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diff fragpipe.xml @ 4:e969a182e3cb draft default tip

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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
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--- a/fragpipe.xml	Thu Sep 12 08:06:44 2024 +0000
+++ b/fragpipe.xml	Fri Dec 13 15:17:28 2024 +0000
@@ -200,6 +200,57 @@
         </output_collection>
       </test>
       <test expect_num_outputs="11">
+        <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="workflow_name" value="Default"/>
+        <param name="label_free_quantification_run" value="ionquant"/>
+        <param name="output_options" value="workflow,log,combined_outputs,concatenated_outputs"/>
+        <param name="license_agreements" value="true"/>
+        <param name="run_psm_validation" value="msbooster_percolator"/>
+        <output name="concat_psm_tsv" ftype="tabular">
+            <assert_contents>
+                <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;SpectralSim&#x9;RTScore&#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&#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&#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&#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_msbooster_percolator.txt" compare="contains">
+            <assert_contents>
+                <has_text text="crystalc.run-crystalc=false"/>
+            </assert_contents>
+        </output>
+        <output name="log" ftype="txt">
+            <assert_contents>
+                <has_text text="FragPipe version 20.0"/>
+            </assert_contents>
+        </output>
+        <output_collection name="combined_outputs" type="list">
+            <element name="combined_protein.tsv" ftype="tabular">
+                <assert_contents>
+                    <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="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"/>