| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/galaxyp/mqppep_preproc/mqppep_preproc/0.1.19+galaxy0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/galaxyp/mqppep_preproc/mqppep_preproc/0.1.18+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/galaxyp/mqppep_preproc/mqppep_preproc/0.1.17+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/galaxyp/mqppep_preproc/mqppep_preproc/0.1.16+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/galaxyp/mqppep_preproc/mqppep_preproc/0.1.15+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/galaxyp/mqppep_preproc/mqppep_preproc/0.1.13+galaxy0 |
| mqppep_preproc |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| bioconductor-preprocesscore | 1.56.0 | package |
| gmp | 6.2.1 | package |
| numpy | 1.23.4 | package |
| openblas | 0.3.3 | package |
| pandas | 1.5.1 | package |
| perl-dbd-sqlite | 1.70 | package |
| perl | 5.32.1 | package |
| pyahocorasick | 1.4.4 | package |
| python | 3.10.6 | package |
| r-base | 4.1.3 | package |
| r-caret | 6.0_93 | package |
| r-data.table | 1.14.4 | package |
| r-dbi | 1.1.3 | package |
| r-ggplot2 | 3.3.6 | package |
| r-gplots | 3.1.3 | package |
| r-latex2exp | 0.9.5 | package |
| r-optparse | 1.7.3 | package |
| r-reshape2 | 1.4.4 | package |
| r-rmarkdown | 2.17 | package |
| r-sessioninfo | 1.2.2 | package |
| r-sqldf | 0.4_11 | package |
| r-stringr | 1.4.1 | package |
| r-tinytex | 0.42 | package |
| r-vioplot | 0.3.7 | package |
| Additional information about this tool |
echo '--- localization-filter step:'
&& (
Rscript '$__tool_directory__/MaxQuantProcessingScript.R'
-i '$phosphoSites'
#if $pst_py_selector == "y"
--enriched Y
#else
--enriched ST
#end if
--phosphoCol '$phosphocol_script'
--startCol '$startcol_script'
--intervalCol $intervalCol
--localProbCutoff $localProbCutoff
--collapse_func $merge_function
-o '$phosphoPepIntensities'
--locProbCutoffGraph $locProbCutoffGraph
--enrichGraph $enrichGraph
--locProbCutoffGraph_svg $locProbCutoffGraph_svg
--enrichGraph_svg $enrichGraph_svg
--filtered_data $filteredData_tabular
--quant_data $quantData_tabular
) &&
echo '... end localization-filter.'
&& (
echo '--- kinase-mapping step:'
) && (
perl '$__tool_directory__/PhosphoPeptide_Upstream_Kinase_Mapping.pl'
-i '$phosphoPepIntensities'
-f '$protein_fasta'
-n '$networkin'
-m '$p_sty_motifs'
-p '$psp_kinase_substrate'
-r '$psp_regulatory_sites'
#if $pst_py_selector == "y"
-P y
#else
-P sty
#end if
-F $merge_function
-o '$mapped_phophopeptides'
-O '$melted_phophopeptide_map'
-D '$mqppep_output_sqlite'
-s '$species'
) &&
echo '... end kinase-mapping.'
&&
echo '--- merge-and-filter step:'
&& (
python '$__tool_directory__/mqppep_mrgfltr.py'
--phosphopeptides='$mapped_phophopeptides'
--ppep_mapping_db='$mqppep_output_sqlite'
--species='$species'
--mrgfltr_tab='$preproc_tab'
--mrgfltr_csv='$preproc_csv'
--mrgfltr_sqlite='$preproc_sqlite'
)
&& echo '... end merge-and-filter.'
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
phosphoSites: test_input_for_preproc.tabular phosphoCol: ^Number of Phospho [(][STY][STY]*[)]$ startCol: ^Intensity[^_] intervalCol: 1 pst_py_selector: st merge_function: sum localProbCutoff: 0.75 protein_fasta: test_swissprot.fasta networkin: test_networkin.tabular p_sty_motifs: pSTY_motifs.tabular psp_kinase_substrate: test_kinase_substrate.tabular psp_regulatory_sites: test_regulatory_sites.tabular species: human |
name: value name: value name: value |
test_input_for_preproc.tabular test_swissprot.fasta test_networkin.tabular pSTY_motifs.tabular test_kinase_substrate.tabular test_regulatory_sites.tabular value |
| Test-2 |
phosphoSites: test_input_for_preproc.tabular phosphoCol: ^Number of Phospho [(][STY][STY]*[)]$ startCol: ^Intensity[^_] intervalCol: 1 pst_py_selector: y merge_function: sum localProbCutoff: 0.75 protein_fasta: test_swissprot.fasta networkin: test_networkin.tabular p_sty_motifs: pSTY_motifs.tabular psp_kinase_substrate: test_kinase_substrate.tabular psp_regulatory_sites: test_regulatory_sites.tabular species: human |
name: value name: value name: value |
test_input_for_preproc.tabular test_swissprot.fasta test_networkin.tabular pSTY_motifs.tabular test_kinase_substrate.tabular test_regulatory_sites.tabular value |