Mercurial > repos > iuc > pangolin

comparison pangolin.xml @ 4:6b5a64c4cb34 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit ab174c9f8cbfc741501068dfa4f6ccf229a54489"
author iuc
date Thu, 03 Jun 2021 06:37:39 +0000
parents 68e94cfc9e6d
children a4f59b43cba3
comparison
equal deleted inserted replaced
3:68e94cfc9e6d 4:6b5a64c4cb34
1 <tool id="pangolin" name="Pangolin" version="@TOOL_VERSION@+galaxy1" profile="20.01"> 1 <tool id="pangolin" name="Pangolin" version="@TOOL_VERSION@+galaxy0" profile="20.01">
2 <description>Phylogenetic Assignment of Outbreak Lineages</description> 2 <description>Phylogenetic Assignment of Outbreak Lineages</description>
3 <macros> 3 <macros>
4 <token name="@TOOL_VERSION@">2.3.8</token> 4 <token name="@TOOL_VERSION@">3.0.3</token>
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
7 <requirement type="package" version="@TOOL_VERSION@">pangolin</requirement> 7 <requirement type="package" version="@TOOL_VERSION@">pangolin</requirement>
8 <requirement type="package" version="0.22.0">csvtk</requirement> 8 <requirement type="package" version="0.22.0">csvtk</requirement>
9 </requirements> 9 </requirements>
16 pangolin 16 pangolin
17 --threads \${GALAXY_SLOTS:-1} 17 --threads \${GALAXY_SLOTS:-1}
18 #if str($db.source) == "download" or str($db.source) == "builtin" 18 #if str($db.source) == "download" or str($db.source) == "builtin"
19 --datadir 'datadir' 19 --datadir 'datadir'
20 #end if 20 #end if
21 $usher
21 $alignment 22 $alignment
22 --outfile report.csv 23 --outfile report.csv
23 --max-ambig $max_ambig 24 --max-ambig $max_ambig
24 --min-length $min_length 25 --min-length $min_length
25 '$input1' 26 '$input1'
32 && mv sequences.aln.fasta '$align1' 33 && mv sequences.aln.fasta '$align1'
33 #end if 34 #end if
34 ]]></command> 35 ]]></command>
35 <inputs> 36 <inputs>
36 <param type="data" name="input1" format="fasta" label="Input FASTA File(s)" /> 37 <param type="data" name="input1" format="fasta" label="Input FASTA File(s)" />
37 <param name="alignment" type="boolean" label="Generate output alignment" 38 <param argument="--usher" type="boolean" label="Use UShER model" truevalue="--usher" falsevalue="" help="Use UShER model instead of default pangoLEARN model" />
39 <param argument="--alignment" type="boolean" label="Generate output alignment"
38 truevalue="--alignment" falsevalue="" /> 40 truevalue="--alignment" falsevalue="" />
39 <param argument="--max-ambig" type="float" label="Maximum proportion of Ns allowed" 41 <param argument="--max-ambig" type="float" label="Maximum proportion of Ns allowed"
40 value="0.5" min="0" max="1" help="Maximum proportion of Ns allowed for pangolin to attempt assignment" /> 42 value="0.5" min="0" max="1" help="Maximum proportion of Ns allowed for pangolin to attempt assignment" />
41 <param argument="--min-length" type="integer" label="Minimum query length allowed" 43 <param argument="--min-length" type="integer" label="Minimum query length allowed"
42 value="10000" min="0" help="Minimum query length allowed for pangolin to attempt assignment"/> 44 value="10000" min="0" help="Minimum query length allowed for pangolin to attempt assignment"/>
54 <param name="db_release" label="pangoLEARN release" type="select"> 56 <param name="db_release" label="pangoLEARN release" type="select">
55 <options from_data_table="pangolearn"> 57 <options from_data_table="pangolearn">
56 <column name="value" index="0" /> 58 <column name="value" index="0" />
57 <column name="name" index="1" /> 59 <column name="name" index="1" />
58 <column name="path" index="3" /> 60 <column name="path" index="3" />
59 <filter type="sort_by" column="0"/> 61 <filter type="sort_by" column="0" />
62 <filter type="static_value" column="2" value="3.0" />
60 </options> 63 </options>
61 </param> 64 </param>
62 </when> 65 </when>
63 <when value="default"> 66 <when value="default">
64 </when> 67 </when>
65 </conditional> 68 </conditional>
66 </inputs> 69 </inputs>
67 <outputs> 70 <outputs>
68 <data name="output1" format="tabular" label="pangolin on ${on_string}"> 71 <data name="output1" format="tabular" label="pangolin on ${on_string}">
69 <actions> 72 <actions>
70 <action name="column_names" type="metadata" default="taxon,lineage,probability,pangoLEARN_version,status,note" /> 73 <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" />
71 </actions> 74 </actions>
72 </data> 75 </data>
73 <data name="align1" format="fasta" label="pangolin alignment on ${on_string}"> 76 <data name="align1" format="fasta" label="pangolin alignment on ${on_string}">
74 <filter>alignment</filter> 77 <filter>alignment</filter>
75 </data> 78 </data>
80 <conditional name="db"> 83 <conditional name="db">
81 <param name="source" value="download" /> 84 <param name="source" value="download" />
82 </conditional> 85 </conditional>
83 <output name="output1" ftype="tabular"> 86 <output name="output1" ftype="tabular">
84 <assert_contents> 87 <assert_contents>
85 <has_text text="B.1.1" /> 88 <has_text_matching expression="B.1.1\t0.0" />
89 <has_text text="passed_qc" />
90 <has_n_lines n="1" />
91 </assert_contents>
92 </output>
93 </test>
94 <!-- test UShER mode -->
95 <test expect_num_outputs="1">
96 <param name="input1" value="test1.fasta"/>
97 <param name="usher" value="true" />
98 <conditional name="db">
99 <param name="source" value="download" />
100 </conditional>
101 <output name="output1" ftype="tabular">
102 <assert_contents>
103 <has_text_matching expression="B.1.1.409\t\t*PUSHER" />
86 <has_text text="passed_qc" /> 104 <has_text text="passed_qc" />
87 <has_n_lines n="1" /> 105 <has_n_lines n="1" />
88 </assert_contents> 106 </assert_contents>
89 </output> 107 </output>
90 </test> 108 </test>
94 <conditional name="db"> 112 <conditional name="db">
95 <param name="source" value="download" /> 113 <param name="source" value="download" />
96 </conditional> 114 </conditional>
97 <output name="output1" ftype="tabular"> 115 <output name="output1" ftype="tabular">
98 <assert_contents> 116 <assert_contents>
99 <has_text text="B.1.1" /> 117 <has_text_matching expression="B.1.1\t0.0" />
100 <has_text text="passed_qc" /> 118 <has_text text="passed_qc" />
101 <has_n_lines n="1" /> 119 <has_n_lines n="1" />
102 </assert_contents> 120 </assert_contents>
103 </output> 121 </output>
104 <output name="align1" file="aln1.fasta" ftype="fasta"> 122 <output name="align1" file="aln1.fasta" ftype="fasta">
106 <has_text text="Consensus_EB232-crude-prep_S297" /> 124 <has_text text="Consensus_EB232-crude-prep_S297" />
107 <has_n_lines n="2" /> 125 <has_n_lines n="2" />
108 </assert_contents> 126 </assert_contents>
109 </output> 127 </output>
110 </test> 128 </test>
111 <test expect_num_outputs="1"> 129 <!-- testing with builtin data is too large -->
130 <!-- <test expect_num_outputs="1">
112 <param name="input1" value="test1.fasta"/> 131 <param name="input1" value="test1.fasta"/>
113 <conditional name="db"> 132 <conditional name="db">
114 <param name="source" value="builtin" /> 133 <param name="source" value="builtin" />
115 </conditional> 134 </conditional>
116 <output name="output1" ftype="tabular"> 135 <output name="output1" ftype="tabular">
117 <assert_contents> 136 <assert_contents>
118 <has_text text="Consensus_EB232-crude-prep_S297" /> 137 <has_text text="Consensus_EB232-crude-prep_S297" />
119 <has_n_lines n="1" /> 138 <has_n_lines n="1" />
120 </assert_contents> 139 </assert_contents>
121 </output> 140 </output>
122 </test> 141 </test>
123 <test expect_num_outputs="1"> 142 <test expect_num_outputs="1">
124 <param name="input1" value="multiple_alignment.fasta.gz"/> 143 <param name="input1" value="multiple_alignment.fasta.gz"/>
125 <conditional name="db"> 144 <conditional name="db">
126 <param name="source" value="builtin" /> 145 <param name="source" value="builtin" />
127 </conditional> 146 </conditional>
131 <has_text text="Poland" /> 150 <has_text text="Poland" />
132 <has_text text="USA" /> 151 <has_text text="USA" />
133 <has_n_lines n="34" /> 152 <has_n_lines n="34" />
134 </assert_contents> 153 </assert_contents>
135 </output> 154 </output>
136 </test> 155 </test> -->
137 <!-- test include-header option --> 156 <!-- test include-header option -->
138 <test expect_num_outputs="1"> 157 <test expect_num_outputs="1">
139 <param name="input1" value="multiple_alignment.fasta.gz"/> 158 <param name="input1" value="multiple_alignment.fasta.gz"/>
140 <param name="include_header" value="true" /> 159 <param name="include_header" value="true" />
141 <conditional name="db"> 160 <conditional name="db">
142 <param name="source" value="builtin" /> 161 <param name="source" value="download" />
143 </conditional> 162 </conditional>
144 <output name="output1" ftype="tabular"> 163 <output name="output1" ftype="tabular">
145 <assert_contents> 164 <assert_contents>
146 <has_text text="pangoLEARN_version" /> 165 <has_text text="pangoLEARN_version" />
147 <has_text text="lineage" /> 166 <has_text text="lineage" />