Mercurial > repos > jjohnson > encyclopedia_encyclopedia

comparison encyclopedia_encyclopedia.xml @ 6:61692bb2c78f draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 17dcc85ebd7507af5557a1aee4816ac437a3f27b"
author jjohnson
date Fri, 21 Aug 2020 16:07:21 -0400
parents aeda6093dd40
children b3c5daaea8f4
comparison
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5:aeda6093dd40 6:61692bb2c78f
33 <option value="first_rt_fit_pdf" selected="false">encyclopedia.txt.first.rt_fit.pdf</option> 33 <option value="first_rt_fit_pdf" selected="false">encyclopedia.txt.first.rt_fit.pdf</option>
34 <option value="first_rt_fit_txt" selected="false">encyclopedia.txt.first.rt_fit.txt</option> 34 <option value="first_rt_fit_txt" selected="false">encyclopedia.txt.first.rt_fit.txt</option>
35 <option value="final_delta_rt_pdf" selected="false">encyclopedia.txt.final.delta_rt.pdf</option> 35 <option value="final_delta_rt_pdf" selected="false">encyclopedia.txt.final.delta_rt.pdf</option>
36 <option value="final_rt_fit_pdf" selected="false">encyclopedia.txt.final.rt_fit.pdf</option> 36 <option value="final_rt_fit_pdf" selected="false">encyclopedia.txt.final.rt_fit.pdf</option>
37 <option value="final_rt_fit_txt" selected="false">encyclopedia.txt.final.rt_fit.txt</option> 37 <option value="final_rt_fit_txt" selected="false">encyclopedia.txt.final.rt_fit.txt</option>
38 <option value="features" selected="true">features.txt</option> 38 <option value="features" selected="false">features.txt</option>
39 <option value="encyclopedia" selected="true">encyclopedia.txt</option> 39 <option value="encyclopedia" selected="true">encyclopedia.txt</option>
40 <option value="encyclopedia_decoy" selected="false">encyclopedia.decoy.txt</option> 40 <option value="encyclopedia_decoy" selected="false">encyclopedia.decoy.txt</option>
41 </param> 41 </param>
42 </inputs> 42 </inputs>
43 <outputs> 43 <outputs>
93 <tests> 93 <tests>
94 <test> 94 <test>
95 <param name="scan_input" ftype="mzml" value="BCS_hela_wide_500_900_1.mzML"/> 95 <param name="scan_input" ftype="mzml" value="BCS_hela_wide_500_900_1.mzML"/>
96 <param name="library" ftype="elib" value="BCS_hela.elib"/> 96 <param name="library" ftype="elib" value="BCS_hela.elib"/>
97 <param name="fasta" ftype="fasta" value="uniprot_human.fasta"/> 97 <param name="fasta" ftype="fasta" value="uniprot_human.fasta"/>
98 <param name="select_outputs" values="log,features,encyclopedia"/>
98 <output name="features" ftype="tabular"> 99 <output name="features" ftype="tabular">
99 <assert_contents> 100 <assert_contents>
100 <has_text text="ESYDDVSSFR"/> 101 <has_text text="ESYDDVSSFR"/>
101 </assert_contents> 102 </assert_contents>
102 </output> 103 </output>
116 EncyclopeDIA extracts peptide fragmentation chromatograms from MZML files, matches them to spectra in libraries, and calculates various scoring features. These features are interpreted by Percolator to identify peptides. 117 EncyclopeDIA extracts peptide fragmentation chromatograms from MZML files, matches them to spectra in libraries, and calculates various scoring features. These features are interpreted by Percolator to identify peptides.
117 118
118 119
119 **Inputs** 120 **Inputs**
120 121
121
122 - A spectrum file in mzML format 122 - A spectrum file in mzML format
123 - A chromatogram library that can be generated by SearchToLib 123 - A chromatogram library that can be generated by SearchToLib
124 - A protein data base in fasta format 124 - A protein data base in fasta format
125 125
126 126
127 @MSCONVERT_HELP@ 127 @MSCONVERT_HELP@
128 128
129 **Outputs** 129 **Outputs**
130 130
131 - A log file 131 - A log file
132 - The identified features in tabular format 132 - A Chromatogram Library (.elib)
133 - The identified proteins in tabular format 133 - The identified features in tabular format
134 Feature values of scans that are used by percolator to determine matches.
135 - The identified Peptide Spectral Match results in tabular format
136 Columns: PSMId, score, q-value, posterior_error_prob, peptide, proteinIds
137 - The identified peptides in tabular format
138 Per peptide: the normalized intensity for each scan file.
139 Columns: Peptide, Protein, numFragments, intensity_in_file1, intensity_in_file2, ...
140 - The identified proteins in tabular format
141 Per protein: the normalized intensity for each scan file.
142 Columns: Protein, NumPeptides, PeptideSequences, intensity_in_file1, intensity_in_file2, ...
134 143
135 ]]></help> 144 ]]></help>
136 <expand macro="citations" /> 145 <expand macro="citations" />
137 </tool> 146 </tool>