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comparison kraken_taxonomy_report.xml @ 5:bfae8da6082c draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report commit 5b5fa1a3d9492fbbf01aa6ddceca9d4525c7cba5
author iuc
date Tue, 12 Mar 2024 09:52:55 +0000
parents 27d65c78863c
children
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4:27d65c78863c 5:bfae8da6082c
1 <tool id="kraken_taxonomy_report" name="Kraken taxonomic report" version="0.0.3" profile="16.04"> 1 <tool id="kraken_taxonomy_report" name="Kraken taxonomic report" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="16.04">
2 <description>view report of classification for multiple samples</description> 2 <description>view report of classification for multiple samples</description>
3 <macros>
4 <token name="@TOOL_VERSION@">0.0.3</token>
5 <token name="@VERSION_SUFFIX@">1</token>
6 </macros>
7 <xrefs>
8 <xref type="bio.tools">Kraken-Taxonomy-Report</xref>
9 </xrefs>
3 <requirements> 10 <requirements>
4 <requirement type="package" version="1.66">biopython</requirement> 11 <requirement type="package" version="1.66">biopython</requirement>
5 </requirements> 12 </requirements>
13
6 <version_command>python '${__tool_directory__}/kraken_taxonomy_report.py' --version</version_command> 14 <version_command>python '${__tool_directory__}/kraken_taxonomy_report.py' --version</version_command>
7 <command><![CDATA[ 15 <command><![CDATA[
8 #for $input_classification in $classification: 16 #for $input_classification in $classification:
9 ln -s "${input_classification}" "${input_classification.element_identifier}" && 17 ln -s "${input_classification}" "${input_classification.element_identifier}" &&
10 #end for 18 #end for
11 19
12 export KRAKEN_DB_PATH='${kraken_database.fields.path}' && 20 export KRAKEN_DB_PATH='${kraken_database.fields.path}' &&
13 python '${__tool_directory__}/kraken_taxonomy_report.py' 21 python '${__tool_directory__}/kraken_taxonomy_report.py'
14 22
15 --db '${kraken_database.fields.name}' 23 --db '${kraken_database.fields.name}'
16 ${show_zeros} 24 ${show_zeros_param}
17 ${header_line} 25 ${header_line_param}
18 ${otu_name} 26 ${otu_name}
19 ${taxonomy} 27 ${taxo}
20 ${show_rank} 28 ${rank}
21 ${intermediate} 29 ${intermediate_rank}
22 ${sanitize_names} 30 ${sanitize_names_param}
23 #if str( $cluster.cluster ): 31 #if str( $cluster.cluster_param ):
24 --cluster ${cluster.cluster} 32 --cluster ${cluster.cluster_param}
25 #else: 33 #else:
26 ${cluster.summation} 34 ${cluster.summ}
27 #end if 35 #end if
28 36
29 --output '${output_report}' 37 --output '${output_report}'
30 38
31 #if $output_tree: 39 #if $output_tree:
36 '${input_classification.element_identifier}' 44 '${input_classification.element_identifier}'
37 #end for 45 #end for
38 ]]></command> 46 ]]></command>
39 <inputs> 47 <inputs>
40 <param format="tabular" label="Kraken output" multiple="True" name="classification" type="data" /> 48 <param format="tabular" label="Kraken output" multiple="True" name="classification" type="data" />
41 <param checked="False" falsevalue="" argument="--show-zeros" label="Display taxa even if they lack a read in any sample" name="show_zeros" truevalue="--show-zeros" type="boolean" /> 49 <param checked="False" falsevalue="" argument="--show-zeros" label="Display taxa even if they lack a read in any sample" name="show_zeros_param" truevalue="--show-zeros" type="boolean" />
42 <param checked="True" falsevalue="" argument="--header-line" label="Display a header line indicating sample IDs" name="header_line" truevalue="--header-line" type="boolean" /> 50 <param checked="True" falsevalue="" argument="--header-line" label="Display a header line indicating sample IDs" name="header_line_param" truevalue="--header-line" type="boolean" />
43 <param label="Select a Kraken database" name="kraken_database" type="select" help="Select the same database used to classify reads"> 51 <param label="Select a Kraken database" name="kraken_database" type="select" help="Select the same database used to classify reads">
44 <options from_data_table="kraken_databases"> 52 <options from_data_table="kraken_databases">
45 <validator message="No Kraken databases are available" type="no_options" /> 53 <validator message="No Kraken databases are available" type="no_options" />
46 </options> 54 </options>
47 </param> 55 </param>
48 <param label="How to name OTUs" name="otu_name" type="select" multiple="False"> 56 <param label="How to name OTUs" name="otu_name" type="select" multiple="False">
49 <option value="" selected="True">Node name only</option> 57 <option value="" selected="True">Node name only</option>
50 <option value="--name-long">Taxonified Name</option> 58 <option value="--name-long">Taxonified Name</option>
51 <option value="--name-id">Node ID</option> 59 <option value="--name-id">Node ID</option>
52 </param> 60 </param>
53 <param checked="True" falsevalue="" argument="--sanitize-names" label="Sanitize Names" name="sanitize_names" truevalue="--sanitize-names" type="boolean" help="Replace special chars (\t| |\||\.;) with underscore (_)" /> 61 <param checked="True" falsevalue="" argument="--sanitize-names" label="Sanitize Names" name="sanitize_names_param" truevalue="--sanitize-names" type="boolean" help="Replace special chars (\t| |\||\.;) with underscore (_)" />
54 <param checked="False" falsevalue="" argument="--show-rank" label="Output Rank Name in (second to) last column" name="show_rank" truevalue="--show-rank" type="boolean" /> 62 <param checked="False" falsevalue="" argument="--show-rank" label="Output Rank Name in (second to) last column" name="rank" truevalue="--show-rank" type="boolean" />
55 <param checked="False" falsevalue="" argument="--taxonomy" label="Output taxonomy in last column" name="taxonomy" truevalue="--taxonomy" type="boolean" /> 63 <param checked="False" falsevalue="" argument="--taxonomy" label="Output taxonomy in last column" name="taxo" truevalue="--taxonomy" type="boolean" />
56 <param checked="True" falsevalue="" argument="--intermediate" label="Display intermediate ranks" name="intermediate" truevalue="--intermediate" type="boolean" /> 64 <param checked="True" falsevalue="" argument="--intermediate" label="Display intermediate ranks" name="intermediate_rank" truevalue="--intermediate" type="boolean" />
57 <conditional name="cluster"> 65 <conditional name="cluster">
58 <param argument="--cluster" help="Combines rows under the selected taxon and reports only selected rank." label="Cluster by taxonomic rank" name="cluster" type="select"> 66 <param argument="--cluster" help="Combines rows under the selected taxon and reports only selected rank." label="Cluster by taxonomic rank" name="cluster_param" type="select">
59 <option value="Superkingdom">Superkingdom</option> 67 <option value="Superkingdom">Superkingdom</option>
60 <option value="Kingdom">Kingdom</option> 68 <option value="Kingdom">Kingdom</option>
61 <option value="Subkingdom">Subkingdom</option> 69 <option value="Subkingdom">Subkingdom</option>
62 <option value="Superphylum">Superphylum</option> 70 <option value="Superphylum">Superphylum</option>
63 <option value="Phylum">Phylum</option> 71 <option value="Phylum">Phylum</option>
85 <option value="Varietas">Varietas</option> 93 <option value="Varietas">Varietas</option>
86 <option value="Forma">Forma</option> 94 <option value="Forma">Forma</option>
87 <option value="" selected="True">No Clustering</option> 95 <option value="" selected="True">No Clustering</option>
88 </param> 96 </param>
89 <when value=""> 97 <when value="">
90 <param checked="False" falsevalue="" argument="--summation" label="Summation of lower ranks into higher ranks" name="summation" truevalue="--summation" type="boolean" /> 98 <param checked="False" falsevalue="" argument="--summation" label="Summation of lower ranks into higher ranks" name="summ" truevalue="--summation" type="boolean" />
91 </when> 99 </when>
92 <when value="Superkingdom"/> 100 <when value="Superkingdom"/>
93 <when value="Kingdom"/> 101 <when value="Kingdom"/>
94 <when value="Subkingdom"/> 102 <when value="Subkingdom"/>
95 <when value="Superphylum"/> 103 <when value="Superphylum"/>
125 <data format="txt" name="output_tree" label="${tool.name} on ${on_string} (Newick Tree)"> 133 <data format="txt" name="output_tree" label="${tool.name} on ${on_string} (Newick Tree)">
126 <filter>tree</filter> 134 <filter>tree</filter>
127 </data> 135 </data>
128 </outputs> 136 </outputs>
129 <tests> 137 <tests>
130 <test> 138 <test expect_num_outputs="2">
131 <param name="classification" value="input_kraken_1.tabular" ftype="tabular"/> 139 <param name="classification" value="input_kraken_1.tabular" ftype="tabular"/>
132 <param name="show_zeros" value="True"/> 140 <param name="show_zeros_param" value="True"/>
133 <param name="header_line" value="True"/> 141 <param name="header_line_param" value="True"/>
134 <param name="kraken_database" value="test_db"/> 142 <param name="kraken_database" value="test_db"/>
135 <param name="otu_name" value=""/> 143 <param name="otu_name" value=""/>
136 <param name="sanitize_names" value="True"/> 144 <param name="sanitize_names_param" value="True"/>
137 <param name="show_rank" value="True"/> 145 <param name="rank" value="True"/>
138 <param name="taxonomy" value="True"/> 146 <param name="taxo" value="True"/>
139 <param name="intermediate" value="True"/> 147 <param name="intermediate_rank" value="True"/>
140 <conditional name="cluster"> 148 <conditional name="cluster">
141 <param name="cluster" value=""/> 149 <param name="cluster_param" value=""/>
142 <param name="summation" value="True"/> 150 <param name="summ" value="True"/>
143 </conditional> 151 </conditional>
144 <param name="tree" value="True"/> 152 <param name="tree" value="True"/>
145 <output name="output_report" file="output_abundance_1.tabular" ftype="tabular"/> 153 <output name="output_report" file="output_abundance_1.tabular" ftype="tabular"/>
146 <output name="output_tree" file="output_tree_1.newick" /> 154 <output name="output_tree" file="output_tree_1.newick" />
147 </test> 155 </test>
148 <test> 156 <test expect_num_outputs="2">
149 <param name="classification" value="input_kraken_1.tabular" ftype="tabular"/> 157 <param name="classification" value="input_kraken_1.tabular" ftype="tabular"/>
150 <param name="show_zeros" value="True"/> 158 <param name="show_zeros_param" value="True"/>
151 <param name="header_line" value="True"/> 159 <param name="header_line_param" value="True"/>
152 <param name="kraken_database" value="test_db"/> 160 <param name="kraken_database" value="test_db"/>
153 <param name="otu_name" value=""/> 161 <param name="otu_name" value=""/>
154 <param name="sanitize_names" value="True"/> 162 <param name="sanitize_names_param" value="True"/>
155 <param name="show_rank" value="True"/> 163 <param name="rank" value="True"/>
156 <param name="taxonomy" value="True"/> 164 <param name="taxo" value="True"/>
157 <param name="intermediate" value="True"/> 165 <param name="intermediate_rank" value="True"/>
158 <conditional name="cluster"> 166 <conditional name="cluster">
159 <param name="cluster" value=""/> 167 <param name="cluster_param" value=""/>
160 <param name="summation" value="False"/> 168 <param name="summ" value="False"/>
161 </conditional> 169 </conditional>
162 <param name="tree" value="True"/> 170 <param name="tree" value="True"/>
163 <output name="output_report" file="output_abundance_2.tabular" ftype="tabular"/> 171 <output name="output_report" file="output_abundance_2.tabular" ftype="tabular"/>
164 <output name="output_tree" file="output_tree_1.newick" /> 172 <output name="output_tree" file="output_tree_1.newick" />
165 </test> 173 </test>
166 <test> 174 <test expect_num_outputs="2">
167 <param name="classification" value="input_kraken_1.tabular" ftype="tabular"/> 175 <param name="classification" value="input_kraken_1.tabular" ftype="tabular"/>
168 <param name="show_zeros" value="True"/> 176 <param name="show_zeros_param" value="True"/>
169 <param name="header_line" value="True"/> 177 <param name="header_line_param" value="True"/>
170 <param name="kraken_database" value="test_db"/> 178 <param name="kraken_database" value="test_db"/>
171 <param name="otu_name" value=""/> 179 <param name="otu_name" value=""/>
172 <param name="sanitize_names" value="True"/> 180 <param name="sanitize_names_param" value="True"/>
173 <param name="show_rank" value="True"/> 181 <param name="rank" value="True"/>
174 <param name="taxonomy" value="True"/> 182 <param name="taxo" value="True"/>
175 <param name="intermediate" value="False"/> 183 <param name="intermediate_rank" value="False"/>
176 <conditional name="cluster"> 184 <conditional name="cluster">
177 <param name="cluster" value="Species"/> 185 <param name="cluster_param" value="Species"/>
178 </conditional> 186 </conditional>
179 <param name="tree" value="True"/> 187 <param name="tree" value="True"/>
180 <output name="output_report" file="output_abundance_3.tabular" ftype="tabular"/> 188 <output name="output_report" file="output_abundance_3.tabular" ftype="tabular"/>
181 <output name="output_tree" file="output_tree_3.newick" /> 189 <output name="output_tree" file="output_tree_3.newick" />
182 </test> 190 </test>
183 <test> 191 <test expect_num_outputs="2">
184 <param name="classification" value="input_kraken_1.tabular,input_kraken_2.tabular" ftype="tabular"/> 192 <param name="classification" value="input_kraken_1.tabular,input_kraken_2.tabular" ftype="tabular"/>
185 <param name="show_zeros" value="True"/> 193 <param name="show_zeros_param" value="True"/>
186 <param name="header_line" value="True"/> 194 <param name="header_line_param" value="True"/>
187 <param name="kraken_database" value="test_db"/> 195 <param name="kraken_database" value="test_db"/>
188 <param name="otu_name" value=""/> 196 <param name="otu_name" value=""/>
189 <param name="sanitize_names" value="True"/> 197 <param name="sanitize_names_param" value="True"/>
190 <param name="show_rank" value="True"/> 198 <param name="rank" value="True"/>
191 <param name="taxonomy" value="True"/> 199 <param name="taxo" value="True"/>
192 <param name="intermediate" value="False"/> 200 <param name="intermediate_rank" value="False"/>
193 <conditional name="cluster"> 201 <conditional name="cluster">
194 <param name="cluster" value="Species"/> 202 <param name="cluster_param" value="Species"/>
195 </conditional> 203 </conditional>
196 <param name="tree" value="True"/> 204 <param name="tree" value="True"/>
197 <output name="output_report" file="output_abundance_4.tabular" ftype="tabular"/> 205 <output name="output_report" file="output_abundance_4.tabular" ftype="tabular"/>
198 <output name="output_tree" file="output_tree_3.newick" /> 206 <output name="output_tree" file="output_tree_3.newick" />
199 </test> 207 </test>