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comparison srst2.xml @ 3:f995ba9f1caa draft default tip

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planemo upload for repository https://github.com/katholt/srst2 commit 90275e51aa271edacdd9d277c441e38e99502c53
author iuc
date Mon, 28 Oct 2024 13:08:53 +0000
parents 81cea47ec685
children
comparison
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2:81cea47ec685 3:f995ba9f1caa
101 #end if 101 #end if
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 ## |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
103 #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"
104 && mkdir -p allelesOutput/ && cp *.output__input.*.pileup allelesOutput | true 104 && mkdir -p allelesOutput/ && cp *.output__input.*.pileup allelesOutput | true
105 #end if 105 #end if
106
106 #if $use_gene_db.selector == "yes" and $use_gene_db.no_gene_details 107 #if $use_gene_db.selector == "yes" and $use_gene_db.no_gene_details
107 && mkdir -p geneTypingOutput/ && cp output__genes__*__results.txt geneTypingOutput | true && cp output__fullgenes__*__results.txt geneTypingOutput | true 108 && mkdir -p geneTypingOutput/ geneTypingOutputFull/ && cp output__genes__*__results.txt geneTypingOutput | true && cp output__fullgenes__*__results.txt geneTypingOutputFull | true
108 #end if 109 #end if
110
109 #if 'save_scores' in str($output_files_selector) 111 #if 'save_scores' in str($output_files_selector)
110 && mkdir -p scoresOutput/ && cp *.scores scoresOutput | true 112 && mkdir -p scoresOutput/ && cp *.scores scoresOutput | true
111 #end if 113 #end if
112 #if $input.selector == "single" or $input.selector == "paired" 114 #if $input.selector == "single" or $input.selector == "paired"
113 && mkdir -p bowtie2Alignments/ && cp *.sorted.bam bowtie2Alignments | true 115 && mkdir -p bowtie2Alignments/ && cp *.sorted.bam bowtie2Alignments | true
152 <add value="=" /> 154 <add value="=" />
153 <add value=" " /> 155 <add value=" " />
154 <add value="_" /> 156 <add value="_" />
155 </valid> 157 </valid>
156 </sanitizer> 158 </sanitizer>
157 <validator type="regex">[A-Za-z0-9 =-_/+]+</validator> 159 <validator type="regex">[A-Za-z0-9 =_/+-]+</validator>
158 </param> 160 </param>
159 <param argument="--mlst_max_mismatch" type="integer" value="10" label="Maximum number of mismatches per read for MLST allele calling"/> 161 <param argument="--mlst_max_mismatch" type="integer" value="10" label="Maximum number of mismatches per read for MLST allele calling"/>
160 <param argument="--min_depth" type="integer" value="5" label="Minimum mean depth to flag as dubious allele call"/> 162 <param argument="--min_depth" type="integer" value="5" label="Minimum mean depth to flag as dubious allele call"/>
161 <param argument="--min_edge_depth" type="integer" value="2" label="Minimum edge depth to flag as dubious allele call"/> 163 <param argument="--min_edge_depth" type="integer" value="2" label="Minimum edge depth to flag as dubious allele call"/>
162 </when> 164 </when>
196 <outputs> 198 <outputs>
197 <data name="mlst_results" format="tabular" from_work_dir="output__mlst__mlst_db__results.txt" label="${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 ${on_string}: MLST Results">
198 <filter>use_mlst_db['selector'] == "yes"</filter> 200 <filter>use_mlst_db['selector'] == "yes"</filter>
199 </data> 201 </data>
200 <collection name="gene_typing" type="list" label="${tool.name} on ${on_string}: Gene typing results files" > 202 <collection name="gene_typing" type="list" label="${tool.name} on ${on_string}: Gene typing results files" >
201 <discover_datasets pattern="(?P&lt;designation&gt;.+)" directory="geneTypingOutput" format="txt,tabular"/> 203 <discover_datasets pattern="(?P&lt;designation&gt;.+)" directory="geneTypingOutput" format="tabular"/>
204 <filter>use_gene_db['selector'] == "yes" and use_gene_db['no_gene_details'] is True</filter>
205 </collection>
206 <collection name="gene_typing_full" type="list" label="${tool.name} on ${on_string}: Full Gene typing results files" >
207 <discover_datasets pattern="(?P&lt;designation&gt;.+)" directory="geneTypingOutputFull" format="tabular"/>
202 <filter>use_gene_db['selector'] == "yes" and use_gene_db['no_gene_details'] is True</filter> 208 <filter>use_gene_db['selector'] == "yes" and use_gene_db['no_gene_details'] is True</filter>
203 </collection> 209 </collection>
204 <data name="Compiled_gene_and_mlst_output" format="tabular" from_work_dir="output__compiledResults.txt" label="${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 ${on_string}: Compiled MLST and Gene databases Results">
205 </data> 211 </data>
206 <data name="all_consensus" format="fasta" from_work_dir="output.all_consensus_alleles.fasta" label="${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 ${on_string}: All consensus Results">
225 <data name="log_output" format="tabular" from_work_dir="output.log" label="${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">
226 <filter>"log" in output_files_selector</filter> 232 <filter>"log" in output_files_selector</filter>
227 </data> 233 </data>
228 </outputs> 234 </outputs>
229 <tests> 235 <tests>
230 <test expect_num_outputs="9"> 236 <test expect_num_outputs="10">
231 <param name="prob_err" value="0.01"/> 237 <param name="prob_err" value="0.01"/>
232 <param name="max_unaligned_overlap" value="10"/> 238 <param name="max_unaligned_overlap" value="10"/>
233 <param name="mapq" value="1"/> 239 <param name="mapq" value="1"/>
234 <param name="baseq" value="20"/> 240 <param name="baseq" value="20"/>
235 <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"/>
262 <has_text text="fumC"/> 268 <has_text text="fumC"/>
263 <has_n_lines n="2"/> 269 <has_n_lines n="2"/>
264 </assert_contents> 270 </assert_contents>
265 </output> 271 </output>
266 <output_collection name="gene_typing" type="list"> 272 <output_collection name="gene_typing" type="list">
267 <element name="output__fullgenes__0-gene_db__results.txt"> 273 <element name="output__genes__0-gene_db__results.txt">
268 <assert_contents> 274 <assert_contents>
269 <has_text text="AmpC1_Ecoli_Bla"/> 275 <has_text text="AmpC1_Ecoli_Bla"/>
270 <has_n_lines n="2"/> 276 <has_n_lines n="2"/>
271 </assert_contents> 277 </assert_contents>
272 </element> 278 </element>
273 <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">
274 <assert_contents> 282 <assert_contents>
275 <has_text text="AmpC1_Ecoli_Bla"/> 283 <has_text text="AmpC1_Ecoli_Bla"/>
276 <has_n_lines n="2"/> 284 <has_n_lines n="2"/>
277 </assert_contents> 285 </assert_contents>
278 </element> 286 </element>