Mercurial > repos > iuc > hamronize_tool
comparison hamronize_tool.xml @ 0:d2590ecc4189 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
author | iuc |
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date | Tue, 16 Mar 2021 12:38:42 +0000 |
parents | |
children | ec82fac4eb4b |
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-1:000000000000 | 0:d2590ecc4189 |
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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> |