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comparison srst2.xml @ 1:46c5d7a0393b draft

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planemo upload for repository https://github.com/katholt/srst2 commit 2e3867763a28e217bf5f44558a3f56e7efe041c5
author iuc
date Tue, 06 Sep 2022 14:18:05 +0000
parents f9a0855c792d
children 81cea47ec685
comparison
equal deleted inserted replaced
0:f9a0855c792d 1:46c5d7a0393b
19 #for $i, $s in enumerate($prev_output) 19 #for $i, $s in enumerate($prev_output)
20 #if $s 20 #if $s
21 ln -s $s './$i-prev_output.txt' && 21 ln -s $s './$i-prev_output.txt' &&
22 #end if 22 #end if
23 #end for 23 #end for
24 #for $i, $s in enumerate($use_gene_db.gene_db) 24 #if $use_gene_db.selector == "yes"
25 #if $s 25 #for $i, $s in enumerate($use_gene_db.gene_db)
26 ln -s $s './$i-gene_db.fasta' && 26 #if $s
27 #end if 27 ln -s $s './$i-gene_db.fasta' &&
28 #end for 28 #end if
29 #end for
30 #end if
29 #if $use_mlst_db.selector == "yes" 31 #if $use_mlst_db.selector == "yes"
30 #set ext_3=$use_mlst_db.mlst_definitions.datatype.file_ext 32 #set ext_3=$use_mlst_db.mlst_definitions.datatype.file_ext
31 ln -s $use_mlst_db.mlst_db './mlst_db.fasta' && 33 ln -s $use_mlst_db.mlst_db './mlst_db.fasta' &&
32 ln -s $use_mlst_db.mlst_definitions './mlst_definitions.$ext_3' && 34 ln -s $use_mlst_db.mlst_definitions './mlst_definitions.$ext_3' &&
33 #end if 35 #end if
94 --report_all_consensus 96 --report_all_consensus
95 #end if 97 #end if
96 #if 'keep_interim_alignment' in str($output_files_selector) 98 #if 'keep_interim_alignment' in str($output_files_selector)
97 --keep_interim_alignment 99 --keep_interim_alignment
98 #end if 100 #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
99 #if 'report_new_consensus' in str($output_files_selector) and $use_gene_db.selector == "yes" and $use_mlst_db.selector == "yes" 102 #if 'report_new_consensus' in str($output_files_selector) and $use_gene_db.selector == "yes" and $use_mlst_db.selector == "yes"
100 && mkdir -p allelesOutput/ && cp *.output__input.*.pileup allelesOutput 103 && mkdir -p allelesOutput/ && cp *.output__input.*.pileup allelesOutput | true
101 #end if 104 #end if
102 #if $use_gene_db.selector == "yes" and $use_gene_db.no_gene_details 105 #if $use_gene_db.selector == "yes" and $use_gene_db.no_gene_details
103 && mkdir -p geneTypingOutput/ && cp output__genes__*__results.txt geneTypingOutput && cp output__fullgenes__*__results.txt geneTypingOutput 106 && mkdir -p geneTypingOutput/ && cp output__genes__*__results.txt geneTypingOutput | true && cp output__fullgenes__*__results.txt geneTypingOutput | true
104 #end if 107 #end if
105 #if 'save_scores' in str($output_files_selector) 108 #if 'save_scores' in str($output_files_selector)
106 && mkdir -p scoresOutput/ && cp *.scores scoresOutput 109 && mkdir -p scoresOutput/ && cp *.scores scoresOutput | true
107 #end if 110 #end if
108 #if $input.selector == "single" or $input.selector == "paired" 111 #if $input.selector == "single" or $input.selector == "paired"
109 && mkdir -p bowtie2Alignments/ && cp *.sorted.bam bowtie2Alignments 112 && mkdir -p bowtie2Alignments/ && cp *.sorted.bam bowtie2Alignments | true
110 && mkdir -p samtoolsPileup/ && cp output__input.*.pileup samtoolsPileup 113 && mkdir -p samtoolsPileup/ && cp output__input.*.pileup samtoolsPileup | true
111 #end if 114 #end if
112 ]]></command> 115 ]]></command>
113 <inputs> 116 <inputs>
114 <conditional name="input"> 117 <conditional name="input">
115 <param name="selector" type="select" label="Reads files type for anaylsis"> 118 <param name="selector" type="select" label="Reads files type for anaylsis">
313 <has_text text="Building"/> 316 <has_text text="Building"/>
314 <has_n_lines n="52"/> 317 <has_n_lines n="52"/>
315 </assert_contents> 318 </assert_contents>
316 </output> 319 </output>
317 </test> 320 </test>
321 <test expect_num_outputs="7">
322 <param name="prob_err" value="0.01"/>
323 <param name="max_unaligned_overlap" value="10"/>
324 <param name="mapq" value="1"/>
325 <param name="baseq" value="20"/>
326 <param name="output_files_selector" value="log,save_scores,report_new_consensus,report_all_consensus"/>
327 <conditional name="input">
328 <param name="selector" value="paired"/>
329 <param name="paired_input1" value="ERR024070_1_reduced_forward_reads.fastqsanger.gz"/>
330 <param name="paired_input2" value="ERR024070_2_reduced_reverse_reads.fastqsanger.gz"/>
331 <param name="merge_paired" value="false"/>
332 <param name="read_type" value="q"/>
333 </conditional>
334 <conditional name="use_mlst_db">
335 <param name="selector" value="no"/>
336 </conditional>
337 <conditional name="use_gene_db">
338 <param name="selector" value="no"/>
339 </conditional>
340 <output name="Compiled_gene_and_mlst_output">
341 <assert_contents>
342 <has_n_lines n="0"/>
343 </assert_contents>
344 </output>
345 <output name="all_consensus">
346 <assert_contents>
347 <has_size value="0" delta="0"/>
348 </assert_contents>
349 </output>
350 <output_collection name="new_consensus" type="list">
351 </output_collection>
352 <output_collection name="samtools_pileup_alignment" type="list">
353 </output_collection>
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">
359 <assert_contents>
360 <has_text text="Total paired readsets found:1"/>
361 <has_n_lines n="4"/>
362 </assert_contents>
363 </output>
364 </test>
318 </tests> 365 </tests>
319 <help><![CDATA[ 366 <help><![CDATA[
320 SRST2 367 SRST2
321 ===== 368 =====
322 Short Read Sequence Typing for Bacterial Pathogens 369 Short Read Sequence Typing for Bacterial Pathogens