Mercurial > repos > iuc > hamronize_tool

comparison hamronize_tool.xml @ 0:41acac3dbb79 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
author iuc
date Tue, 16 Mar 2021 12:36:39 +0000
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children d37098dab8ca
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-1:000000000000 0:41acac3dbb79
1 <tool id="hamronize_tool" name="hamronize" version="@VERSION@+galaxy0">
2 <description> parse multiple Antimicrobial Resistance Analysis Reports into a common data structure</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6
7 <expand macro="requirements" />
8 <expand macro="version_command" />
9
10 <command detect_errors="exit_code"><![CDATA[
11 #set $extra_2_params = str("ariba,srax,csstar,groot").split(",")
12 #set $extra_1_param = $extra_2_params + str("amrfinderplus,rgi,resfinder4,deeparg,kmerresistance,srst2,amrplusplus,resfarms").split(",")
13
14 hamronize
15 ${select_tool.tool}
16 --analysis_software_version '${analysis_software_version}'
17 --reference_database_version '${reference_database_version}'
18 --format ${output_format}
19 #if $output_format == "tsv"
20 --output hamronized.tsv
21 #else
22 --output hamronized.json
23 #end if
24
25 #if $select_tool.tool in $extra_1_param
26 --input_file_name $select_tool.input_file_name
27 #end if
28
29 #if $select_tool.tool in $extra_2_params
30 --reference_database_id $select_tool.reference_database_id
31 #end if
32
33 $report
34 ]]> </command>
35
36 <inputs>
37 <param name="report" type="data" format="txt,tabular,tsv" label="Report file"/>
38 <conditional name="select_tool">
39 <param name="tool" type="select" label="Tool">
40 <option value="abricate" selected="true">abricate</option>
41 <option value="amrfinderplus">amrfinderplus</option>
42 <option value="ariba">ariba</option>
43 <option value="rgi">rgi</option>
44 <option value="resfinder">resfinder</option>
45 <option value="resfinder4">resfinder4</option>
46 <option value="srax">srax</option>
47 <option value="deeparg">deeparg</option>
48 <option value="kmerresistance">kmerresistance</option>
49 <option value="srst2">srst2</option>
50 <option value="staramr">staramr</option>
51 <option value="csstar">csstar</option>
52 <option value="amrplusplus">amrplusplus</option>
53 <option value="resfams">resfams</option>
54 <option value="groot">groot</option>
55 </param>
56 <when value="abricate" />
57 <when value="resfinder" />
58 <when value="staramr" />
59 <when value="amrfinderplus">
60 <expand macro="input_file_name"/>
61 </when>
62
63 <when value="ariba">
64 <expand macro="input_file_name"/>
65 <expand macro="reference_database_id"/>
66 </when>
67
68 <when value="rgi">
69 <expand macro="input_file_name"/>
70 </when>
71
72 <when value="resfinder4">
73 <expand macro="input_file_name"/>
74 </when>
75
76 <when value="srax">
77 <expand macro="input_file_name"/>
78 <expand macro="reference_database_id"/>
79 </when>
80
81 <when value="deeparg">
82 <expand macro="input_file_name"/>
83 </when>
84
85 <when value="kmerresistance">
86 <expand macro="input_file_name"/>
87 </when>
88
89 <when value="srst2">
90 <expand macro="input_file_name"/>
91 </when>
92
93 <when value="csstar">
94 <expand macro="input_file_name"/>
95 <expand macro="reference_database_id"/>
96 </when>
97
98 <when value="amrplusplus">
99 <expand macro="input_file_name"/>
100 </when>
101
102 <when value="resfams">
103 <expand macro="input_file_name"/>
104 </when>
105
106 <when value="groot">
107 <expand macro="input_file_name"/>
108 <expand macro="reference_database_id"/>
109 </when>
110 </conditional>
111 <param name="output_format" type="select" label="Output format" multiple="false" display="radio">
112 <option value="tsv" selected="True">tsv</option>
113 <option value="json">json</option>
114 </param>
115 <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>
117 </inputs>
118
119 <outputs>
120 <data format="tsv" name="output_tsv" label="${tool.name} on ${on_string}: Output" from_work_dir="hamronized.tsv">
121 <filter>output_format == "tsv"</filter>
122 </data>
123 <data format="json" name="output_json" label="${tool.name} on ${on_string}: Output" from_work_dir="hamronized.json">
124 <filter>output_format == "json"</filter>
125 </data>
126 </outputs>
127 <tests>
128 <!-- abricate -->
129 <test expect_num_outputs="1">
130 <param name="report" value="abricate/report.tsv" ftype="tsv" />
131 <param name="tool" value="abricate" />
132 <param name="output_format" value="tsv" />
133 <param name="reference_database_version" value="db_v_1" />
134 <param name="analysis_software_version" value="tool_v_1" />
135 <output name="output_tsv" ftype="tsv" file="hamronized_abricate.tsv" />
136 </test>
137 <test expect_num_outputs="1">
138 <param name="report" value="abricate/report.tsv" ftype="tsv" />
139 <param name="tool" value="abricate" />
140 <param name="output_format" value="json" />
141 <param name="reference_database_version" value="db_v_1" />
142 <param name="analysis_software_version" value="tool_v_1" />
143 <output name="output_json" ftype="json" file="hamronized_abricate.json" />
144 </test>
145 <!-- ariba -->
146 <test expect_num_outputs="1">
147 <param name="report" value="ariba/report.tsv" ftype="tsv" />
148 <param name="tool" value="ariba" />
149 <param name="output_format" value="tsv" />
150 <param name="reference_database_version" value="db_v_1" />
151 <param name="analysis_software_version" value="ariba_v1" />
152 <param name="input_file_name" value="ariba_report" />
153 <param name="reference_database_id" value="dbname" />
154 <output name="output_tsv" ftype="tsv" file="hamronized_ariba.tsv" />
155 </test>
156 <!-- rgi -->
157 <test expect_num_outputs="1">
158 <param name="report" value="rgi/rgi.txt" ftype="txt" />
159 <param name="tool" value="rgi" />
160 <param name="output_format" value="tsv" />
161 <param name="reference_database_version" value="card_v1" />
162 <param name="analysis_software_version" value="rgi_v1" />
163 <param name="input_file_name" value="rgi_report" />
164 <output name="output_tsv" ftype="tsv" file="hamronized_rgi.tsv" />
165 </test>
166 </tests>
167 <help><![CDATA[
168 **What it does**
169 Hamronize parse multiple Antimicrobial Resistance Analysis Reports into a common data structure
170
171 **Inputs**
172
173 ::
174
175 Tools with hAMRonizable reports:
176 {abricate,amrfinderplus,ariba,rgi,resfinder,resfinder4,srax,deeparg,kmerresistance,srst2,staramr,csstar,amrplusplus,resfams,groot}
177 abricate hAMRonize abricate's output report i.e., OUTPUT.tsv
178 amrfinderplus hAMRonize amrfinderplus's output report i.e., OUTPUT.tsv
179 ariba hAMRonize ariba's output report i.e., OUTDIR/OUTPUT.tsv
180 rgi hAMRonize rgi's output report i.e., OUTPUT.txt or OUTPUT_bwtoutput.gene_mapping_data.txt
181 resfinder hAMRonize resfinder's output report i.e., data_resfinder.json
182 resfinder4 hAMRonize resfinder4's tabular output report i.e., ResFinder_results_tab.txt
183 srax hAMRonize srax's output report i.e., sraX_detected_ARGs.tsv
184 deeparg hAMRonize deeparg's output report i.e., OUTDIR/OUTPUT.mapping.ARG
185 kmerresistance hAMRonize kmerresistance's output report i.e., OUTPUT.KmerRes
186 srst2 hAMRonize srst2's output report i.e., OUTPUT_srst2_report.tsv
187 staramr hAMRonize staramr's output report i.e., resfinder.tsv
188 csstar hAMRonize csstar's output report i.e., OUTPUT.tsv
189 amrplusplus hAMRonize amrplusplus's output report i.e., gene.tsv
190 resfams hAMRonize resfams's output report i.e., resfams.tblout
191 groot hAMRonize groot's output report i.e., OUTPUT.tsv (from `groot report`)
192
193
194
195 ::
196
197 More: https://github.com/pha4ge/hAMRonization/#usage
198
199 ]]> </help>
200 </tool>