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comparison rna_quast.xml @ 7:3125faf00ffd draft

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planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit d68ebc953fe79f2909c79ef1b133300f450aa822
author iuc
date Fri, 30 Aug 2024 13:23:03 +0000
parents 8e66f695d859
children f73ab5187eed
comparison
equal deleted inserted replaced
6:8e66f695d859 7:3125faf00ffd
11 <command detect_errors="exit_code"><![CDATA[ 11 <command detect_errors="exit_code"><![CDATA[
12 mkdir -p './complete_reports/' && 12 mkdir -p './complete_reports/' &&
13 mkdir -p './fasta_files/' && 13 mkdir -p './fasta_files/' &&
14 #import os, re, glob 14 #import os, re, glob
15 #for $i in $transcripts 15 #for $i in $transcripts
16 ln -s '$i' '${re.sub('[^\w\-.]', '_', i.element_identifier)}' && 16 ln -s '$i' '${re.sub('[^\w.]', '_', i.element_identifier)}' &&
17 #end for 17 #end for
18 #if $reference 18 #if $reference
19 #for $rf in $reference 19 #for $rf in $reference
20 ln -s '$rf' '${re.sub('[^\w\-.]', '_', rf.element_identifier)}' && 20 ln -s '$rf' '${re.sub('[^\w.]', '_', rf.element_identifier)}' &&
21 #end for 21 #end for
22 #end if 22 #end if
23 #if $gene_coordinates.selector == "true" 23 #if $gene_coordinates.selector == "true"
24 #for $g in $gene_coordinates.gtf 24 #for $g in $gene_coordinates.gtf
25 ln -s '$g' '${re.sub('[^\w\-.]', '_', g.element_identifier)}' && 25 ln -s '$g' '${re.sub('[^\w.]', '_', g.element_identifier)}' &&
26 #end for 26 #end for
27 #end if 27 #end if
28 mkdir outputdir && 28 mkdir outputdir &&
29 rnaQUAST.py 29 rnaQUAST.py
30 --threads \${GALAXY_SLOTS:-8} 30 --threads \${GALAXY_SLOTS:-8}
31 --transcripts 31 --transcripts
32 #for $i in $transcripts 32 #for $i in $transcripts
33 '${re.sub('[^\w\-.]', '_', i.element_identifier)}' 33 '${re.sub('[^\w.]', '_', i.element_identifier)}'
34 #end for 34 #end for
35 #if $reads_option.selector == 'paired' 35 #if $reads_option.selector == 'paired'
36 --left_reads '${reads_option.forward_reads}' 36 --left_reads '${reads_option.forward_reads}'
37 --right_reads '${reads_option.reverse_reads}' 37 --right_reads '${reads_option.reverse_reads}'
38 #else if $reads_option.selector == 'single' 38 #else if $reads_option.selector == 'single'
43 --reads_alignment '${reads_alignment}' 43 --reads_alignment '${reads_alignment}'
44 #end if 44 #end if
45 #if $reference 45 #if $reference
46 -r 46 -r
47 #for $rf in $reference 47 #for $rf in $reference
48 '${re.sub('[^\w\-.]', '_', rf.element_identifier)}' 48 '${re.sub('[^\w.]', '_', rf.element_identifier)}'
49 #end for 49 #end for
50 #end if 50 #end if
51 #if $gene_coordinates.selector == "true" 51 #if $gene_coordinates.selector == "true"
52 --gtf 52 --gtf
53 #for $g in $gene_coordinates.gtf 53 #for $g in $gene_coordinates.gtf
54 '${re.sub('[^\w\-.]', '_', g.element_identifier)}' 54 '${re.sub('[^\w.]', '_', g.element_identifier)}'
55 #end for 55 #end for
56 $gene_coordinates.disable_infer_genes 56 $gene_coordinates.disable_infer_genes
57 $gene_coordinates.disable_infer_transcripts 57 $gene_coordinates.disable_infer_transcripts
58 #end if 58 #end if
59 $advanced_options.prokaryote 59 $advanced_options.prokaryote
80 #if 'gz' in $output_options.out_add 80 #if 'gz' in $output_options.out_add
81 && tar -czvf results.tar.gz './outputdir' 81 && tar -czvf results.tar.gz './outputdir'
82 #end if 82 #end if
83 83
84 #if len($transcripts) == 1 84 #if len($transcripts) == 1
85 #set $path = "/".join(['outputdir',($transcripts[0].element_identifier).split(".")[0]]) + "_output" 85 #set $path = "/".join(['outputdir',re.sub('[^\w.]', '_', $transcripts[0].element_identifier).split(".")[0]]) + "_output"
86 && mv '${path}' './results' 86 && mv '${path}' './results'
87 ## rename .list files to .txt files to make them detectable 87 ## rename .list files to .txt files to make them detectable
88 && find './results/' -name "*.list" -exec mv {} {}.txt \; 88 && find './results/' -name "*.list" -exec mv {} {}.txt \;
89 && true 89 && true
90 && printf "************ METRICS/TRANSCRIPTS ***************\n" > stats.txt 90 && printf "************ METRICS/TRANSCRIPTS ***************\n" > stats.txt
97 #end if 97 #end if
98 #else 98 #else
99 && mkdir -p './results/' 99 && mkdir -p './results/'
100 #if $gene_coordinates.selector == 'true' and $reference 100 #if $gene_coordinates.selector == 'true' and $reference
101 #for $i, $transcript in enumerate($transcripts) 101 #for $i, $transcript in enumerate($transcripts)
102 #set $path = "/".join(['outputdir',($transcripts[$i].element_identifier).split(".")[0]]) + "_output" 102 #set $path = "/".join(['outputdir',re.sub('[^\w.]', '_', $transcripts[$i].element_identifier).split(".")[0]]) + "_output"
103 && rm -r ./results 103 && rm -r ./results
104 && cp -r $path './results' 104 && cp -r $path './results'
105 && mv ./results/*fasta './fasta_files/' 105 && mv ./results/*fasta './fasta_files/'
106 #end for 106 #end for
107 #end if 107 #end if
383 </assert_contents> 383 </assert_contents>
384 </output> 384 </output>
385 </test> 385 </test>
386 <!-- Test 08: Multiple inputs--> 386 <!-- Test 08: Multiple inputs-->
387 <test expect_num_outputs="6"> 387 <test expect_num_outputs="6">
388 <param name="transcripts" value="transcriptome01.fasta,transcriptome02.fasta"/> 388 <param name="transcripts" value="transcriptome01.fasta,transcriptome?02.fasta"/>
389 <param name="reference" value="reference.fasta"/> 389 <param name="reference" value="reference.fasta"/>
390 <conditional name="gene_coordinates"> 390 <conditional name="gene_coordinates">
391 <param name="selector" value="true"/> 391 <param name="selector" value="true"/>
392 <param name="gtf" value="reference.gtf"/> 392 <param name="gtf" value="reference.gtf"/>
393 </conditional> 393 </conditional>
405 <conditional name="reads_option"> 405 <conditional name="reads_option">
406 <param name="selector" value="single"/> 406 <param name="selector" value="single"/>
407 <param name="single_reads" value="single_end.fastq.gz"/> 407 <param name="single_reads" value="single_end.fastq.gz"/>
408 </conditional> 408 </conditional>
409 <output name="short_report_tabular" value="test_08_short_report.tab" ftype="tabular"/> 409 <output name="short_report_tabular" value="test_08_short_report.tab" ftype="tabular"/>
410 <output name="short_report_pdf" value="test_08_short_report.pdf" ftype="pdf"/> 410 <output name="short_report_pdf" value="test_08_short_report.pdf" ftype="pdf" compare="sim_size" delta_frac="0.1"/>
411 <output name="stats" value="test_08_complete_report.tab" ftype="txt" lines_diff="6" /> 411 <output name="stats" value="test_08_complete_report.tab" ftype="txt" lines_diff="6" />
412 <output_collection name="fasta_files" type="list" count="14"> 412 <output_collection name="fasta_files" type="list" count="14">
413 <element name="transcriptome01.paralogs" file="test_08_paralogs.fasta" ftype="fasta"/> 413 <element name="transcriptome01.paralogs" file="test_08_paralogs.fasta" ftype="fasta"/>
414 </output_collection> 414 </output_collection>
415 <output_collection name="list_logs" type="list" count="14"> 415 <output_collection name="list_logs" type="list" count="14">
430 <has_text text="Thank you for using rnaQUAST!"/> 430 <has_text text="Thank you for using rnaQUAST!"/>
431 </assert_contents> 431 </assert_contents>
432 </element> 432 </element>
433 </output_collection> 433 </output_collection>
434 </test> 434 </test>
435 435 <!-- Test 09: Multiple inputs with dash in names-->
436 <test expect_num_outputs="6">
437 <param name="transcripts" value="transcriptome01.fasta,transcriptome-02.fasta"/>
438 <param name="reference" value="reference.fasta"/>
439 <conditional name="gene_coordinates">
440 <param name="selector" value="true"/>
441 <param name="gtf" value="reference.gtf"/>
442 </conditional>
443 <section name="output_options">
444 <param name="out_sr" value="tabular,pdf"/>
445 </section>
446 <conditional name="use_busco">
447 <param name="selector" value="true"/>
448 <conditional name="lineage_conditional">
449 <param name="selector" value="cached"/>
450 <param name="cached_db" value="busco-demo-db-20230328"/>
451 </conditional>
452 </conditional>
453 <param name="out_add" value="complete,fasta,logs,gz"/>
454 <conditional name="reads_option">
455 <param name="selector" value="single"/>
456 <param name="single_reads" value="single_end.fastq.gz"/>
457 </conditional>
458 <output name="short_report_tabular" value="test_08_short_report.tab" ftype="tabular"/>
459 <output name="short_report_pdf" value="test_08_short_report.pdf" ftype="pdf" compare="sim_size" delta_frac="0.1"/>
460 <output name="stats" value="test_08_complete_report.tab" ftype="txt" lines_diff="6" />
461 <output_collection name="fasta_files" type="list" count="14">
462 <element name="transcriptome01.paralogs" file="test_08_paralogs.fasta" ftype="fasta"/>
463 </output_collection>
464 <output_collection name="list_logs" type="list" count="14">
465 <element name="STAR.out" ftype="txt">
466 <assert_contents>
467 <has_text text="STAR --runThreadN"/>
468 <has_text text="finished successfully"/>
469 </assert_contents>
470 </element>
471 <element name="gmap_build.out" ftype="txt">
472 <assert_contents>
473 <has_text text="No alternate scaffolds observed"/>
474 </assert_contents>
475 </element>
476 <element name="rnaQUAST" ftype="txt">
477 <assert_contents>
478 <has_text text="THE QUALITY OF TRANSCRIPTOME ASSEMBLY DONE"/>
479 <has_text text="Thank you for using rnaQUAST!"/>
480 </assert_contents>
481 </element>
482 </output_collection>
483 </test>
436 </tests> 484 </tests>
437 <help><![CDATA[ 485 <help><![CDATA[
438 486
439 .. class:: infomark 487 .. class:: infomark
440 488