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planemo upload for repository https://github.com/katholt/srst2 commit 90275e51aa271edacdd9d277c441e38e99502c53
author iuc
date Mon, 28 Oct 2024 13:08:41 +0000
parents 4e0b819bf73e
children
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1:4e0b819bf73e 2:1f1738444233
2 <description>Short Read Sequence Typing for Bacterial Pathogens</description> 2 <description>Short Read Sequence Typing for Bacterial Pathogens</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 <token name="@FAST_A_Q_FORMATS@">fasta,fasta.gz,fastq,fastq.gz,fastqsanger,fastqsanger.gz</token> 5 <token name="@FAST_A_Q_FORMATS@">fasta,fasta.gz,fastq,fastq.gz,fastqsanger,fastqsanger.gz</token>
6 </macros> 6 </macros>
7 <expand macro="xrefs"/>
7 <expand macro="requirements"/> 8 <expand macro="requirements"/>
8 <version_command>srst2 --version</version_command> 9 <version_command>srst2 --version</version_command>
9 <command detect_errors="exit_code"><![CDATA[ 10 <command detect_errors="exit_code"><![CDATA[
10 #if $input.selector == "single" 11 #if $input.selector == "single"
11 #set ext=$input.single_input.datatype.file_ext 12 #set ext=$input.single_input.datatype.file_ext
100 #end if 101 #end if
101 ## |true here is added in order not to search for a file that is not produced at all, such that if the user provided no gene/MLST databases or there are no outputs found, the tool will run successfully and only notify the user that no outputs are found 102 ## |true here is added in order not to search for a file that is not produced at all, such that if the user provided no gene/MLST databases or there are no outputs found, the tool will run successfully and only notify the user that no outputs are found
102 #if 'report_new_consensus' in str($output_files_selector) and $use_gene_db.selector == "yes" and $use_mlst_db.selector == "yes" 103 #if 'report_new_consensus' in str($output_files_selector) and $use_gene_db.selector == "yes" and $use_mlst_db.selector == "yes"
103 && mkdir -p allelesOutput/ && cp *.output__input.*.pileup allelesOutput | true 104 && mkdir -p allelesOutput/ && cp *.output__input.*.pileup allelesOutput | true
104 #end if 105 #end if
106
105 #if $use_gene_db.selector == "yes" and $use_gene_db.no_gene_details 107 #if $use_gene_db.selector == "yes" and $use_gene_db.no_gene_details
106 && mkdir -p geneTypingOutput/ && cp output__genes__*__results.txt geneTypingOutput | true && cp output__fullgenes__*__results.txt geneTypingOutput | true 108 && mkdir -p geneTypingOutput/ geneTypingOutputFull/ && cp output__genes__*__results.txt geneTypingOutput | true && cp output__fullgenes__*__results.txt geneTypingOutputFull | true
107 #end if 109 #end if
110
108 #if 'save_scores' in str($output_files_selector) 111 #if 'save_scores' in str($output_files_selector)
109 && mkdir -p scoresOutput/ && cp *.scores scoresOutput | true 112 && mkdir -p scoresOutput/ && cp *.scores scoresOutput | true
110 #end if 113 #end if
111 #if $input.selector == "single" or $input.selector == "paired" 114 #if $input.selector == "single" or $input.selector == "paired"
112 && mkdir -p bowtie2Alignments/ && cp *.sorted.bam bowtie2Alignments | true 115 && mkdir -p bowtie2Alignments/ && cp *.sorted.bam bowtie2Alignments | true
151 <add value="=" /> 154 <add value="=" />
152 <add value=" " /> 155 <add value=" " />
153 <add value="_" /> 156 <add value="_" />
154 </valid> 157 </valid>
155 </sanitizer> 158 </sanitizer>
156 <validator type="regex">[A-Za-z0-9 =-_/+]+</validator> 159 <validator type="regex">[A-Za-z0-9 =_/+-]+</validator>
157 </param> 160 </param>
158 <param argument="--mlst_max_mismatch" type="integer" value="10" label="Maximum number of mismatches per read for MLST allele calling"/> 161 <param argument="--mlst_max_mismatch" type="integer" value="10" label="Maximum number of mismatches per read for MLST allele calling"/>
159 <param argument="--min_depth" type="integer" value="5" label="Minimum mean depth to flag as dubious allele call"/> 162 <param argument="--min_depth" type="integer" value="5" label="Minimum mean depth to flag as dubious allele call"/>
160 <param argument="--min_edge_depth" type="integer" value="2" label="Minimum edge depth to flag as dubious allele call"/> 163 <param argument="--min_edge_depth" type="integer" value="2" label="Minimum edge depth to flag as dubious allele call"/>
161 </when> 164 </when>
195 <outputs> 198 <outputs>
196 <data name="mlst_results" format="tabular" from_work_dir="output__mlst__mlst_db__results.txt" label="${tool.name} on ${on_string}: MLST Results"> 199 <data name="mlst_results" format="tabular" from_work_dir="output__mlst__mlst_db__results.txt" label="${tool.name} on ${on_string}: MLST Results">
197 <filter>use_mlst_db['selector'] == "yes"</filter> 200 <filter>use_mlst_db['selector'] == "yes"</filter>
198 </data> 201 </data>
199 <collection name="gene_typing" type="list" label="${tool.name} on ${on_string}: Gene typing results files" > 202 <collection name="gene_typing" type="list" label="${tool.name} on ${on_string}: Gene typing results files" >
200 <discover_datasets pattern="(?P&lt;designation&gt;.+)" directory="geneTypingOutput" format="txt,tabular"/> 203 <discover_datasets pattern="(?P&lt;designation&gt;.+)" directory="geneTypingOutput" format="tabular"/>
204 <filter>use_gene_db['selector'] == "yes" and use_gene_db['no_gene_details'] is True</filter>
205 </collection>
206 <collection name="gene_typing_full" type="list" label="${tool.name} on ${on_string}: Full Gene typing results files" >
207 <discover_datasets pattern="(?P&lt;designation&gt;.+)" directory="geneTypingOutputFull" format="tabular"/>
201 <filter>use_gene_db['selector'] == "yes" and use_gene_db['no_gene_details'] is True</filter> 208 <filter>use_gene_db['selector'] == "yes" and use_gene_db['no_gene_details'] is True</filter>
202 </collection> 209 </collection>
203 <data name="Compiled_gene_and_mlst_output" format="tabular" from_work_dir="output__compiledResults.txt" label="${tool.name} on ${on_string}: Compiled MLST and Gene databases Results"> 210 <data name="Compiled_gene_and_mlst_output" format="tabular" from_work_dir="output__compiledResults.txt" label="${tool.name} on ${on_string}: Compiled MLST and Gene databases Results">
204 </data> 211 </data>
205 <data name="all_consensus" format="fasta" from_work_dir="output.all_consensus_alleles.fasta" label="${tool.name} on ${on_string}: All consensus Results"> 212 <data name="all_consensus" format="fasta" from_work_dir="output.all_consensus_alleles.fasta" label="${tool.name} on ${on_string}: All consensus Results">
224 <data name="log_output" format="tabular" from_work_dir="output.log" label="${tool.name} on ${on_string}: Log file"> 231 <data name="log_output" format="tabular" from_work_dir="output.log" label="${tool.name} on ${on_string}: Log file">
225 <filter>"log" in output_files_selector</filter> 232 <filter>"log" in output_files_selector</filter>
226 </data> 233 </data>
227 </outputs> 234 </outputs>
228 <tests> 235 <tests>
229 <test expect_num_outputs="9"> 236 <test expect_num_outputs="10">
230 <param name="prob_err" value="0.01"/> 237 <param name="prob_err" value="0.01"/>
231 <param name="max_unaligned_overlap" value="10"/> 238 <param name="max_unaligned_overlap" value="10"/>
232 <param name="mapq" value="1"/> 239 <param name="mapq" value="1"/>
233 <param name="baseq" value="20"/> 240 <param name="baseq" value="20"/>
234 <param name="output_files_selector" value="log,save_scores,report_new_consensus,report_all_consensus"/> 241 <param name="output_files_selector" value="log,save_scores,report_new_consensus,report_all_consensus"/>
261 <has_text text="fumC"/> 268 <has_text text="fumC"/>
262 <has_n_lines n="2"/> 269 <has_n_lines n="2"/>
263 </assert_contents> 270 </assert_contents>
264 </output> 271 </output>
265 <output_collection name="gene_typing" type="list"> 272 <output_collection name="gene_typing" type="list">
266 <element name="output__fullgenes__0-gene_db__results.txt"> 273 <element name="output__genes__0-gene_db__results.txt">
267 <assert_contents> 274 <assert_contents>
268 <has_text text="AmpC1_Ecoli_Bla"/> 275 <has_text text="AmpC1_Ecoli_Bla"/>
269 <has_n_lines n="2"/> 276 <has_n_lines n="2"/>
270 </assert_contents> 277 </assert_contents>
271 </element> 278 </element>
272 <element name="output__genes__0-gene_db__results.txt"> 279 </output_collection>
280 <output_collection name="gene_typing_full" type="list">
281 <element name="output__fullgenes__0-gene_db__results.txt">
273 <assert_contents> 282 <assert_contents>
274 <has_text text="AmpC1_Ecoli_Bla"/> 283 <has_text text="AmpC1_Ecoli_Bla"/>
275 <has_n_lines n="2"/> 284 <has_n_lines n="2"/>
276 </assert_contents> 285 </assert_contents>
277 </element> 286 </element>
286 <assert_contents> 295 <assert_contents>
287 <has_text text="49__AmpC1_Ecoli_Bla__AmpC1__1670"/> 296 <has_text text="49__AmpC1_Ecoli_Bla__AmpC1__1670"/>
288 <has_n_lines n="2"/> 297 <has_n_lines n="2"/>
289 </assert_contents> 298 </assert_contents>
290 </output> 299 </output>
291 <output_collection name="new_consensus" type="list"> 300 <output_collection name="new_consensus" type="list" count="1">
292 <element name="49__AmpC1_Ecoli_Bla__AmpC1__1670.output__input.0-gene_db.pileup"> 301 <element name="49__AmpC1_Ecoli_Bla__AmpC1__1670.output__input.0-gene_db.pileup">
293 <assert_contents> 302 <assert_contents>
294 <has_text text="49__AmpC1_Ecoli_Bla__AmpC1__1670"/> 303 <has_text text="49__AmpC1_Ecoli_Bla__AmpC1__1670"/>
295 <has_n_lines n="1196"/> 304 <has_n_lines n="1196"/>
296 </assert_contents> 305 </assert_contents>
297 </element> 306 </element>
298 </output_collection> 307 </output_collection>
299 <output_collection name="samtools_pileup_alignment" type="list"> 308 <output_collection name="samtools_pileup_alignment" type="list" count="1">
300 <element name="output__input.0-gene_db.pileup"> 309 <element name="output__input.0-gene_db.pileup">
301 <assert_contents> 310 <assert_contents>
302 <has_text text="49__AmpC1_Ecoli_Bla__AmpC1__1670"/> 311 <has_text text="49__AmpC1_Ecoli_Bla__AmpC1__1670"/>
303 <has_n_lines n="1196"/> 312 <has_n_lines n="1196"/>
304 </assert_contents> 313 </assert_contents>
305 </element> 314 </element>
306 </output_collection> 315 </output_collection>
307 <output_collection name="bowtie2_alignment_output" type="list"> 316 <output_collection name="bowtie2_alignment_output" type="list" count="1">
308 <element name="output__input.0-gene_db.sorted.bam"> 317 <element name="output__input.0-gene_db.sorted.bam">
309 <assert_contents> 318 <assert_contents>
310 <has_size value="18500" delta="1000"/> 319 <has_size value="18500" delta="1000"/>
311 </assert_contents> 320 </assert_contents>
312 </element> 321 </element>
345 <output name="all_consensus"> 354 <output name="all_consensus">
346 <assert_contents> 355 <assert_contents>
347 <has_size value="0" delta="0"/> 356 <has_size value="0" delta="0"/>
348 </assert_contents> 357 </assert_contents>
349 </output> 358 </output>
350 <output_collection name="new_consensus" type="list"> 359 <output_collection name="new_consensus" type="list" count="0"/>
351 </output_collection> 360 <output_collection name="samtools_pileup_alignment" type="list" count="0"/>
352 <output_collection name="samtools_pileup_alignment" type="list"> 361 <output_collection name="bowtie2_alignment_output" type="list" count="0"/>
353 </output_collection> 362 <output_collection name="scores_ofEachAllele" type="list" count="0"/>
354 <output_collection name="bowtie2_alignment_output" type="list">
355 </output_collection>
356 <output_collection name="scores_ofEachAllele" type="list">
357 </output_collection>
358 <output name="log_output"> 363 <output name="log_output">
359 <assert_contents> 364 <assert_contents>
360 <has_text text="Total paired readsets found:1"/> 365 <has_text text="Total paired readsets found:1"/>
361 <has_n_lines n="4"/> 366 <has_n_lines n="4"/>
362 </assert_contents> 367 </assert_contents>