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comparison pangolin.xml @ 3:68e94cfc9e6d draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
author iuc
date Wed, 19 May 2021 13:31:57 +0000
parents de3ceb419d91
children 6b5a64c4cb34
comparison
equal deleted inserted replaced
2:832862510ae8 3:68e94cfc9e6d
1 <tool id="pangolin" name="Pangolin" version="@TOOL_VERSION@" profile="20.01"> 1 <tool id="pangolin" name="Pangolin" version="@TOOL_VERSION@+galaxy1" 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@">2.3.8</token>
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
21 $alignment 21 $alignment
22 --outfile report.csv 22 --outfile report.csv
23 --max-ambig $max_ambig 23 --max-ambig $max_ambig
24 --min-length $min_length 24 --min-length $min_length
25 '$input1' 25 '$input1'
26 && csvtk csv2tab report.csv | tail -n-1 >'$output1' 26 && csvtk csv2tab report.csv
27 #if not $include_header:
28 | tail -n+2
29 #end if
30 > '$output1'
27 #if $alignment 31 #if $alignment
28 && mv sequences.aln.fasta '$align1' 32 && mv sequences.aln.fasta '$align1'
29 #end if 33 #end if
30 ]]></command> 34 ]]></command>
31 <inputs> 35 <inputs>
32 <param type="data" name="input1" format="fasta" label="Input FASTA File(s)" /> 36 <param type="data" name="input1" format="fasta" label="Input FASTA File(s)" />
33 <param name="alignment" type="boolean" label="Generate output alignment" 37 <param name="alignment" type="boolean" label="Generate output alignment"
34 truevalue="--alignment" falsevalue="" /> 38 truevalue="--alignment" falsevalue="" />
35 <param argument="--max-ambig" type="float" label="Maximum proportion of Ns allowed" 39 <param argument="--max-ambig" type="float" label="Maximum proportion of Ns allowed"
36 value="0.5" min="0" max="1" help="Maximum proportion of Ns allowed for pangolin to attempt assignment" /> 40 value="0.5" min="0" max="1" help="Maximum proportion of Ns allowed for pangolin to attempt assignment" />
37 <param argument="--min-length" type="integer" label="Minimum query length allowed" 41 <param argument="--min-length" type="integer" label="Minimum query length allowed"
38 value="10000" min="0" help="Minimum query length allowed for pangolin to attempt assignment"/> 42 value="10000" min="0" help="Minimum query length allowed for pangolin to attempt assignment"/>
39 <conditional name="db"> 43 <param name="include_header" type="boolean" label="Include header line in output file"
44 truevalue="true" falsevalue="false" />
45 <conditional name="db">
40 <param type="select" name="source" label="pangoLEARN source" help="Where to find the pangoLEARN database"> 46 <param type="select" name="source" label="pangoLEARN source" help="Where to find the pangoLEARN database">
41 <option value="download">Download latest from web</option> 47 <option value="download">Download latest from web</option>
42 <option value="builtin">Use database from Galaxy server</option> 48 <option value="builtin">Use database from Galaxy server</option>
43 <option value="default">Use default database built in to pangolin (not recommended)</option> 49 <option value="default">Use default database built in to pangolin (not recommended)</option>
44 </param> 50 </param>
47 <when value="builtin"> 53 <when value="builtin">
48 <param name="db_release" label="pangoLEARN release" type="select"> 54 <param name="db_release" label="pangoLEARN release" type="select">
49 <options from_data_table="pangolearn"> 55 <options from_data_table="pangolearn">
50 <column name="value" index="0" /> 56 <column name="value" index="0" />
51 <column name="name" index="1" /> 57 <column name="name" index="1" />
52 <column name="path" index="3" /> 58 <column name="path" index="3" />
53 <filter type="sort_by" column="0"/> 59 <filter type="sort_by" column="0"/>
54 </options> 60 </options>
55 </param> 61 </param>
56 </when> 62 </when>
57 <when value="default"> 63 <when value="default">
67 <data name="align1" format="fasta" label="pangolin alignment on ${on_string}"> 73 <data name="align1" format="fasta" label="pangolin alignment on ${on_string}">
68 <filter>alignment</filter> 74 <filter>alignment</filter>
69 </data> 75 </data>
70 </outputs> 76 </outputs>
71 <tests> 77 <tests>
72 <test expect_num_outputs="1"> 78 <test expect_num_outputs="1">
73 <param name="input1" value="test1.fasta"/> 79 <param name="input1" value="test1.fasta"/>
74 <conditional name="db"> 80 <conditional name="db">
75 <param name="source" value="download" /> 81 <param name="source" value="download" />
76 </conditional> 82 </conditional>
77 <output name="output1"> 83 <output name="output1" ftype="tabular">
78 <assert_contents> 84 <assert_contents>
79 <has_text text="B.1.1" /> 85 <has_text text="B.1.1" />
80 <has_text text="passed_qc" /> 86 <has_text text="passed_qc" />
81 </assert_contents> 87 <has_n_lines n="1" />
82 </output> 88 </assert_contents>
83 </test> 89 </output>
84 <test expect_num_outputs="2"> 90 </test>
85 <param name="alignment" value="--alignment" /> 91 <test expect_num_outputs="2">
86 <param name="input1" value="test1.fasta" /> 92 <param name="alignment" value="--alignment" />
87 <conditional name="db"> 93 <param name="input1" value="test1.fasta" />
88 <param name="source" value="download" /> 94 <conditional name="db">
89 </conditional> 95 <param name="source" value="download" />
90 <output name="output1"> 96 </conditional>
91 <assert_contents> 97 <output name="output1" ftype="tabular">
92 <has_text text="B.1.1" /> 98 <assert_contents>
93 <has_text text="passed_qc" /> 99 <has_text text="B.1.1" />
94 </assert_contents> 100 <has_text text="passed_qc" />
95 </output> 101 <has_n_lines n="1" />
96 <output name="align1" file="aln1.fasta" ftype="fasta" /> 102 </assert_contents>
97 </test> 103 </output>
98 <test expect_num_outputs="1"> 104 <output name="align1" file="aln1.fasta" ftype="fasta">
99 <param name="input1" value="test1.fasta"/> 105 <assert_contents>
100 <conditional name="db"> 106 <has_text text="Consensus_EB232-crude-prep_S297" />
101 <param name="source" value="builtin" /> 107 <has_n_lines n="2" />
102 </conditional> 108 </assert_contents>
103 <output name="output1"> 109 </output>
104 <assert_contents> 110 </test>
105 <has_text text="2021-04-21" /> 111 <test expect_num_outputs="1">
106 </assert_contents> 112 <param name="input1" value="test1.fasta"/>
107 </output> 113 <conditional name="db">
108 </test> 114 <param name="source" value="builtin" />
115 </conditional>
116 <output name="output1" ftype="tabular">
117 <assert_contents>
118 <has_text text="Consensus_EB232-crude-prep_S297" />
119 <has_n_lines n="1" />
120 </assert_contents>
121 </output>
122 </test>
123 <test expect_num_outputs="1">
124 <param name="input1" value="multiple_alignment.fasta.gz"/>
125 <conditional name="db">
126 <param name="source" value="builtin" />
127 </conditional>
128 <output name="output1" ftype="tabular">
129 <assert_contents>
130 <has_text text="Serbia" />
131 <has_text text="Poland" />
132 <has_text text="USA" />
133 <has_n_lines n="34" />
134 </assert_contents>
135 </output>
136 </test>
137 <!-- test include-header option -->
138 <test expect_num_outputs="1">
139 <param name="input1" value="multiple_alignment.fasta.gz"/>
140 <param name="include_header" value="true" />
141 <conditional name="db">
142 <param name="source" value="builtin" />
143 </conditional>
144 <output name="output1" ftype="tabular">
145 <assert_contents>
146 <has_text text="pangoLEARN_version" />
147 <has_text text="lineage" />
148 <has_text text="Serbia" />
149 <has_text text="Poland" />
150 <has_text text="USA" />
151 <has_n_lines n="35" />
152 </assert_contents>
153 </output>
154 </test>
109 </tests> 155 </tests>
110 <help><![CDATA[ 156 <help><![CDATA[
111 157
112 .. class:: infomark 158 .. class:: infomark
113 159