| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/computational-metabolomics/mspurity_dimspredictpuritysingle/mspurity_dimspredictpuritysingle/1.16.2+galaxy1 (this tool) |
| toolshed.g2.bx.psu.edu/repos/computational-metabolomics/mspurity_dimspredictpuritysingle/mspurity_dimspredictpuritysingle/1.16.2+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/computational-metabolomics/mspurity_dimspredictpuritysingle/mspurity_dimspredictpuritysingle/1.12.2+galaxy3 |
| toolshed.g2.bx.psu.edu/repos/computational-metabolomics/mspurity_dimspredictpuritysingle/mspurity_dimspredictpuritysingle/1.12.2+galaxy2 |
| toolshed.g2.bx.psu.edu/repos/computational-metabolomics/mspurity_dimspredictpuritysingle/mspurity_dimspredictpuritysingle/1.12.2+galaxy1 |
| toolshed.g2.bx.psu.edu/repos/computational-metabolomics/mspurity_dimspredictpuritysingle/mspurity_dimspredictpuritysingle/1.12.2+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/computational-metabolomics/mspurity_dimspredictpuritysingle/mspurity_dimspredictpuritysingle/1.12.0+galaxy1 |
| toolshed.g2.bx.psu.edu/repos/computational-metabolomics/mspurity_dimspredictpuritysingle/mspurity_dimspredictpuritysingle/1.12.0+galaxy0 |
| mspurity_dimspredictpuritysingle |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| bioconductor-mspurity | 1.16.2 | package |
| bioconductor-camera | 1.46.0 | package |
| bioconductor-xcms | 3.12.0 | package |
| bioconductor-mspuritydata | 1.16.0 | package |
| r-optparse | 1.6.6 | package |
| r-rpostgres | 1.3.1 | package |
| r-rmysql | 0.10.21 | package |
| Additional information about this tool |
Rscript '$__tool_directory__/dimsPredictPuritySingle.R'
#if $mzML_data.format == 'mzML_file'
--mzML_file '$mzML_data.source'
#elif $mzML_data.format == 'library'
--mzML_file '$__app__.config.user_library_import_dir/$__user_email__/$mzML_data.source'
#elif $mzML_data.format == 'mzML_data_collection'
--mzML_files='
#for $i in $mzML_data.source
$i,
#end for
'
--galaxy_names='
#for $i in $mzML_data.source
$i.name,
#end for
'
--mzML_filename=' $mzML_data.mzML_filename'
#end if
--peaks_file='$peaks_file'
--out_dir='.'
--minoffset=$minoffset
--maxoffset=$maxoffset
--ppm=$ppm
--iwNorm=$iw_norm
--ilim=$ilim
#if $sim
--sim
#end if
#if $remove_NAs
--remove_nas
#end if
#if $dimspy_usage.usage == "dimspy"
--dimspy
--file_num_dimspy $dimspy_usage.file_num_dimspy
#end if
#if $isotopes.isotopes == "exclude_default":
--exclude_isotopes
#elif $isotopes.isotopes == "user"
--exclude_isotopes
--isotope_matrix = '$isotopes.im'
#end if
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
peaks_file: dimsPredictPuritySingle_input_dimspy_peakmatrix.tsv mzML_data|source: dimsPredictPuritySingle_full_scan.mzML mzML_data|format: mzML_file remove_NAs: True dimspy_usage|file_num_dimspy: 1 dimspy_usage|usage: dimspy |
name: value |
dimsPredictPuritySingle_input_dimspy_peakmatrix.tsv dimsPredictPuritySingle_full_scan.mzML value |