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Fix tabs in tests.
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@reid-wagner
reid-wagner committed Jun 14, 2024
1 parent 1c7d2a6 commit fa446d8
Showing 1 changed file with 16 additions and 15 deletions.
31 changes: 16 additions & 15 deletions tools/fragpipe/fragpipe.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -167,25 +167,25 @@
<param name="license_agreements" value="true"/>
<output name="concat_psm_tsv" ftype="tabular">
<assert_contents>
<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 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"/>
<has_text text="Experiment&#x9;Spectrum&#x9;Spectrum File&#x9;Peptide&#x9;Modified Peptide&#x9;Extended Peptide&#x9;Prev AA&#x9;Next AA&#x9;Peptide Length&#x9;Charge&#x9;Retention&#x9;Observed Mass&#x9;Calibrated Observed Mass&#x9;Observed M/Z&#x9;Calibrated Observed M/Z&#x9;Calculated Peptide Mass&#x9;Calculated M/Z&#x9;Delta Mass&#x9;Expectation&#x9;Hyperscore&#x9;Nextscore&#x9;PeptideProphet Probability&#x9;Number of Enzymatic Termini&#x9;Number of Missed Cleavages&#x9;Protein Start&#x9;Protein End&#x9;Intensity&#x9;Assigned Modifications&#x9;Observed Modifications&#x9;Purity&#x9;Is Unique&#x9;Protein&#x9;Protein ID&#x9;Entry Name&#x9;Gene&#x9;Protein Description&#x9;Mapped Genes&#x9;Mapped Proteins"/>
<has_text text="sample1"/>
</assert_contents>
</output>
<output name="concat_ion_tsv" ftype="tabular">
<assert_contents>
<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"/>
<has_text text="Experiment&#x9;Peptide Sequence&#x9;Modified Sequence&#x9;Prev AA&#x9;Next AA&#x9;Peptide Length&#x9;Protein Start&#x9;Protein End&#x9;M/Z&#x9;Charge&#x9;Observed Mass&#x9;Probability&#x9;Expectation&#x9;Spectral Count&#x9;Intensity&#x9;Assigned Modifications&#x9;Observed Modifications&#x9;Protein&#x9;Protein ID&#x9;Entry Name&#x9;Gene&#x9;Protein Description&#x9;Mapped Genes&#x9;Mapped Proteins"/>
<has_text text="sample1"/>
</assert_contents>
</output>
<output name="concat_peptide_tsv" ftype="tabular">
<assert_contents>
<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"/>
<has_text text="Experiment&#x9;Peptide&#x9;Prev AA&#x9;Next AA&#x9;Peptide Length&#x9;Protein Start&#x9;Protein End&#x9;Charges&#x9;Probability&#x9;Spectral Count&#x9;Intensity&#x9;Assigned Modifications&#x9;Observed Modifications&#x9;Protein&#x9;Protein ID&#x9;Entry Name&#x9;Gene&#x9;Protein Description&#x9;Mapped Genes&#x9;Mapped Proteins"/>
<has_text text="sample1"/>
</assert_contents>
</output>
<output name="concat_protein_tsv" ftype="tabular">
<assert_contents>
<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"/>
<has_text text="Experiment&#x9;Protein&#x9;Protein ID&#x9;Entry Name&#x9;Gene&#x9;Length&#x9;Organism&#x9;Protein Description&#x9;Protein Existence&#x9;Coverage&#x9;Protein Probability&#x9;Top Peptide Probability&#x9;Total Peptides&#x9;Unique Peptides&#x9;Razor Peptides&#x9;Total Spectral Count&#x9;Unique Spectral Count&#x9;Razor Spectral Count&#x9;Total Intensity&#x9;Unique Intensity&#x9;Razor Intensity&#x9;Razor Assigned Modifications&#x9;Razor Observed Modifications&#x9;Indistinguishable Proteins"/>
<has_text text="sample1"/>
</assert_contents>
</output>
Expand All @@ -202,44 +202,45 @@
<output_collection name="combined_outputs" type="list">
<element name="combined_protein.tsv" ftype="tabular">
<assert_contents>
<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"/>
<has_text text="Protein&#x9;Protein ID&#x9;Entry Name&#x9;Gene&#x9;Protein Length&#x9;Organism&#x9;Protein Existence&#x9;Description&#x9;Protein Probability&#x9;Top Peptide Probability&#x9;Combined Total Peptides&#x9;Combined Spectral Count&#x9;Combined Unique Spectral Count&#x9;Combined Total Spectral Count&#x9;sample1 Spectral Count&#x9;sample2 Spectral Count&#x9;sample1 Intensity&#x9;sample2 Intensity&#x9;Indistinguishable Proteins"/>
</assert_contents>
</element>
</output_collection>
</test>
<test expect_num_outputs="11">
<param name="scanformat" value="mzML"/>
<param name="inputs" value="default/test1.mzML,default/test2.mzML" ftype="mzml"/>
<param name="database_name" value="default/test.fasta" ftype="fasta"/>
<param name="manifest" value="default/test.manifest" ftype="tabular"/>
<param name="inputs" value="tmt11/test1.mzML,tmt11/test2.mzML" ftype="mzml"/>
<param name="database_name" value="tmt11/test.fasta" ftype="fasta"/>
<param name="manifest" value="tmt11/test.manifest" ftype="tabular"/>
<param name="annotation" value="tmt11/test.annotation" ftype="tabular"/>
<param name="workflow_name" value="TMT11"/>
<param name="output_options" value="workflow,log,concatenated_outputs"/>
<param name="license_agreements" value="true"/>
<output name="concat_psm_tsv" ftype="tabular">
<assert_contents>
<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 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"/>
<has_text text="Experiment&#x9;Spectrum&#x9;Spectrum File&#x9;Peptide&#x9;Modified Peptide&#x9;Extended Peptide&#x9;Prev AA&#x9;Next AA&#x9;Peptide Length&#x9;Charge&#x9;Retention&#x9;Observed Mass&#x9;Calibrated Observed Mass&#x9;Observed M/Z&#x9;Calibrated Observed M/Z&#x9;Calculated Peptide Mass&#x9;Calculated M/Z&#x9;Delta Mass&#x9;Expectation&#x9;Hyperscore&#x9;Nextscore&#x9;PeptideProphet Probability&#x9;Number of Enzymatic Termini&#x9;Number of Missed Cleavages&#x9;Protein Start&#x9;Protein End&#x9;Intensity&#x9;Assigned Modifications&#x9;Observed Modifications&#x9;Purity&#x9;Is Unique&#x9;Protein&#x9;Protein ID&#x9;Entry Name&#x9;Gene&#x9;Protein Description&#x9;Mapped Genes&#x9;Mapped Proteins"/>
<has_text text="sample1"/>
</assert_contents>
</output>
<output name="concat_ion_tsv" ftype="tabular">
<assert_contents>
<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"/>
<has_text text="Experiment&#x9;Peptide Sequence&#x9;Modified Sequence&#x9;Prev AA&#x9;Next AA&#x9;Peptide Length&#x9;Protein Start&#x9;Protein End&#x9;M/Z&#x9;Charge&#x9;Observed Mass&#x9;Probability&#x9;Expectation&#x9;Spectral Count&#x9;Intensity&#x9;Assigned Modifications&#x9;Observed Modifications&#x9;Protein&#x9;Protein ID&#x9;Entry Name&#x9;Gene&#x9;Protein Description&#x9;Mapped Genes&#x9;Mapped Proteins"/>
<has_text text="sample1"/>
</assert_contents>
</output>
<output name="concat_peptide_tsv" ftype="tabular">
<assert_contents>
<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"/>
<has_text text="Experiment&#x9;Peptide&#x9;Prev AA&#x9;Next AA&#x9;Peptide Length&#x9;Protein Start&#x9;Protein End&#x9;Charges&#x9;Probability&#x9;Spectral Count&#x9;Intensity&#x9;Assigned Modifications&#x9;Observed Modifications&#x9;Protein&#x9;Protein ID&#x9;Entry Name&#x9;Gene&#x9;Protein Description&#x9;Mapped Genes&#x9;Mapped Proteins"/>
<has_text text="sample1"/>
</assert_contents>
</output>
<output name="concat_protein_tsv" ftype="tabular">
<assert_contents>
<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"/>
<has_text text="Experiment&#x9;Protein&#x9;Protein ID&#x9;Entry Name&#x9;Gene&#x9;Length&#x9;Organism&#x9;Protein Description&#x9;Protein Existence&#x9;Coverage&#x9;Protein Probability&#x9;Top Peptide Probability&#x9;Total Peptides&#x9;Unique Peptides&#x9;Razor Peptides&#x9;Total Spectral Count&#x9;Unique Spectral Count&#x9;Razor Spectral Count&#x9;Total Intensity&#x9;Unique Intensity&#x9;Razor Intensity&#x9;Razor Assigned Modifications&#x9;Razor Observed Modifications&#x9;Indistinguishable Proteins"/>
<has_text text="sample1"/>
</assert_contents>
</output>
<output name="output_workflow" ftype="txt" file="default/outputs/workflow.txt" compare="contains">
<output name="output_workflow" ftype="txt" file="tmt11/outputs/workflow.txt" compare="contains">
<assert_contents>
<has_text text="crystalc.run-crystalc=false"/>
</assert_contents>
Expand All @@ -252,12 +253,12 @@
<output_collection name="tmt_results" type="list">
<element name="abundance_gene_MD.tsv" ftype="tabular">
<assert_contents>
<has_text text="Index NumberPSM ProteinID MaxPepProb ReferenceIntensity sample-01 sample-02 sample-03 sample-04 sample-05 sample-06 sample-07 sample-08 sample-09 sample-10 Bridge"/>
<has_text text="Index&#x9;NumberPSM&#x9;ProteinID&#x9;MaxPepProb&#x9;ReferenceIntensity&#x9;sample-01&#x9;sample-02&#x9;sample-03&#x9;sample-04&#x9;sample-05&#x9;sample-06&#x9;sample-07&#x9;sample-08&#x9;sample-09&#x9;sample-10&#x9;Bridge"/>
</assert_contents>
</element>
<element name="ratio_gene_MD.tsv" ftype="tabular">
<assert_contents>
<has_text text="Index NumberPSM ProteinID MaxPepProb ReferenceIntensity sample-01 sample-02 sample-03 sample-04 sample-05 sample-06 sample-07 sample-08 sample-09 sample-10 Bridge"/>
<has_text text="Index&#x9;NumberPSM&#x9;ProteinID&#x9;MaxPepProb&#x9;ReferenceIntensity&#x9;sample-01&#x9;sample-02&#x9;sample-03&#x9;sample-04&#x9;sample-05&#x9;sample-06&#x9;sample-07&#x9;sample-08&#x9;sample-09&#x9;sample-10&#x9;Bridge"/>
</assert_contents>
</element>
</output_collection>
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