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comparison abromics_galaxy_json_extractor.xml @ 0:c49ec8c0b046 draft

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planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty
author pimarin
date Sun, 04 Jun 2023 17:16:20 +0000
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1 <tool id="abromics_galaxy_json_extractor" name="abromics_galaxy_json_extractor" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>
3 Result extractor to json format
4 </description>
5 <macros>
6 <import>macro.xml</import>
7 </macros>
8 <expand macro='edam'/>
9 <expand macro="requirements"/>
10 <expand macro="version_command"/>
11
12 <command detect_errors="aggressive"><![CDATA[
13 mkdir "abromics_extracted_folder" &&
14 #*=================================================================
15 Paramaters to add Database and tool version if available
16 =================================================================*#
17 #set $software_with_database = str("abricate,bakta,bracken,kraken2,plasmidfinder,recentrifuge").split(",")
18 #set $counter = len($tool_section.tools)-1
19 #*======================================================
20 Loop to include some different tool in one time
21 ======================================================*#
22 #for $i, $tool in enumerate( $tool_section.tools )
23 abromics_extract
24 "$tool.select_tool.tool_list"
25 --hid $tool.select_tool.input.hid
26 "$tool.select_tool.input"
27 --analysis_software_version "$tool.select_tool.analysis_software_version"
28 #if str($tool.select_tool.tool_list) in str($software_with_database)
29 --reference_database_version "$tool.select_tool.reference_database_version"
30 #end if
31 #if "$tool.select_tool.tool_list" == "bakta"
32 --summary_result_path "$tool.select_tool.summary_result_path"
33 --nucleotide_annotation_path "$tool.select_tool.nucleotide_annotation_path"
34 --amino_acid_annotation_path "$tool.select_tool.amino_acid_annotation_path"
35 --gff_file_path "$tool.select_tool.gff_file_path"
36 #elif "$tool.select_tool.tool_list" == "bracken"
37 --kraken_report_path "tool.select_tool.kraken_report_path"
38 --threshold "tool.select_tool.threshold"
39 --read_length "tool.select_tool.read_length"
40 --level "tool.select_tool.level"
41 #elif"$tool.select_tool.tool_list" == "integronfinder2"
42 --summary_file_path "tool.select_tool.summary_file_path"
43 #elif "$tool.select_tool.tool_list" == "isescan"
44 --orf_fna_file "tool.select_tool.orf_fna_file"
45 --orf_faa_file "tool.select_tool.orf_faa_file"
46 --is_fna_file "tool.select_tool.is_fna_file"
47 #elif "$tool.select_tool.tool_list" == "kraken2"
48 --seq_classification_file_path "tool.select_tool.seq_classification_file_path"
49 #elif "$tool.select_tool.tool_list" == "plasmidfinder"
50 --genome_hit_file_path "tool.select_tool.genome_hit_file_path"
51 --plasmid_sequence_file_path "tool.select_tool.plasmid_sequence_file_path"
52 #elif "$tool.select_tool.tool_list" == "recentrifuge"
53 --rcf_stat_file_path "tool.select_tool.rcf_stat_file_path"
54 --rcf_html_path "tool.select_tool.rcf_html_path"
55 #elif "$tool.select_tool.tool_list" == "shovill"
56 --contig_graph_path "tool.select_tool.contig_graph_path"
57 --bam_file_path "tool.select_tool.bam_file_path"
58 #elif "$tool.select_tool.tool_list" == "staramr"
59 --mlst_file_path "tool.select_tool.mlst_file_path"
60 --plasmidfinder_file_path "tool.select_tool.plasmidfinder_file_path"
61 --pointfinder_file_path "tool.select_tool.pointfinder_file_path"
62 --setting_file_path "tool.select_tool.setting_file_path"
63 #elif "$tool.select_tool.tool_list" == "tabular_file"
64 --analysis_software_name "tool.select_tool.analysis_software_name"
65 #end if
66 -o "abromics_extracted_folder/$($tool.select_tool.tool_list)_$(i)_output.json"
67 | tee "$logfile"
68 #if $i < $counter
69 &&
70 #end if
71 #end for
72
73 ]]>
74 </command>
75 <inputs>
76 <section name="tool_section" title="Available tools" expanded="true">
77 <repeat name="tools" title="Tool" min="0">
78 <conditional name="select_tool">
79 <param name="tool_list" type="select" label="Available tools">
80 <option value="abricate">abricate</option>
81 <option value="bakta">bakta</option>
82 <option value="bandage">bandage</option>
83 <option value="bracken">bracken</option>
84 <option value="fastp">fastp</option>
85 <option value="integronfinder2">integronfinder2</option>
86 <option value="isescan">isescan</option>
87 <option value="kraken2">kraken2</option>
88 <option value="plasmidfinder">plasmidfinder</option>
89 <option value="quast">quast</option>
90 <option value="recentrifuge">recentrifuge</option>
91 <option value="refseqmasher">refseqmasher</option>
92 <option value="shovill">shovill</option>
93 <option value="staramr">staramr</option>
94 <option value="tabular_file">tabular_generic_file</option>
95 </param>
96 <when value="abricate">
97 <param name="input" type="data" format="tabular" multiple="false" label="Abricate report file" help="Tabular file from abricate output"/>
98 <expand macro="analysis_software_version"/>
99 <expand macro="reference_database_version"/>
100 </when>
101 <when value="bakta">
102 <param name="input" type="data" format="json" multiple="false" label="Bakta report file" help="Json file from bakta output"/>
103 <param argument="--summary_result_path" type="data" format="txt" multiple="false" optional="true" label="Bakta summary file" help="Summary file from bakta output"/>
104 <param argument="--nucleotide_annotation_path" type="data" format="fasta" multiple="false" optional="true" label="Bakta nucleotide file" help="Nucleotide sequence annotation file"/>
105 <param argument="--amino_acid_annotation_path" type="data" format="fasta" multiple="false" optional="true" label="Bakta amino acide file" help="Amino acid sequence annotation file"/>
106 <param argument="--gff_file_path" type="data" format="gff3" multiple="false" optional="true" label="Bakta annotation file" help="Annotation file"/>
107 <expand macro="analysis_software_version"/>
108 <expand macro="reference_database_version"/>
109 </when>
110 <when value="bandage">
111 <param name="input" type="data" format="txt,tabular" multiple="false" label="Bandage report file" help="Tabular file from bandage output"/>
112 <expand macro="analysis_software_version"/>
113 </when>
114 <when value="bracken">
115 <param name="input" type="data" format="txt,tabular" multiple="false" label="Bracken report file" help="Tabular file from bracken output"/>
116 <expand macro="analysis_software_version"/>
117 <expand macro="reference_database_version"/>
118 <param argument="--kraken_report_path" type="data" format="txt,tabular" multiple="false" label="Kraken re-estimated report" help="New kraken report from bracken tool"/>
119 <param argument="--threshold" type="integer" min="0" optional="true" label="PRIOR on read numbers" help="Prior of read for estimation, default is 0"/>
120 <param argument="--read_length" type="integer" min="0" optional="true" label="Read length"/>
121 <param argument="--level" type="select" label="Taxonomic level estimation" help="Level of final abundance (from Domain to subspecies, default on species)">
122 <option value="D">Domain</option>
123 <option value="P">Phylum</option>
124 <option value="C">Class</option>
125 <option value="O">Order</option>
126 <option value="F">Family</option>
127 <option value="G">Genus</option>
128 <option value="S">Species</option>
129 <option value="S+">Subspecies</option>
130 </param>
131 </when>
132 <when value="fastp">
133 <param name="input" type="data" format="json" multiple="false" label="Fastp report file" help="Fastp result in json format"/>
134 <expand macro="analysis_software_version"/>
135 </when>
136 <when value="integronfinder2">
137 <param name="input" type="data" format="txt,tabular" multiple="false" label="Integronfinder report" help="Integron file from integronfinder2"/>
138 <param argument="--summary_file_path" type="data" format="txt,tabular" multiple="false" label="Summary report" help="Summary file from integronfinder2"/>
139 <expand macro="analysis_software_version"/>
140 </when>
141 <when value="isescan">
142 <param name="input" type="data" format="txt,tabular" multiple="false" label="Isescan report" help="IseScan file from integronfinder2"/>
143 <param argument="--orf_fna_file" type="data" format="fasta" optional="true" multiple="false" label="ORF fna file" help="Nuleotide sequence to the ORFs"/>
144 <param argument="--orf_faa_file" type="data" format="fasta" optional="true" multiple="false" label="ORF faa file" help="Amino acid sequence to the ORFs"/>
145 <param argument="--is_fna_file" type="data" format="fasta" optional="true" multiple="false" label="IS fna file" help="Nuleotide sequence to the inserted elements"/>
146 <expand macro="analysis_software_version"/>
147 </when>
148 <when value="kraken2">
149 <param name="input" type="data" format="txt,tabular" multiple="false" label="kraken report" help="Taxonomic assignation file from kraken2"/>
150 <param argument="--seq_classification_file_path" type="data" format="txt,tabular" optional="true" multiple="false" label="Sequence assignation" help="Reads assignation file"/>
151 <expand macro="analysis_software_version"/>
152 <expand macro="reference_database_version"/>
153 </when>
154 <when value="plasmidfinder">
155 <param name="input" type="data" format="json" multiple="false" label="Json report" help="Plasmidfinder result from json file"/>
156 <param argument="--genome_hit_file_path" type="data" format="fasta" optional="true" multiple="false" label="Genome hits" help="Sequence hit in the analyzed genome"/>
157 <param argument="--plasmid_sequence_file_path" type="data" format="fasta" optional="true" multiple="false" label="Plasmid hits" help="Plasmid sequence identified"/>
158 <expand macro="analysis_software_version"/>
159 <expand macro="reference_database_version"/>
160 </when>
161 <when value="quast">
162 <param name="input" type="data" format="txt,tabular" multiple="false" label="Quast report" help="Tabular Quast report"/>
163 <expand macro="analysis_software_version"/>
164 </when>
165 <when value="recentrifuge">
166 <param name="input" type="data" format="txt,tabular" multiple="false" label="Recentrifuge data file"/>
167 <param argument="--rcf_stat_file_path" type="data" format="txt,tabular" optional="true" multiple="false" label="Recentrifuge stat file"/>
168 <param argument="--rcf_html_path" type="data" format="html" optional="true" multiple="false" label="Recentrifuge html report file"/>
169 <expand macro="analysis_software_version"/>
170 <expand macro="reference_database_version"/>
171 </when>
172 <when value="refseqmasher">
173 <param name="input" type="data" format="txt,tabular" multiple="false" label="RefsesMasher results"/>
174 <expand macro="analysis_software_version"/>
175 </when>
176 <when value="shovill">
177 <param name="input" type="data" format="fasta" multiple="false" label="Contigs file" help="Contig fasta file from assembly"/>
178 <param argument="--contig_graph_path" type="data" format="txt" optional="true" multiple="false" label="Contig graph file" help="Graphic file assembly"/>
179 <param argument="--bam_file_path" type="data" format="bam" optional="true" multiple="false" label="Bam file" help="Alignemnt file in bam format"/>
180 <expand macro="analysis_software_version"/>
181
182 </when>
183 <when value="staramr">
184 <param name="input" type="data" format="txt,tabular" multiple="false" label="Resfinder report" help="Resfinder result from starAMR"/>
185 <param argument="--mlst_file_path" type="data" format="txt,tabular" optional="true" multiple="false" label="MLST results" help="mlst scheme file result from starAMR"/>
186 <param argument="--plasmidfinder_file_path" type="data" optional="true" format="txt,tabular" multiple="false" label="Plasmid results" help="Plasmidfinder result from starAMR"/>
187 <param argument="--pointfinder_file_path" type="data" optional="true" format="txt,tabular" multiple="false" label="Pointfinder results" help="PointFinder result from starAMR"/>
188 <param argument="--setting_file_path" type="data" optional="true" format="txt,tabular" multiple="false" label="Setting informations" help="Settings file from starAMR"/>
189 <expand macro="analysis_software_version"/>
190 </when>
191 <when value="tabular_file">
192 <param name="input" type="data" format="txt,tabular" multiple="false" label="Tabular file type" help="Generic result file in tabular format with header"/>
193 <param argument="--analysis_software_name" type="text" multiple="false" label="Tool name" help="Tool name which generated the result file"/>
194 <expand macro="analysis_software_version"/>
195 </when>
196 </conditional>
197 </repeat>
198 </section>
199 <param name="log" type="boolean" truevalue="true" falsevalue="" label="Add log" help="Activate/Deactivate the log"/>
200 </inputs>
201 <outputs>
202 <collection name="output_json" type="list" label="${tool.name} on ${on_string}: abromics formated json results">
203 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.json" format="json" directory="abromics_extracted_folder" />
204 </collection>
205 <data name="logfile" format="txt" label="${tool.name} on ${on_string}: log file">
206 <filter> log == True </filter>
207 </data>
208 </outputs>
209 <tests>
210 <test expect_num_outputs="2"> <!-- TEST_1 abricate with logfile -->
211 <section name="tool_section">
212 <repeat name="tools">
213 <conditional name="select_tool">
214 <param name="tool_list" value="abricate"/>
215 <param name="input" value="abricate/report.tsv" ftype="tabular"/>
216 <param name="analysis_software_version" value="1.0"/>
217 <param name="reference_database_version" value="2.0" />
218 </conditional>
219 </repeat>
220 </section>
221 <param name="log" value="true"/>
222 <output_collection name="output_json" type="list">
223 <expand macro="element_assert" name="abricate_0_output" text="Enterococcus faecalis V583"/>
224 </output_collection>
225 <output name="logfile" value="abricate_logfile.txt"/>
226 </test>
227 <test expect_num_outputs="1"> <!-- TEST_2 bakta all files -->
228 <section name="tool_section">
229 <repeat name="tools">
230 <conditional name="select_tool">
231 <param name="tool_list" value="bakta"/>
232 <param name="input" value="bakta/bakta.json" ftype="json"/>
233 <param name="summary_result_path" value="bakta/bakta_summary.txt" ftype="txt"/>
234 <param name="nucleotide_annotation_path" value="bakta/bakta_nucleotide.fasta" ftype="fasta"/>
235 <param name="amino_acid_annotation_path" value="bakta/bakta_aminoacid.faa" ftype="fasta"/>
236 <param name="gff_file_path" value="bakta/bakta_annotation.gff3" ftype="gff3"/>
237 <param name="reference_database_version" value="1.6.1"/>
238 </conditional>
239 </repeat>
240 </section>
241 <output_collection name="output_json" type="list" count="1">
242 <expand macro="element_assert" name="bakta_0_output" text="UniRef50_A0A0H2ZNL3"/>
243 </output_collection>
244 </test>
245 <test expect_num_outputs="1"> <!-- TEST_3 All tool in repeat -->
246 <section name="tool_section">
247 <repeat name="tools">
248 <conditional name="select_tool">
249 <param name="tool_list" value="abricate"/>
250 <param name="input" value="abricate/report.tsv" ftype="tabular"/>
251 <param name="analysis_software_version" value="1.0"/>
252 <param name="reference_database_version" value="2.0" />
253 </conditional>
254 </repeat>
255 <repeat name="tools">
256 <conditional name="select_tool">
257 <param name="tool_list" value="bakta"/>
258 <param name="input" value="bakta/bakta.json" ftype="json"/>
259 </conditional>
260 </repeat>
261 <repeat name="tools">
262 <conditional name="select_tool">
263 <param name="tool_list" value="bandage"/>
264 <param name="input" value="bandage/bandage_info.txt" ftype="txt"/>
265 </conditional>
266 </repeat>
267 <repeat name="tools">
268 <conditional name="select_tool">
269 <param name="tool_list" value="bracken"/>
270 <param name="input" value="bracken/bracken_report.tsv" ftype="tabular"/>
271 <param name="bracken/bracken_kraken_report" ftype="tabular" />
272 <param name="threshold" value="0" />
273 <param name="read_length" value="100"/>
274 <param name="level" value="S"/>
275 </conditional>
276 </repeat>
277 <repeat name="tools">
278 <conditional name="select_tool">
279 <param name="tool_list" value="fastp"/>
280 <param name="input" value="fastp/fastp_report.json" ftype="json"/>
281 </conditional>
282 </repeat>
283 <repeat name="tools">
284 <conditional name="select_tool">
285 <param name="tool_list" value="integronfinder2"/>
286 <param name="input" value="integronfinder2/results.integrons" ftype="tabular"/>
287 <param name="summary_file_path" value="integronfinder2/results.summary" ftype="tabular"/>
288 </conditional>
289 </repeat>
290 <repeat name="tools">
291 <conditional name="select_tool">
292 <param name="tool_list" value="isescan"/>
293 <param name="input" value="isescan/results.tsv" ftype="tabular"/>
294 <param name="orf_fna_file" value="isescan/orf.fna" ftype="fasta"/>
295 <param name="orf_faa_file" value="isescan/orf.faa" ftype="fasta"/>
296 <param name="is_fna_file" value="isescan/is.fna" ftype="fasta"/>
297 </conditional>
298 </repeat>
299 <repeat name="tools">
300 <conditional name="select_tool">
301 <param name="tool_list" value="kraken2"/>
302 <param name="input" value="kraken2/taxonomy_report.tsv" ftype="tabular"/>
303 <param name="seq_classification_file_path" value="kraken2/taxonomy_result.tsv" ftype="tabular"/>
304 </conditional>
305 </repeat>
306 <repeat name="tools">
307 <conditional name="select_tool">
308 <param name="tool_list" value="plasmidfinder"/>
309 <param name="input" value="plasmidfinder/plasmidfinder_result.json" ftype="json"/>
310 <param name="genome_hit_file_path" value="plasmidfinder/genome_hit.fasta" ftype="fasta"/>
311 <param name="plasmid_sequence_file_path" value="plasmidfinder/plasmid_hit.fasta" ftype="fasta"/>
312 </conditional>
313 </repeat>
314 <repeat name="tools">
315 <conditional name="select_tool">
316 <param name="tool_list" value="quast"/>
317 <param name="input" value="quast/quast_result.tsv" ftype="tabular"/>
318 </conditional>
319 </repeat>
320 <repeat name="tools">
321 <conditional name="select_tool">
322 <param name="tool_list" value="recentrifuge"/>
323 <param name="input" value="recentrifuge/rcf_data.tsv" ftype="tabular"/>
324 <param name="rcf_stat_file_path" value="recentrifuge/rcf_stat.tsv" ftype="tabular"/>
325 <param name="rcf_html_path" value="recentrifuge/rcf_report.html"/>
326 </conditional>
327 </repeat>
328 <repeat name="tools">
329 <conditional name="select_tool">
330 <param name="tool_list" value="refseqmasher"/>
331 <param name="input" value="refseqmasher/refsesqmasher.tsv" ftype="tabular"/>
332 </conditional>
333 </repeat>
334 <repeat name="tools">
335 <conditional name="select_tool">
336 <param name="tool_list" value="shovill"/>
337 <param name="input" value="shovill/contigs.fa" ftype="fasta"/>
338 <param name="contig_graph_path" value="shovill/contigs.gfa" ftype="txt"/>
339 <param name="bam_file_path" value="shovill/alignment.bam" ftype="bam"/>
340 </conditional>
341 </repeat>
342 <repeat name="tools">
343 <conditional name="select_tool">
344 <param name="tool_list" value="staramr"/>
345 <param name="input" value="staramr/resfinder.tsv" ftype="tabular"/>
346 <param name="mlst_file_path" value="staramr/mlst.tsv" ftype="tabular"/>
347 <param name="plasmidfinder_file_path" value="staramr/plasmidfinder.tsv" ftype="tabular"/>
348 <param name="pointfinder_file_path" value="staramr/pointfinder.tsv" ftype="tabular"/>
349 <param name="setting_file_path" value="staramr/settings.txt" ftype="tabular"/>
350 </conditional>
351 </repeat>
352 <repeat name="tools">
353 <conditional name="select_tool">
354 <param name="tool_list" value="tabular_file"/>
355 <param name="input" value="tabular_file/report.tsv" ftype="tabular"/>
356 </conditional>
357 </repeat>
358 </section>
359 <output_collection name="output_json" type="list" count="15">
360 <expand macro="element_assert" name="abricate_0_output" text="Enterococcus faecalis V583"/>
361 <expand macro="element_assert" name="bakta_1_output" text="UniRef50_A0A0H2ZNL3"/>
362 <expand macro="element_assert" name="bandage_2_output" text="3042326"/>
363 <expand macro="element_assert" name="bracken_3_output" text="Staphylococcus_aureus"/>
364 <expand macro="element_assert" name="fastp_4_output" text="705053822"/>
365 <expand macro="element_assert" name="integronfinder2_5_output" text="2353.0"/>
366 <expand macro="element_assert" name="isescan_6_output" text="IS200/IS605"/>
367 <expand macro="element_assert" name="kraken2_7_output" text="Enterococcus_faecalis_ATCC_29212"/>
368 <expand macro="element_assert" name="plasmidfinder_8_output" text="repUS40_1_repB"/>
369 <expand macro="element_assert" name="quast_9_output" text="2944723"/>
370 <expand macro="element_assert" name="recentrifuge_10_output" text="6.4917947578"/>
371 <expand macro="element_assert" name="refseqmasher_11_output" text="GCF_000519925.1"/>
372 <expand macro="element_assert" name="shovill_12_output" text="436224"/>
373 <expand macro="element_assert" name="staramr_13_output" text="10_Enterococcus_faecalis_S17_L001"/>
374 <expand macro="element_assert" name="tabular_file_14_output" text="NP_814691"/>
375 </output_collection>
376 </test>
377 </tests>
378 <help><![CDATA[**What it does**
379 ** Tool input**
380 abromics_galaxy_json_extractor can use several input type from at least 14 different tools :
381 | Tools | Version | Default input file| Optional files |
382 | -: | :-: | :- | :- |
383 | Abricate | 1.0.1 | output.tsv | |
384 | Bakta | 1.7.0 | output.json | protein.faa, nucleotide.fna, annotation.gff3, summary.txt |
385 | Bandage | 0.8.1 | info.txt | |
386 | Bracken | 2.8 | output.tsv | taxonomy.tsv |
387 | Fastp | 0.23.2 | output.json | |
388 | Integronfinder2| 2.0.2 | output.integrons | output.summary |
389 | ISEScan | 1.7.2.3 | output.tsv | is.fna, orf.faa, orf.fna |
390 | Kraken2 | 2.1.2 | taxonomy.tsv | reads_assignation.txt |
391 | Plasmidfinder | 2.1.6 | output.json | genome_hits.fasta, plasmid_hits.fasta |
392 | Quast | 5.2.0 | output.tsv | |
393 | Recentrifuge | 1.10.0 | data.tsv | report.html, stat.tsv |
394 | Refseqmasher | 0.1.2 | output.tsv | |
395 | Shovill | 1.1.0 | contigs.fasta | alignment.bam, contigs.gfa |
396 | Staramr | 0.9.1 | resfinder.tsv | mlst.tsv, pointfinder.tsv, plasmidfinder.tsv, settings.tsv |
397 | tabular_file | 0 | output.tsv | no optional files |
398
399 ** Options **
400 You can add a tool version and a database version for related tools.
401 For some tools you can add optional files previously produced by the tool
402 ]]></help>
403 <expand macro="citations"/>
404 </tool>