| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/computational-metabolomics/mspurity_createmsp/mspurity_createmsp/1.28.0+galaxy1 (this tool) |
| toolshed.g2.bx.psu.edu/repos/computational-metabolomics/mspurity_createmsp/mspurity_createmsp/1.28.0+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/computational-metabolomics/mspurity_createmsp/mspurity_createmsp/1.16.2+galaxy2 |
| toolshed.g2.bx.psu.edu/repos/computational-metabolomics/mspurity_createmsp/mspurity_createmsp/1.16.2+galaxy1 |
| toolshed.g2.bx.psu.edu/repos/computational-metabolomics/mspurity_createmsp/mspurity_createmsp/1.16.2+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/computational-metabolomics/mspurity_createmsp/mspurity_createmsp/1.12.2+galaxy3 |
| toolshed.g2.bx.psu.edu/repos/computational-metabolomics/mspurity_createmsp/mspurity_createmsp/1.12.2+galaxy2 |
| toolshed.g2.bx.psu.edu/repos/computational-metabolomics/mspurity_createmsp/mspurity_createmsp/1.12.2+galaxy1 |
| toolshed.g2.bx.psu.edu/repos/computational-metabolomics/mspurity_createmsp/mspurity_createmsp/1.12.2+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/computational-metabolomics/mspurity_createmsp/mspurity_createmsp/1.12.0+galaxy1 |
| toolshed.g2.bx.psu.edu/repos/computational-metabolomics/mspurity_createmsp/mspurity_createmsp/1.12.0+galaxy0 |
| mspurity_createmsp |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| bioconductor-mspurity | 1.28.0 | package |
| bioconductor-camera | 1.58.0 | package |
| bioconductor-xcms | 4.0.0 | package |
| bioconductor-mspuritydata | 1.30.0 | package |
| r-optparse | 1.7.5 | package |
| r-rpostgres | 1.4.7 | package |
| r-rmysql | 0.10.27 | package |
| Additional information about this tool |
Rscript '$__tool_directory__/createMSP.R'
--rdata_input '$rdata_input'
--method '$method'
#if $metadata_cond.metadata_select == "true"
--metadata '$metadata_cond.metadata'
--metadata_cols '$metadata_cond.metadata_cols'
--metadata_cols_filter '$metadata_cond.metadata_cols_filter'
#end if
#if $xcms_group_cond.xcms_group_select == "true"
--xcms_groupids '$xcms_group_cond.xcms_groupids'
#end if
$filter
$adduct_split
--msp_schema $msp_schema
--intensity_ra $intensity_ra
--include_adducts $include_adducts
#if $include_adducts_custom
--include_adducts_custom "$include_adducts_custom"
#end if
--out_dir '.'
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
rdata_input: averageFragSpectra_output_all.RData method: av_all metadata_cond|metadata: createMSP_input_metadata.tsv metadata_cond|metadata_select: True xcms_group_cond|xcms_groupids: 8,12 xcms_group_cond|xcms_group_select: True |
name: value |
averageFragSpectra_output_all.RData createMSP_input_metadata.tsv value |
| Test-2 |
rdata_input: averageFragSpectra_output_all.RData method: av_all metadata_cond|metadata: createMSP_input_metadata.tsv metadata_cond|metadata_select: True xcms_group_cond|xcms_groupids: 8,12 xcms_group_cond|xcms_group_select: True include_adducts_custom: [M+]+,[M-H]-,[M+TEST SPACE+]+ |
name: value |
averageFragSpectra_output_all.RData createMSP_input_metadata.tsv value |