From fa446d84782592b262d52f359949905338fa03ab Mon Sep 17 00:00:00 2001
From: Reid Wagner <wagnerr@umn.edu>
Date: Fri, 14 Jun 2024 09:27:56 -0500
Subject: [PATCH] Fix tabs in tests.

---
 tools/fragpipe/fragpipe.xml | 31 ++++++++++++++++---------------
 1 file changed, 16 insertions(+), 15 deletions(-)

diff --git a/tools/fragpipe/fragpipe.xml b/tools/fragpipe/fragpipe.xml
index c5da6433c..f7ce883f1 100644
--- a/tools/fragpipe/fragpipe.xml
+++ b/tools/fragpipe/fragpipe.xml
@@ -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>
@@ -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>
@@ -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>