Mercurial > repos > galaxyp > fragpipe
comparison fragpipe.xml @ 4:e969a182e3cb draft default tip
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit f98d62a3e8aef1dd26fa64eff5c19f5773652d43
| author | galaxyp |
|---|---|
| date | Fri, 13 Dec 2024 15:17:28 +0000 |
| parents | da9ebef968bd |
| children |
comparison
equal
deleted
inserted
replaced
| 3:da9ebef968bd | 4:e969a182e3cb |
|---|---|
| 180 <has_text text="Experiment	Protein	Protein ID	Entry Name	Gene	Length	Organism	Protein Description	Protein Existence	Coverage	Protein Probability	Top Peptide Probability	Total Peptides	Unique Peptides	Razor Peptides	Total Spectral Count	Unique Spectral Count	Razor Spectral Count	Total Intensity	Unique Intensity	Razor Intensity	Razor Assigned Modifications	Razor Observed Modifications	Indistinguishable Proteins"/> | 180 <has_text text="Experiment	Protein	Protein ID	Entry Name	Gene	Length	Organism	Protein Description	Protein Existence	Coverage	Protein Probability	Top Peptide Probability	Total Peptides	Unique Peptides	Razor Peptides	Total Spectral Count	Unique Spectral Count	Razor Spectral Count	Total Intensity	Unique Intensity	Razor Intensity	Razor Assigned Modifications	Razor Observed Modifications	Indistinguishable Proteins"/> |
| 181 <has_text text="sample1"/> | 181 <has_text text="sample1"/> |
| 182 </assert_contents> | 182 </assert_contents> |
| 183 </output> | 183 </output> |
| 184 <output name="output_workflow" ftype="txt" file="default/outputs/workflow.txt" compare="contains"> | 184 <output name="output_workflow" ftype="txt" file="default/outputs/workflow.txt" compare="contains"> |
| 185 <assert_contents> | |
| 186 <has_text text="crystalc.run-crystalc=false"/> | |
| 187 </assert_contents> | |
| 188 </output> | |
| 189 <output name="log" ftype="txt"> | |
| 190 <assert_contents> | |
| 191 <has_text text="FragPipe version 20.0"/> | |
| 192 </assert_contents> | |
| 193 </output> | |
| 194 <output_collection name="combined_outputs" type="list"> | |
| 195 <element name="combined_protein.tsv" ftype="tabular"> | |
| 196 <assert_contents> | |
| 197 <has_text text="Protein	Protein ID	Entry Name	Gene	Protein Length	Organism	Protein Existence	Description	Protein Probability	Top Peptide Probability	Combined Total Peptides	Combined Spectral Count	Combined Unique Spectral Count	Combined Total Spectral Count	sample1 Spectral Count	sample2 Spectral Count	sample1 Intensity	sample2 Intensity	Indistinguishable Proteins"/> | |
| 198 </assert_contents> | |
| 199 </element> | |
| 200 </output_collection> | |
| 201 </test> | |
| 202 <test expect_num_outputs="11"> | |
| 203 <param name="inputs" value="default/test1.mzML,default/test2.mzML" ftype="mzml"/> | |
| 204 <param name="database_name" value="default/test.fasta" ftype="fasta"/> | |
| 205 <param name="manifest" value="default/test.manifest" ftype="tabular"/> | |
| 206 <param name="workflow_name" value="Default"/> | |
| 207 <param name="label_free_quantification_run" value="ionquant"/> | |
| 208 <param name="output_options" value="workflow,log,combined_outputs,concatenated_outputs"/> | |
| 209 <param name="license_agreements" value="true"/> | |
| 210 <param name="run_psm_validation" value="msbooster_percolator"/> | |
| 211 <output name="concat_psm_tsv" ftype="tabular"> | |
| 212 <assert_contents> | |
| 213 <has_text text="Experiment	Spectrum	Spectrum File	Peptide	Modified Peptide	Extended Peptide	Prev AA	Next AA	Peptide Length	Charge	Retention	Observed Mass	Calibrated Observed Mass	Observed M/Z	Calibrated Observed M/Z	Calculated Peptide Mass	Calculated M/Z	Delta Mass	SpectralSim	RTScore	Expectation	Hyperscore	Nextscore	PeptideProphet Probability	Number of Enzymatic Termini	Number of Missed Cleavages	Protein Start	Protein End	Intensity	Assigned Modifications	Observed Modifications	Purity	Is Unique	Protein	Protein ID	Entry Name	Gene	Protein Description	Mapped Genes	Mapped Proteins"/> | |
| 214 <has_text text="sample1"/> | |
| 215 </assert_contents> | |
| 216 </output> | |
| 217 <output name="concat_ion_tsv" ftype="tabular"> | |
| 218 <assert_contents> | |
| 219 <has_text text="Experiment	Peptide Sequence	Modified Sequence	Prev AA	Next AA	Peptide Length	Protein Start	Protein End	M/Z	Charge	Observed Mass	Probability	Expectation	Spectral Count	Intensity	Assigned Modifications	Observed Modifications	Protein	Protein ID	Entry Name	Gene	Protein Description	Mapped Genes	Mapped Proteins"/> | |
| 220 <has_text text="sample1"/> | |
| 221 </assert_contents> | |
| 222 </output> | |
| 223 <output name="concat_peptide_tsv" ftype="tabular"> | |
| 224 <assert_contents> | |
| 225 <has_text text="Experiment	Peptide	Prev AA	Next AA	Peptide Length	Protein Start	Protein End	Charges	Probability	Spectral Count	Intensity	Assigned Modifications	Observed Modifications	Protein	Protein ID	Entry Name	Gene	Protein Description	Mapped Genes	Mapped Proteins"/> | |
| 226 <has_text text="sample1"/> | |
| 227 </assert_contents> | |
| 228 </output> | |
| 229 <output name="concat_protein_tsv" ftype="tabular"> | |
| 230 <assert_contents> | |
| 231 <has_text text="Experiment	Protein	Protein ID	Entry Name	Gene	Length	Organism	Protein Description	Protein Existence	Coverage	Protein Probability	Top Peptide Probability	Total Peptides	Unique Peptides	Razor Peptides	Total Spectral Count	Unique Spectral Count	Razor Spectral Count	Total Intensity	Unique Intensity	Razor Intensity	Razor Assigned Modifications	Razor Observed Modifications	Indistinguishable Proteins"/> | |
| 232 <has_text text="sample1"/> | |
| 233 </assert_contents> | |
| 234 </output> | |
| 235 <output name="output_workflow" ftype="txt" file="default/outputs/workflow_msbooster_percolator.txt" compare="contains"> | |
| 185 <assert_contents> | 236 <assert_contents> |
| 186 <has_text text="crystalc.run-crystalc=false"/> | 237 <has_text text="crystalc.run-crystalc=false"/> |
| 187 </assert_contents> | 238 </assert_contents> |
| 188 </output> | 239 </output> |
| 189 <output name="log" ftype="txt"> | 240 <output name="log" ftype="txt"> |