Mercurial > repos > galaxyp > diann

comparison diann.xml @ 3:a8f461b7d193 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/vdemichev/DiaNN commit 7066fc6839300c6703770e667f8534ed69248d25
author galaxyp
date Thu, 12 Jun 2025 09:14:41 +0000
parents 65134626eb2b
children
comparison
equal deleted inserted replaced
2:65134626eb2b 3:a8f461b7d193
1 <tool id="diann" name="DIA-NN" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.2"> 1 <tool id="diann" name="DIA-NN" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.2">
2 <description>is a software for DIA/SWATH data processing</description> 2 <description>is a software for DIA/SWATH data processing</description>
3 <macros> 3 <macros>
4 <token name="@TOOL_VERSION@">1.8.1</token> 4 <token name="@TOOL_VERSION@">1.8.1</token>
5 <token name="@VERSION_SUFFIX@">4</token> 5 <token name="@VERSION_SUFFIX@">5</token>
6 </macros> 6 </macros>
7 <requirements> 7 <requirements>
8 <container type="docker">biocontainers/diann:@TOOL_VERSION@_cv2</container> 8 <container type="docker">biocontainers/diann:@TOOL_VERSION@_cv2</container>
9 </requirements> 9 </requirements>
10 <stdio> 10 <stdio>
15 mkdir ./tmp && 15 mkdir ./tmp &&
16 16
17 ## generate string like "--f file1 --f file2 ..." for each input in $input.f, which are comma separated 17 ## generate string like "--f file1 --f file2 ..." for each input in $input.f, which are comma separated
18 #set infiles_str = '' 18 #set infiles_str = ''
19 #for $infile in $input.f 19 #for $infile in $input.f
20 #if not $infile:
21 #continue
22 #end if
20 ## if brukertdf.d.tar, extract to ./input_data and append "./input_data/" to infiles_str 23 ## if brukertdf.d.tar, extract to ./input_data and append "./input_data/" to infiles_str
21 #if $infile.is_of_type("brukertdf.d.tar"): 24 #if $infile.is_of_type("brukertdf.d.tar"):
22 tar -xf '$infile' -C ./input_data && 25 tar -xf '$infile' -C ./input_data &&
23 #set $infiles_str += '--f ./input_data/' + str($infile.element_identifier[:-4]) 26 #set $infiles_str += "--f './input_data/" + str($infile.element_identifier[:-4]) + "' "
24 #else 27 #else
25 #set name = './input_data/' + $infile.element_identifier + '.' + $infile.ext 28 #set name = './input_data/' + $infile.element_identifier + '.' + $infile.ext
26 ln -s '$infile' '$name' && 29 ln -s '$infile' '$name' &&
27 #set $infiles_str += '--f ' + $name + ' ' 30 #set $infiles_str += "--f '" + $name + "' "
28 #end if 31 #end if
29 #end for 32 #end for
30 33
31 #set $fasta_file_str = '' 34 #set $fasta_file_str = ''
32 #for $fasta_file in $input.fasta_db_options.fasta 35 #for $fasta_file in $input.fasta_db_options.fasta
36 #if $input.spectral_lib_options.lib 39 #if $input.spectral_lib_options.lib
37 ln -s '$input.spectral_lib_options.lib' './input_data/report-lib.predicted.speclib' && 40 ln -s '$input.spectral_lib_options.lib' './input_data/report-lib.predicted.speclib' &&
38 #end if 41 #end if
39 42
40 diann 43 diann
41 #if $input.f != 'None' 44 #if $infiles_str != ''
42 '$infiles_str' 45 $infiles_str
43 #end if 46 #end if
44 --dir ./ 47 --dir ./
45 #if $input.spectral_lib_options.lib 48 #if $input.spectral_lib_options.lib
46 --lib './input_data/report-lib.predicted.speclib' 49 --lib './input_data/report-lib.predicted.speclib'
47 #else 50 #else
48 --lib 51 --lib
49 #end if 52 #end if
50 #if $input.f != 'None' 53 #if $infiles_str != ''
51 --out ./report.tsv 54 --out ./report.tsv
52 #end if 55 #end if
53 #if $input.spectral_lib_options.gen_spec_lib 56 #if $input.spectral_lib_options.gen_spec_lib
54 --out-lib ./report-lib.tsv 57 --out-lib ./report-lib.tsv
55 #end if 58 #end if
56 --threads \${GALAXY_SLOTS:-1} 59 --threads \${GALAXY_SLOTS:-1}
226 $output_options.report_lib_info 229 $output_options.report_lib_info
227 #if $output_options.vis 230 #if $output_options.vis
228 --vis '$output_options.vis' 231 --vis '$output_options.vis'
229 #end if 232 #end if
230 --verbose '$output_options.verbose' 233 --verbose '$output_options.verbose'
231
232 #if len($input.f) > 0
233 && cp ./report.tsv '$output_report'
234 #end if
235
236 #if $input.spectral_lib_options.gen_spec_lib
237 && cp ./report-lib.tsv '$output_report_lib'
238 && cp ./report-lib.tsv.speclib '$output_report_speclib'
239 && cp ./report-lib.predicted.speclib '$output_report_pred_speclib'
240 #end if
241 ]]></command> 234 ]]></command>
242 <inputs> 235 <inputs>
243 <!-- not used: cfg, convert, dir, ext, no_quant_files, out, out_lib, out_lib_copy, prefix, temp, threads, use-quant --> 236 <!-- not used: cfg, convert, dir, ext, no_quant_files, out, out_lib, out_lib_copy, prefix, temp, threads, use-quant -->
244 <section name="input" expanded="true" title="Input files"> 237 <section name="input" expanded="true" title="Input files">
245 <param name="f" type="data" format="mzml,wiff,thermo.raw,brukertdf.d.tar" multiple="true" optional="true" label="Input file" help="Specify a run to be analysed"/> 238 <param name="f" type="data" format="mzml,wiff,thermo.raw,brukertdf.d.tar" multiple="true" optional="true" label="Input file" help="Specify a run to be analysed"/>
415 <param name="vis" type="text" optional="true" label="Extract and save chromatograms" help="Instructs DIA-NN to extract and save chromatograms in the vicinity of the detected elution apex, for all PSMs matching the stripped sequences provided, for all runs in the experiment; at least N scans in the vicinity of the apex will be extracted"/> 408 <param name="vis" type="text" optional="true" label="Extract and save chromatograms" help="Instructs DIA-NN to extract and save chromatograms in the vicinity of the detected elution apex, for all PSMs matching the stripped sequences provided, for all runs in the experiment; at least N scans in the vicinity of the apex will be extracted"/>
416 <param name="verbose" type="integer" min="0" max="4" value="1" label="Verbose level" help="Sets the level of detail of the log"/> 409 <param name="verbose" type="integer" min="0" max="4" value="1" label="Verbose level" help="Sets the level of detail of the log"/>
417 </section> 410 </section>
418 </inputs> 411 </inputs>
419 <outputs> 412 <outputs>
420 <data format="tabular" name="output_report" label="${tool.name} on ${on_string}: report.tsv"> 413 <data format="tabular" name="output_report" from_work_dir="report.tsv" label="${tool.name} on ${on_string}: report.tsv">
421 <filter>input['f'] != None</filter> 414 <filter>input['f'] != None</filter>
422 </data> 415 </data>
423 <data format="tabular" name="output_report_lib" label="${tool.name} on ${on_string}: report-lib.tsv"> 416 <data format="tabular" name="output_report_lib" from_work_dir="report-lib.tsv" label="${tool.name} on ${on_string}: report-lib.tsv">
424 <filter>input['spectral_lib_options']['gen_spec_lib'] == True</filter> 417 <filter>input['spectral_lib_options']['gen_spec_lib'] == True</filter>
418 <filter>input['f'] != None</filter>
425 </data> 419 </data>
426 <data format="data" name="output_report_speclib" label="${tool.name} on ${on_string}: report-lib.tsv.speclib"> 420 <data format="data" name="output_report_speclib" from_work_dir="report-lib.tsv.speclib" label="${tool.name} on ${on_string}: report-lib.tsv.speclib">
427 <filter>input['spectral_lib_options']['gen_spec_lib'] == True</filter> 421 <filter>input['spectral_lib_options']['gen_spec_lib'] == True</filter>
422 <filter>input['f'] != None</filter>
428 </data> 423 </data>
429 <data format="data" name="output_report_pred_speclib" label="${tool.name} on ${on_string}: report-lib.predicted.speclib"> 424 <data format="data" name="output_report_pred_speclib" from_work_dir="report-lib.predicted.speclib" label="${tool.name} on ${on_string}: report-lib.predicted.speclib">
430 <filter>input['spectral_lib_options']['gen_spec_lib'] == True</filter> 425 <filter>input['spectral_lib_options']['gen_spec_lib'] == True</filter>
431 </data> 426 </data>
432 </outputs> 427 </outputs>
433 <tests> 428 <tests>
434 <!-- test for default run --> 429 <!-- test for default run -->
455 </assert_contents> 450 </assert_contents>
456 </output> 451 </output>
457 <output name="output_report_speclib" file="report-lib.tsv.speclib" compare="sim_size" delta="100"/> 452 <output name="output_report_speclib" file="report-lib.tsv.speclib" compare="sim_size" delta="100"/>
458 <output name="output_report_pred_speclib" file="report-lib.predicted.speclib" compare="sim_size" delta="100"/> 453 <output name="output_report_pred_speclib" file="report-lib.predicted.speclib" compare="sim_size" delta="100"/>
459 </test> 454 </test>
455 <!-- test for default run wo MS files -->
456 <test expect_num_outputs="1">
457 <section name="input">
458 <section name="spectral_lib_options">
459 <param name="gen_spec_lib" value="True"/>
460 <param name="predictor" value="True"/>
461 </section>
462 <section name="fasta_db_options">
463 <param name="fasta" value="bsa.fasta"/>
464 <param name="fasta_search" value="True"/>
465 </section>
466 </section>
467 <output name="output_report_pred_speclib" file="report-lib.predicted.speclib" compare="sim_size" delta="100"/>
468 </test>
460 <!-- test for multiple fastas --> 469 <!-- test for multiple fastas -->
461 <test expect_num_outputs="1"> 470 <test expect_num_outputs="1">
462 <section name="input"> 471 <section name="input">
463 <param name="f" value="small-peakpicking-cwt-allMS" /> 472 <param name="f" value="small-peakpicking-cwt-allMS" />
464 <section name="fasta_db_options"> 473 <section name="fasta_db_options">
489 <has_text text="PG.Normalised"/> 498 <has_text text="PG.Normalised"/>
490 </assert_contents> 499 </assert_contents>
491 </output> 500 </output>
492 </test> 501 </test>
493 <!-- test for Bruker data --> 502 <!-- test for Bruker data -->
494 <!-- <test expect_num_outputs="2"> 503 <!-- <test expect_num_outputs="2">
495 <section name="input"> 504 <section name="input">
496 <param name="f" value="ThyroglobMRM000003.d.tar" /> 505 <param name="f" value="ThyroglobMRM000003.d.tar" />
497 <section name="spectral_lib_options"> 506 <section name="spectral_lib_options">
498 <param name="gen_spec_lib" value="True"/> 507 <param name="gen_spec_lib" value="True"/>
499 <param name="predictor" value="True"/> 508 <param name="predictor" value="True"/>