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comparison hamronize_tool.xml @ 3:e13b801516dd draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b4943555d76f7e352de3f396c51d3dfb90ed633d
author iuc
date Fri, 09 Feb 2024 21:27:18 +0000
parents ec82fac4eb4b
children cbfa52c8f1ef
comparison
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2:41c7e03b3eab 3:e13b801516dd
1 <tool id="hamronize_tool" name="hamronize" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@"> 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 <expand macro="bio_tools"/>
6 <expand macro="requirements" /> 7 <expand macro="requirements" />
7 <expand macro="version_command" /> 8 <expand macro="version_command" />
8 9
9 <command detect_errors="exit_code"><![CDATA[ 10 <command detect_errors="exit_code"><![CDATA[
10 #set $extra_2_params = str("ariba,srax,csstar,groot").split(",") 11 #set $extra_2_params = str("ariba,srax,csstar,groot").split(",")
56 <when value="resfinder" /> 57 <when value="resfinder" />
57 <when value="staramr" /> 58 <when value="staramr" />
58 <when value="amrfinderplus"> 59 <when value="amrfinderplus">
59 <expand macro="input_file_name"/> 60 <expand macro="input_file_name"/>
60 </when> 61 </when>
61
62 <when value="ariba"> 62 <when value="ariba">
63 <expand macro="input_file_name"/> 63 <expand macro="input_file_name"/>
64 <expand macro="reference_database_id"/> 64 <expand macro="reference_database_id"/>
65 </when> 65 </when>
66
67 <when value="rgi"> 66 <when value="rgi">
68 <expand macro="input_file_name"/> 67 <expand macro="input_file_name"/>
69 </when> 68 </when>
70
71 <when value="resfinder4"> 69 <when value="resfinder4">
72 <expand macro="input_file_name"/> 70 <expand macro="input_file_name"/>
73 </when> 71 </when>
74
75 <when value="srax"> 72 <when value="srax">
76 <expand macro="input_file_name"/> 73 <expand macro="input_file_name"/>
77 <expand macro="reference_database_id"/> 74 <expand macro="reference_database_id"/>
78 </when> 75 </when>
79
80 <when value="deeparg"> 76 <when value="deeparg">
81 <expand macro="input_file_name"/> 77 <expand macro="input_file_name"/>
82 </when> 78 </when>
83
84 <when value="kmerresistance"> 79 <when value="kmerresistance">
85 <expand macro="input_file_name"/> 80 <expand macro="input_file_name"/>
86 </when> 81 </when>
87
88 <when value="srst2"> 82 <when value="srst2">
89 <expand macro="input_file_name"/> 83 <expand macro="input_file_name"/>
90 </when> 84 </when>
91
92 <when value="csstar"> 85 <when value="csstar">
93 <expand macro="input_file_name"/> 86 <expand macro="input_file_name"/>
94 <expand macro="reference_database_id"/> 87 <expand macro="reference_database_id"/>
95 </when> 88 </when>
96
97 <when value="amrplusplus"> 89 <when value="amrplusplus">
98 <expand macro="input_file_name"/> 90 <expand macro="input_file_name"/>
99 </when> 91 </when>
100
101 <when value="resfams"> 92 <when value="resfams">
102 <expand macro="input_file_name"/> 93 <expand macro="input_file_name"/>
103 </when> 94 </when>
104
105 <when value="groot"> 95 <when value="groot">
106 <expand macro="input_file_name"/> 96 <expand macro="input_file_name"/>
107 <expand macro="reference_database_id"/> 97 <expand macro="reference_database_id"/>
108 </when> 98 </when>
109 </conditional> 99 </conditional>
114 <param name="analysis_software_version" type="text" label="Analysis software version"></param> 104 <param name="analysis_software_version" type="text" label="Analysis software version"></param>
115 <param name="reference_database_version" type="text" label="Reference database version"></param> 105 <param name="reference_database_version" type="text" label="Reference database version"></param>
116 </inputs> 106 </inputs>
117 107
118 <outputs> 108 <outputs>
119 <data format="tabular" name="output_tsv" label="${tool.name} on ${on_string}: Output" from_work_dir="hamronized.tsv"> 109 <data format="tabular" name="output_tsv" label="${tool.name} on ${on_string}: Table" from_work_dir="hamronized.tsv">
120 <filter>output_format == "tsv"</filter> 110 <filter>output_format == "tsv"</filter>
121 </data> 111 </data>
122 <data format="json" name="output_json" label="${tool.name} on ${on_string}: Output" from_work_dir="hamronized.json"> 112 <data format="json" name="output_json" label="${tool.name} on ${on_string}: JSON" from_work_dir="hamronized.json">
123 <filter>output_format == "json"</filter> 113 <filter>output_format == "json"</filter>
124 </data> 114 </data>
125 </outputs> 115 </outputs>
126 <tests> 116 <tests>
127 <!-- abricate --> 117 <!-- abricate -->
162 <param name="input_file_name" value="rgi_report" /> 152 <param name="input_file_name" value="rgi_report" />
163 <output name="output_tsv" file="hamronized_rgi.tsv" ftype="tabular"/> 153 <output name="output_tsv" file="hamronized_rgi.tsv" ftype="tabular"/>
164 </test> 154 </test>
165 </tests> 155 </tests>
166 <help><![CDATA[ 156 <help><![CDATA[
167 **What it does** 157 **What it does**
168 Hamronize parse multiple Antimicrobial Resistance Analysis Reports into a common data structure
169 158
170 **Inputs** 159 Hamronize parse multiple Antimicrobial Resistance Analysis Reports into a common data structure
171
172 ::
173 160
174 Tools with hAMRonizable reports: 161 **Inputs**
175 {abricate,amrfinderplus,ariba,rgi,resfinder,resfinder4,srax,deeparg,kmerresistance,srst2,staramr,csstar,amrplusplus,resfams,groot}
176 abricate hAMRonize abricate's output report i.e., OUTPUT.tsv
177 amrfinderplus hAMRonize amrfinderplus's output report i.e., OUTPUT.tsv
178 ariba hAMRonize ariba's output report i.e., OUTDIR/OUTPUT.tsv
179 rgi hAMRonize rgi's output report i.e., OUTPUT.txt or OUTPUT_bwtoutput.gene_mapping_data.txt
180 resfinder hAMRonize resfinder's output report i.e., data_resfinder.json
181 resfinder4 hAMRonize resfinder4's tabular output report i.e., ResFinder_results_tab.txt
182 srax hAMRonize srax's output report i.e., sraX_detected_ARGs.tsv
183 deeparg hAMRonize deeparg's output report i.e., OUTDIR/OUTPUT.mapping.ARG
184 kmerresistance hAMRonize kmerresistance's output report i.e., OUTPUT.KmerRes
185 srst2 hAMRonize srst2's output report i.e., OUTPUT_srst2_report.tsv
186 staramr hAMRonize staramr's output report i.e., resfinder.tsv
187 csstar hAMRonize csstar's output report i.e., OUTPUT.tsv
188 amrplusplus hAMRonize amrplusplus's output report i.e., gene.tsv
189 resfams hAMRonize resfams's output report i.e., resfams.tblout
190 groot hAMRonize groot's output report i.e., OUTPUT.tsv (from `groot report`)
191
192 162
163 Depends on the tools with hAMRonizable reports:
193 164
194 :: 165 * abricate: abricate's output report i.e., OUTPUT.tsv
195 166 * amrfinderplus: amrfinderplus's output report i.e., OUTPUT.tsv
196 More: https://github.com/pha4ge/hAMRonization/#usage 167 * ariba: ariba's output report i.e., OUTDIR/OUTPUT.tsv
168 * rgi: rgi's output report i.e., OUTPUT.txt or OUTPUT_bwtoutput.gene_mapping_data.txt
169 * resfinder: resfinder's output report i.e., data_resfinder.json
170 * resfinder4: resfinder4's tabular output report i.e., ResFinder_results_tab.txt
171 * srax: srax's output report i.e., sraX_detected_ARGs.tsv
172 * deeparg: deeparg's output report i.e., OUTDIR/OUTPUT.mapping.ARG
173 * kmerresistance: kmerresistance's output report i.e., OUTPUT.KmerRes
174 * srst2: srst2's output report i.e., OUTPUT_srst2_report.tsv
175 * staramr: staramr's output report i.e., resfinder.tsv
176 * csstar: csstar's output report i.e., OUTPUT.tsv
177 * amrplusplus: amrplusplus's output report i.e., gene.tsv
178 * resfams: resfams's output report i.e., resfams.tblout
179 * groot: groot's output report i.e., OUTPUT.tsv (from `groot report`)
197 180
198 ]]> </help> 181 More: https://github.com/pha4ge/hAMRonization/#usage
182
183 ]]></help>
184 <expand macro="citations"/>
199 </tool> 185 </tool>