Mercurial > repos > jjohnson > encyclopedia_searchtolib
comparison encyclopedia_searchtolib.xml @ 2:a74d446c8f5f draft
"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 |
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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" /> |