
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203 <citations>
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204 <citation type="bibtex">
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205 @misc{githubpangolin,
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206 author = {O'Toole, Áine},
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207 year = {2020},
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208 title = {pangolin},
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209 publisher = {GitHub},
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210 journal = {GitHub repository},
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211 url = {https://github.com/cov-lineages/pangolin},
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212 }</citation>
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213 </citations>
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214 </tool>