Miscellaneous |
Version lineage of this tool (guids ordered most recent to oldest) |
toolshed.g2.bx.psu.edu/repos/galaxyp/pepquery/pepquery/1.6.2+galaxy1 (this tool) |
toolshed.g2.bx.psu.edu/repos/galaxyp/pepquery/pepquery/1.6.2+galaxy0 |
toolshed.g2.bx.psu.edu/repos/galaxyp/pepquery/pepquery/1.6.0.0 |
toolshed.g2.bx.psu.edu/repos/galaxyp/pepquery/pepquery/1.3.0.0 |
pepquery |
Requirements (dependencies defined in the <requirements> tag set) |
name | version | type |
pepquery | 1.6.2 | package |
Additional information about this tool |
#import re #set $spectrum_file = $re.sub('\s','_',$re.sub('[.][^.]*$','',$req_inputs.spectrum_file.display_name.split('/')[-1])) + ".mgf" #set $db_file = $re.sub('\s','_',$re.sub('[.][^.]*$','',$req_inputs.db_file.display_name.split('/')[-1])) + ".fa" ln -s '$req_inputs.spectrum_file' '$spectrum_file' && ln -s '$req_inputs.db_file' '$db_file' && #if $req_inputs.tags.tagType == 'pFind': pepquery main.java.util.generateTags '$req_inputs.tags.qry_res' > qry.tags && #end if pepquery -ms '$spectrum_file' -db '$db_file' #if $req_inputs.input_type.input_type_selector == 'peptide' -pep '$req_inputs.input_type.multiple.input' #else -t '$req_inputs.input_type.input_type_selector' #if int(str($req_inputs.input_type.input_type_selector)) == 1 -i '$req_inputs.input_type.multiple.input' #else -i '$req_inputs.input_type.input' #if int(str($req_inputs.input_type.input_type_selector)) == 2 #if $req_inputs.input_type.frame == 'None' -f '0' #else -f '$req_inputs.input_type.frame' #end if #else -anno '$req_inputs.input_type.anno' #end if #end if #end if -indexType $req_inputs.indexType #if $req_inputs.tags.tagType == 'PepQuery': -tag '$req_inputs.tags.tag_file' -tagIndexType $req_inputs.tags.tagIndexType #elif $req_inputs.tags.tagType == 'pFind': -tag qry.tags -tagIndexType 2 #end if #if $modifications.fixed_mod -fixMod '$modifications.fixed_mod' #end if #if $modifications.var_mod -varMod '$modifications.var_mod' #end if -maxVar '$modifications.max_mods' $modifications.unmodified $modifications.aa -tol '$ms_params.tolerance_params.precursor_tolerance' -tolu '$ms_params.tolerance_params.precursor_unit' -itol '$ms_params.tolerance_params.tolerance' -e '$ms_params.digestion.enzyme' -fragmentMethod '$ms_params.search.frag_method' -m '$ms_params.search.scoring_method' -maxCharge '$ms_params.search.max_charge' -minCharge '$ms_params.search.min_charge' -minPeaks '$ms_params.search.min_peaks' -minScore '$ms_params.search.min_score' -maxLength '$ms_params.search.max_length' -n '$ms_params.search.num_random_peptides' -o pepquery_output | sed 's/No valid peptide/Error: No valid peptide/' | tee >(cat 1>&2) #if $report_spectrum_file: && for f in pepquery_output/psm.txt pepquery_output/psm_annotation.txt pepquery_output/detail.txt pepquery_output/psm_rank.txt; do if [ -e \${f} ]; then cp \${f} \${f}.orig; awk 'BEGIN{FS="\t"; OFS="\t"; stc = 0;}; NR==1{for (i = 1; i <= NF; i++) {if (\$i == "spectrum_title") stc = i;}}; NR==1{if (stc>0){\$stc = "spectrum_file" FS \$stc}; print}; NR>1{if (stc>0){\$stc = "$spectrum_file" FS \$stc}; print}' \${f}.orig > \${f};fi;done #end if
Functional tests |
name | inputs | outputs | required files |
Test-1 |
req_inputs|input_type|multiple|input: ELGSSDLTAR req_inputs|input_type|multiple|peptide_input_selector: single req_inputs|input_type|input_type_selector: peptide req_inputs|db_file: Uniprot.fasta req_inputs|spectrum_file: iTRAQ_f4.mgf modifications|fixed_mod: ['6', '103', '157'] modifications|var_mod: 117 modifications|max_mods: 3 modifications|unmodified: False modifications|aa: True ms_params|tolerance_params|precursor_tolerance: 10 ms_params|tolerance_params|precursor_unit: ppm ms_params|tolerance_params|tolerance: 0.6 ms_params|digestion|enzyme: 0 ms_params|digestion|max_missed_cleavages: 2 ms_params|search|frag_method: 1 ms_params|search|scoring_method: 1 ms_params|search|max_charge: 3 ms_params|search|min_charge: 2 ms_params|search|min_peaks: 10 ms_params|search|min_score: 12 ms_params|search|max_length: 45 ms_params|search|num_random_peptides: 1000 report_spectrum_file: True |
name: value |
Uniprot.fasta iTRAQ_f4.mgf value |
Test-2 |
req_inputs|input_type|multiple|input: novel_peptides req_inputs|input_type|multiple|peptide_input_selector: multiple req_inputs|input_type|input_type_selector: peptide req_inputs|db_file: Uniprot.fasta req_inputs|spectrum_file: iTRAQ_f4.mgf modifications|fixed_mod: ['6', '103', '157'] modifications|var_mod: 117 modifications|max_mods: 3 modifications|unmodified: False modifications|aa: True ms_params|tolerance_params|precursor_tolerance: 10 ms_params|tolerance_params|precursor_unit: ppm ms_params|tolerance_params|tolerance: 0.6 ms_params|digestion|enzyme: 0 ms_params|digestion|max_missed_cleavages: 2 ms_params|search|frag_method: 1 ms_params|search|scoring_method: 1 ms_params|search|max_charge: 3 ms_params|search|min_charge: 2 ms_params|search|min_peaks: 10 ms_params|search|min_score: 12 ms_params|search|max_length: 45 ms_params|search|num_random_peptides: 1000 report_spectrum_file: True |
name: value |
novel_peptides Uniprot.fasta iTRAQ_f4.mgf value |
Test-3 |
req_inputs|input_type|multiple|input: novel_peptides req_inputs|input_type|multiple|peptide_input_selector: multiple req_inputs|input_type|input_type_selector: peptide req_inputs|db_file: Uniprot.fasta req_inputs|spectrum_file: iTRAQ_f4.mgf modifications|fixed_mod: ['6', '103', '157'] modifications|var_mod: 117 modifications|max_mods: 3 modifications|unmodified: True modifications|aa: True ms_params|tolerance_params|precursor_tolerance: 10 ms_params|tolerance_params|precursor_unit: ppm ms_params|tolerance_params|tolerance: 0.6 ms_params|digestion|enzyme: 0 ms_params|digestion|max_missed_cleavages: 1 ms_params|search|frag_method: 1 ms_params|search|scoring_method: 1 ms_params|search|max_charge: 3 ms_params|search|min_charge: 2 ms_params|search|min_peaks: 7 ms_params|search|min_score: 10 ms_params|search|max_length: 45 ms_params|search|num_random_peptides: 1000 report_spectrum_file: False |
name: value |
novel_peptides Uniprot.fasta iTRAQ_f4.mgf value |
Test-4 |
req_inputs|input_type|multiple|input: novel_proteins.fa req_inputs|input_type|multiple|protein_input_selector: multiple req_inputs|input_type|input_type_selector: 1 req_inputs|db_file: Uniprot.fasta req_inputs|spectrum_file: iTRAQ_f4.mgf modifications|fixed_mod: ['6', '103', '157'] modifications|var_mod: 117 modifications|max_mods: 3 modifications|unmodified: False modifications|aa: True ms_params|tolerance_params|precursor_tolerance: 10 ms_params|tolerance_params|precursor_unit: ppm ms_params|tolerance_params|tolerance: 0.6 ms_params|digestion|enzyme: 0 ms_params|digestion|max_missed_cleavages: 2 ms_params|search|frag_method: 1 ms_params|search|scoring_method: 1 ms_params|search|max_charge: 3 ms_params|search|min_charge: 2 ms_params|search|min_peaks: 10 ms_params|search|min_score: 12 ms_params|search|max_length: 45 ms_params|search|num_random_peptides: 1000 report_spectrum_file: True |
name: value |
novel_proteins.fa Uniprot.fasta iTRAQ_f4.mgf value |
Test-5 |
req_inputs|input_type|input: gaactgggcagcagcgatctgaccgcgcgcagcccgtatcgcgaatttaccgatcatctggtgaaa req_inputs|input_type|input_type_selector: 2 req_inputs|db_file: Uniprot.fasta req_inputs|spectrum_file: iTRAQ_f4.mgf modifications|fixed_mod: ['6', '103', '157'] modifications|var_mod: 117 modifications|max_mods: 3 modifications|unmodified: False modifications|aa: True ms_params|tolerance_params|precursor_tolerance: 10 ms_params|tolerance_params|precursor_unit: ppm ms_params|tolerance_params|tolerance: 0.6 ms_params|digestion|enzyme: 0 ms_params|digestion|max_missed_cleavages: 2 ms_params|search|frag_method: 1 ms_params|search|scoring_method: 1 ms_params|search|max_charge: 3 ms_params|search|min_charge: 2 ms_params|search|min_peaks: 10 ms_params|search|min_score: 12 ms_params|search|max_length: 45 ms_params|search|num_random_peptides: 1000 report_spectrum_file: True |
name: value |
Uniprot.fasta iTRAQ_f4.mgf value |
Test-6 |
req_inputs|input_type|multiple|input: novel_peptides req_inputs|input_type|multiple|peptide_input_selector: multiple req_inputs|input_type|input_type_selector: peptide req_inputs|db_file: Uniprot.fasta req_inputs|spectrum_file: immunopeptidomics.mgf req_inputs|indexType: 2 req_inputs|tags|tag_file: test.tags req_inputs|tags|tagIndexType: 2 req_inputs|tags|tagType: PepQuery modifications|fixed_mod: modifications|var_mod: ['117', '114', '118', '128'] modifications|max_mods: 3 modifications|unmodified: True modifications|aa: True ms_params|tolerance_params|precursor_tolerance: 20 ms_params|tolerance_params|precursor_unit: ppm ms_params|tolerance_params|tolerance: 0.02 ms_params|digestion|enzyme: 0 ms_params|digestion|max_missed_cleavages: 0 ms_params|search|frag_method: 1 ms_params|search|scoring_method: 1 ms_params|search|max_charge: 3 ms_params|search|min_charge: 2 ms_params|search|min_peaks: 10 ms_params|search|min_score: 12 ms_params|search|max_length: 25 ms_params|search|num_random_peptides: 1000 report_spectrum_file: True |
name: value |
novel_peptides Uniprot.fasta immunopeptidomics.mgf test.tags value |
Test-7 |
req_inputs|input_type|multiple|input: novel_peptides req_inputs|input_type|multiple|peptide_input_selector: multiple req_inputs|input_type|input_type_selector: peptide req_inputs|db_file: Uniprot.fasta req_inputs|spectrum_file: immunopeptidomics.mgf req_inputs|indexType: 2 req_inputs|tags|qry_res: pFind.qry.res req_inputs|tags|tagType: pFind modifications|fixed_mod: modifications|var_mod: ['117', '114', '118', '128'] modifications|max_mods: 3 modifications|unmodified: True modifications|aa: True ms_params|tolerance_params|precursor_tolerance: 20 ms_params|tolerance_params|precursor_unit: ppm ms_params|tolerance_params|tolerance: 0.02 ms_params|digestion|enzyme: 0 ms_params|digestion|max_missed_cleavages: 0 ms_params|search|frag_method: 1 ms_params|search|scoring_method: 1 ms_params|search|max_charge: 3 ms_params|search|min_charge: 2 ms_params|search|min_peaks: 10 ms_params|search|min_score: 12 ms_params|search|max_length: 25 ms_params|search|num_random_peptides: 1000 report_spectrum_file: True |
name: value name: value |
novel_peptides Uniprot.fasta immunopeptidomics.mgf pFind.qry.res value |