Mercurial > repos > iuc > hamronize_tool

comparison hamronize_tool.xml @ 1:d37098dab8ca draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b872ea086ebd98be64839e7bbb1ddf7a181943d0"
author iuc
date Sat, 23 Oct 2021 21:36:38 +0000
parents 41acac3dbb79
children
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0:41acac3dbb79 1:d37098dab8ca
1 <tool id="hamronize_tool" name="hamronize" version="@VERSION@+galaxy0"> 1 <tool id="hamronize_tool" name="hamronize" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
2 <description> parse multiple Antimicrobial Resistance Analysis Reports into a common data structure</description> 2 <description> parse multiple Antimicrobial Resistance Analysis Reports into a common data structure</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6
7 <expand macro="requirements" /> 6 <expand macro="requirements" />
8 <expand macro="version_command" /> 7 <expand macro="version_command" />
9 8
10 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
11 #set $extra_2_params = str("ariba,srax,csstar,groot").split(",") 10 #set $extra_2_params = str("ariba,srax,csstar,groot").split(",")
32 31
33 $report 32 $report
34 ]]> </command> 33 ]]> </command>
35 34
36 <inputs> 35 <inputs>
37 <param name="report" type="data" format="txt,tabular,tsv" label="Report file"/> 36 <param name="report" type="data" format="txt,tabular" label="Report file"/>
38 <conditional name="select_tool"> 37 <conditional name="select_tool">
39 <param name="tool" type="select" label="Tool"> 38 <param name="tool" type="select" label="Tool">
40 <option value="abricate" selected="true">abricate</option> 39 <option value="abricate" selected="true">abricate</option>
41 <option value="amrfinderplus">amrfinderplus</option> 40 <option value="amrfinderplus">amrfinderplus</option>
42 <option value="ariba">ariba</option> 41 <option value="ariba">ariba</option>
115 <param name="analysis_software_version" type="text" label="Analysis software version"></param> 114 <param name="analysis_software_version" type="text" label="Analysis software version"></param>
116 <param name="reference_database_version" type="text" label="Reference database version"></param> 115 <param name="reference_database_version" type="text" label="Reference database version"></param>
117 </inputs> 116 </inputs>
118 117
119 <outputs> 118 <outputs>
120 <data format="tsv" name="output_tsv" label="${tool.name} on ${on_string}: Output" from_work_dir="hamronized.tsv"> 119 <data format="tabular" name="output_tsv" label="${tool.name} on ${on_string}: Output" from_work_dir="hamronized.tsv">
121 <filter>output_format == "tsv"</filter> 120 <filter>output_format == "tsv"</filter>
122 </data> 121 </data>
123 <data format="json" name="output_json" label="${tool.name} on ${on_string}: Output" from_work_dir="hamronized.json"> 122 <data format="json" name="output_json" label="${tool.name} on ${on_string}: Output" from_work_dir="hamronized.json">
124 <filter>output_format == "json"</filter> 123 <filter>output_format == "json"</filter>
125 </data> 124 </data>
126 </outputs> 125 </outputs>
127 <tests> 126 <tests>
128 <!-- abricate --> 127 <!-- abricate -->
129 <test expect_num_outputs="1"> 128 <test expect_num_outputs="1">
130 <param name="report" value="abricate/report.tsv" ftype="tsv" /> 129 <param name="report" value="abricate/report.tsv" ftype="tabular" />
131 <param name="tool" value="abricate" /> 130 <param name="tool" value="abricate" />
132 <param name="output_format" value="tsv" /> 131 <param name="output_format" value="tsv" />
133 <param name="reference_database_version" value="db_v_1" /> 132 <param name="reference_database_version" value="db_v_1" />
134 <param name="analysis_software_version" value="tool_v_1" /> 133 <param name="analysis_software_version" value="tool_v_1" />
135 <output name="output_tsv" ftype="tsv" file="hamronized_abricate.tsv" /> 134 <output name="output_tsv" file="hamronized_abricate.tsv" ftype="tabular" />
136 </test> 135 </test>
137 <test expect_num_outputs="1"> 136 <test expect_num_outputs="1">
138 <param name="report" value="abricate/report.tsv" ftype="tsv" /> 137 <param name="report" value="abricate/report.tsv" ftype="tabular" />
139 <param name="tool" value="abricate" /> 138 <param name="tool" value="abricate" />
140 <param name="output_format" value="json" /> 139 <param name="output_format" value="json" />
141 <param name="reference_database_version" value="db_v_1" /> 140 <param name="reference_database_version" value="db_v_1" />
142 <param name="analysis_software_version" value="tool_v_1" /> 141 <param name="analysis_software_version" value="tool_v_1" />
143 <output name="output_json" ftype="json" file="hamronized_abricate.json" /> 142 <output name="output_json" file="hamronized_abricate.json" ftype="json" />
144 </test> 143 </test>
145 <!-- ariba --> 144 <!-- ariba -->
146 <test expect_num_outputs="1"> 145 <test expect_num_outputs="1">
147 <param name="report" value="ariba/report.tsv" ftype="tsv" /> 146 <param name="report" value="ariba/report.tsv" ftype="tabular" />
148 <param name="tool" value="ariba" /> 147 <param name="tool" value="ariba" />
149 <param name="output_format" value="tsv" /> 148 <param name="output_format" value="tsv" />
150 <param name="reference_database_version" value="db_v_1" /> 149 <param name="reference_database_version" value="db_v_1" />
151 <param name="analysis_software_version" value="ariba_v1" /> 150 <param name="analysis_software_version" value="ariba_v1" />
152 <param name="input_file_name" value="ariba_report" /> 151 <param name="input_file_name" value="ariba_report" />
153 <param name="reference_database_id" value="dbname" /> 152 <param name="reference_database_id" value="dbname" />
154 <output name="output_tsv" ftype="tsv" file="hamronized_ariba.tsv" /> 153 <output name="output_tsv" file="hamronized_ariba.tsv" ftype="tabular" />
155 </test> 154 </test>
156 <!-- rgi --> 155 <!-- rgi -->
157 <test expect_num_outputs="1"> 156 <test expect_num_outputs="1">
158 <param name="report" value="rgi/rgi.txt" ftype="txt" /> 157 <param name="report" value="rgi/rgi.txt" ftype="txt" />
159 <param name="tool" value="rgi" /> 158 <param name="tool" value="rgi" />
160 <param name="output_format" value="tsv" /> 159 <param name="output_format" value="tsv" />
161 <param name="reference_database_version" value="card_v1" /> 160 <param name="reference_database_version" value="card_v1" />
162 <param name="analysis_software_version" value="rgi_v1" /> 161 <param name="analysis_software_version" value="rgi_v1" />
163 <param name="input_file_name" value="rgi_report" /> 162 <param name="input_file_name" value="rgi_report" />
164 <output name="output_tsv" ftype="tsv" file="hamronized_rgi.tsv" /> 163 <output name="output_tsv" file="hamronized_rgi.tsv" ftype="tabular"/>
165 </test> 164 </test>
166 </tests> 165 </tests>
167 <help><![CDATA[ 166 <help><![CDATA[
168 **What it does** 167 **What it does**
169 Hamronize parse multiple Antimicrobial Resistance Analysis Reports into a common data structure 168 Hamronize parse multiple Antimicrobial Resistance Analysis Reports into a common data structure