Mercurial > repos > jjohnson > encyclopedia_searchtolib

comparison encyclopedia_searchtolib.xml @ 2:a74d446c8f5f draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
author jjohnson
date Wed, 01 Jul 2020 11:25:18 -0400
parents a7d52df6763f
children 54f4d8c5fbe0
comparison
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1:a7d52df6763f 2:a74d446c8f5f
43 <inputs> 43 <inputs>
44 <expand macro="scan_inputs"/> 44 <expand macro="scan_inputs"/>
45 <expand macro="lib_input" optional="true" libhelp="Use a Prosit dlib spectral library to make a chromatogram elib using EncyclopeDIA, or else leave blank to make a Chromatogram library from just the fasta using Walnut"/> 45 <expand macro="lib_input" optional="true" libhelp="Use a Prosit dlib spectral library to make a chromatogram elib using EncyclopeDIA, or else leave blank to make a Chromatogram library from just the fasta using Walnut"/>
46 <expand macro="fasta_input"/> 46 <expand macro="fasta_input"/>
47 <expand macro="target_fasta"/> 47 <expand macro="target_fasta"/>
48 <param argument="-a" type="boolean" truevalue="true" falsevalue="false" checked="false" label="align between files" help="retention-time alignment of peptides is generally not needed when using narrow-window spectrums"/> 48 <expand macro="options_section"/>
49 <expand macro="common_options"/> 49 <param argument="-a" type="boolean" truevalue="true" falsevalue="false" checked="false" label="align between files" help="retention-time alignment of peptides is generally not needed when when building a library from narrow-window spectrums"/>
50 <expand macro="mass_library_tolerance"/>
51 <expand macro="percolator_options"/>
52 <expand macro="peak_options"/>
53 <expand macro="window_options"/>
54 <expand macro="modification_options"/>
55 <expand macro="search_options"/>
56 <param name="select_outputs" type="select" label="Select outputs" multiple="true"> 50 <param name="select_outputs" type="select" label="Select outputs" multiple="true">
57 <option value="log" selected="true">log</option> 51 <option value="log" selected="true">log</option>
58 <option value="elib" selected="true">elib</option> 52 <option value="elib" selected="true">elib</option>
59 <option value="features" selected="false">concatenated_features.txt</option> 53 <option value="features" selected="false">concatenated_features.txt</option>
60 <option value="results" selected="false">concatenated_results.txt</option> 54 <option value="results" selected="false">concatenated_results.txt</option>
130 124
131 125
132 2. EncyclopeDIA Quantify is then run on the wide-window quantitative replicate mzML files using that chromatogram library to produce quantification results. 126 2. EncyclopeDIA Quantify is then run on the wide-window quantitative replicate mzML files using that chromatogram library to produce quantification results.
133 127
134 .. image:: SearchToLib_Workflow.png 128 .. image:: SearchToLib_Workflow.png
135 :height: 439 129 :width: 810
136 :width: 768 130 :height: 580
137 131
138 .. _Prosit: https://www.proteomicsdb.org/prosit 132 .. _Prosit: https://www.proteomicsdb.org/prosit
139 133
140 ]]></help> 134 ]]></help>
141 <expand macro="citations" /> 135 <expand macro="citations" />