Mercurial > repos > iuc > hamronize_tool
comparison hamronize_tool.xml @ 3:e13b801516dd draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b4943555d76f7e352de3f396c51d3dfb90ed633d
author | iuc |
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date | Fri, 09 Feb 2024 21:27:18 +0000 |
parents | ec82fac4eb4b |
children | cbfa52c8f1ef |
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2:41c7e03b3eab | 3:e13b801516dd |
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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> |