| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/galaxyp/maxquant/maxquant_mqpar/2.0.3.0+galaxy0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/galaxyp/maxquant/maxquant_mqpar/1.6.17.0+galaxy2 |
| toolshed.g2.bx.psu.edu/repos/galaxyp/maxquant/maxquant_mqpar/1.6.17.0+galaxy1 |
| toolshed.g2.bx.psu.edu/repos/galaxyp/maxquant/maxquant_mqpar/1.6.17.0+galaxy0 |
| maxquant_mqpar |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| maxquant | 2.0.3.0 | package |
| pyyaml | 5.4.1 | package |
| dotnet | 3.1.418 | package |
| r-ptxqc | 1.0.16 | package |
| tar | 1.32 | package |
| Additional information about this tool |
export COMPlus_EnableDiagnostics=0 &&
## link galaxy datasets to filenames accepted by maxquant
#import re
#set names = [re.sub('[^\w\-\s\.]', '_', str($n.element_identifier)) for $n in $input_opts.infiles]
#set names_with_ext = [($name if ($name).lower().endswith(str($input_opts.ftype)) else $name + str($input_opts.ftype)) for $name in $names]
#for $target, $link in zip($infiles, $names_with_ext)
#if str($input_opts.ftype) == '.thermo.raw':
cp '$target' '$link' &&
#else:
ln -s '$target' '$link' &&
#end if
#end for
python3 '$__tool_directory__/modify_mqpar.py'
#set inf = ','.join($names_with_ext)
--infiles='$inf'
--version=2.0.3.0
--num_threads=\${GALAXY_SLOTS:-1}
--substitution_rx='[^\w\-\s\.]'
--fasta_files='$fasta_files'
--description_parse_rule='$description_parse_rule'
--identifier_parse_rule='$identifier_parse_rule'
'$mqpar_input'
&&
maxquant mqpar.xml
#if 'log' in $output:
>> '$log'
#end if
&& mv mqpar.xml combined/txt/mqpar.xml
#if 'output_all' in $output:
&&
tar -zcf '$output_all' ./combined/txt
#end if
#if $qc.do_it == 'true':
&&
Rscript '$qr' '$qr_yaml'
#if 'log' in $output:
>> '$log' 2>&1
#end if
&&
cp ./combined/txt/report_v1.0.16_combined.pdf '$ptxqc_report'
#end if
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
input_opts|infiles: ['BSA_min_22', 'BSA_min_21.mzXML'] input_opts|ftype: .mzxml fasta_files: bsa.fasta identifier_parse_rule: >([^\s]*) description_parse_rule: >(.*) mqpar_input: mqpar/mqpar.xml output: ['evidence', 'msms', 'mzTab', 'allPeptides', 'msmsScans', 'mzRange', 'parameters', 'peptides', 'proteinGroups', 'summary', 'modificationSpecificPeptides', 'mqpar', 'output_all'] |
name: value name: value name: value name: value name: value name: value name: value name: value name: value name: value name: value |
BSA_min_22 BSA_min_21.mzXML bsa.fasta mqpar/mqpar.xml value |