Mercurial > repos > thanhlv > hamronization
comparison hamronize_tool.xml @ 0:5fca34360c12 draft default tip
"planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/hamronization commit f4357e288c6ab3d1abf0dd8a8b4ccee72cbf1924-dirty"
author | thanhlv |
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date | Tue, 02 Feb 2021 21:18:52 +0000 |
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-1:000000000000 | 0:5fca34360c12 |
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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 <param name="input_file_name" type="text" label="Input file name" help="A string of sample name which the tool scanned for..."></param> | |
61 </when> | |
62 | |
63 <when value="ariba"> | |
64 <param name="input_file_name" type="text" label="Input file name" help="Sample name which the tool scanned for..."></param> | |
65 <param name="reference_database_id" type="text" label="Reference database ID" help="String containing the reference_database_id for | |
66 ariba"></param> | |
67 </when> | |
68 | |
69 <when value="rgi"> | |
70 <param name="input_file_name" type="text" label="Input file name" help="Sample name which the tool scanned for..."></param> | |
71 </when> | |
72 | |
73 <when value="resfinder4"> | |
74 <param name="input_file_name" type="text" label="Input file name" help="Sample name which the tool scanned for..."></param> | |
75 </when> | |
76 | |
77 <when value="srax"> | |
78 <param name="input_file_name" type="text" label="Input file name" help="Sample name which the tool scanned for..."></param> | |
79 <param name="reference_database_id" type="text" label="Reference database ID" help="String containing the reference_database_id for | |
80 srax"></param> | |
81 </when> | |
82 | |
83 <when value="deeparg"> | |
84 <param name="input_file_name" type="text" label="Input file name" help="Sample name which the tool scanned for..."></param> | |
85 </when> | |
86 | |
87 <when value="kmerresistance"> | |
88 <param name="input_file_name" type="text" label="Input file name" help="Sample name which the tool scanned for..."></param> | |
89 </when> | |
90 | |
91 <when value="srst2"> | |
92 <param name="input_file_name" type="text" label="Input file name" help="Sample name which the tool scanned for..."></param> | |
93 </when> | |
94 | |
95 <when value="csstar"> | |
96 <param name="input_file_name" type="text" label="Input file name" help="Sample name which the tool scanned for..."></param> | |
97 <param name="reference_database_id" type="text" label="Reference database ID" help="String containing the reference_database_id for | |
98 csstar"></param> | |
99 </when> | |
100 | |
101 <when value="amrplusplus"> | |
102 <param name="input_file_name" type="text" label="Input file name" help="Sample name which the tool scanned for..."></param> | |
103 </when> | |
104 | |
105 <when value="resfams"> | |
106 <param name="input_file_name" type="text" label="Input file name" help="Sample name which the tool scanned for..."></param> | |
107 </when> | |
108 | |
109 <when value="groot"> | |
110 <param name="input_file_name" type="text" label="Input file name" help="Sample name which the tool scanned for..."></param> | |
111 <param name="reference_database_id" type="text" label="Reference database ID" help="String containing the reference_database_id for | |
112 grotm"></param> | |
113 </when> | |
114 </conditional> | |
115 <param name="output_format" type="select" label="Output format" multiple="false" display="radio"> | |
116 <option value="tsv" selected="True">tsv</option> | |
117 <option value="json">json</option> | |
118 </param> | |
119 <param name="analysis_software_version" type="text" label="Analysis software version"></param> | |
120 <param name="reference_database_version" type="text" label="Reference database version"></param> | |
121 </inputs> | |
122 | |
123 <outputs> | |
124 <data format="tsv" name="output_tsv" label="${tool.name} on ${on_string}: Output" from_work_dir="hamronized.tsv"> | |
125 <filter>output_format == "tsv"</filter> | |
126 </data> | |
127 <data format="json" name="output_json" label="${tool.name} on ${on_string}: Output" from_work_dir="hamronized.json"> | |
128 <filter>output_format == "json"</filter> | |
129 </data> | |
130 </outputs> | |
131 <tests> | |
132 <!-- abricate --> | |
133 <test expect_num_outputs="1"> | |
134 <param name="report" value="abricate/report.tsv" ftype="tsv" /> | |
135 <param name="tool" value="abricate" /> | |
136 <param name="output_format" value="tsv" /> | |
137 <param name="reference_database_version" value="db_v_1" /> | |
138 <param name="analysis_software_version" value="tool_v_1" /> | |
139 <output name="output_tsv" ftype="tsv" file="hamronized_abricate.tsv" /> | |
140 </test> | |
141 <test expect_num_outputs="1"> | |
142 <param name="report" value="abricate/report.tsv" ftype="tsv" /> | |
143 <param name="tool" value="abricate" /> | |
144 <param name="output_format" value="json" /> | |
145 <param name="reference_database_version" value="db_v_1" /> | |
146 <param name="analysis_software_version" value="tool_v_1" /> | |
147 <output name="output_json" ftype="json" file="hamronized_abricate.json" /> | |
148 </test> | |
149 <!-- ariba --> | |
150 <test expect_num_outputs="1"> | |
151 <param name="report" value="ariba/report.tsv" ftype="tsv" /> | |
152 <param name="tool" value="ariba" /> | |
153 <param name="output_format" value="tsv" /> | |
154 <param name="reference_database_version" value="db_v_1" /> | |
155 <param name="analysis_software_version" value="ariba_v1" /> | |
156 <param name="input_file_name" value="ariba_report" /> | |
157 <param name="reference_database_id" value="dbname" /> | |
158 <output name="output_tsv" ftype="tsv" file="hamronized_ariba.tsv" /> | |
159 </test> | |
160 <!-- rgi --> | |
161 <test expect_num_outputs="1"> | |
162 <param name="report" value="rgi/rgi.txt" ftype="txt" /> | |
163 <param name="tool" value="rgi" /> | |
164 <param name="output_format" value="tsv" /> | |
165 <param name="reference_database_version" value="card_v1" /> | |
166 <param name="analysis_software_version" value="rgi_v1" /> | |
167 <param name="input_file_name" value="rgi_report" /> | |
168 <output name="output_tsv" ftype="tsv" file="hamronized_rgi.tsv" /> | |
169 </test> | |
170 </tests> | |
171 <help><![CDATA[ | |
172 Hamronize parse multiple Antimicrobial Resistance Analysis Reports into a common data structure | |
173 ]]> </help> | |
174 </tool> |