Mercurial > repos > jjohnson > encyclopedia_quantify

comparison encyclopedia_quantify.xml @ 1:acf6acfc8632 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 11:24:39 -0400
parents d3a6bc607825
children aa52f0eadc85
comparison
equal deleted inserted replaced
0:d3a6bc607825 1:acf6acfc8632
37 <inputs> 37 <inputs>
38 <expand macro="scan_inputs"/> 38 <expand macro="scan_inputs"/>
39 <expand macro="lib_input" optional="false" libhelp="Use a Chromatogram elib from SearchToLib"/> 39 <expand macro="lib_input" optional="false" libhelp="Use a Chromatogram elib from SearchToLib"/>
40 <expand macro="fasta_input"/> 40 <expand macro="fasta_input"/>
41 <expand macro="target_fasta"/> 41 <expand macro="target_fasta"/>
42 <expand macro="options_section"/>
42 <param argument="-a" type="boolean" truevalue="true" falsevalue="false" checked="true" label="align between files" help="retention-time alignment of peptides should be enabled when quantifying samples"/> 43 <param argument="-a" type="boolean" truevalue="true" falsevalue="false" checked="true" label="align between files" help="retention-time alignment of peptides should be enabled when quantifying samples"/>
43 <expand macro="common_options"/>
44 <expand macro="mass_library_tolerance"/>
45 <expand macro="percolator_options"/>
46 <expand macro="peak_options"/>
47 <expand macro="window_options"/>
48 <expand macro="modification_options"/>
49 <expand macro="search_options"/>
50 <param name="select_outputs" type="select" label="Select outputs" multiple="true"> 44 <param name="select_outputs" type="select" label="Select outputs" multiple="true">
51 <option value="log" selected="true">log</option> 45 <option value="log" selected="true">log</option>
52 <option value="elib" selected="true">elib</option> 46 <option value="elib" selected="true">elib</option>
53 <option value="features" selected="true">concatenated_features.txt</option> 47 <option value="features" selected="true">concatenated_features.txt</option>
54 <option value="results" selected="true">concatenated_results.txt</option> 48 <option value="results" selected="true">concatenated_results.txt</option>
118 112
119 113
120 2. EncyclopeDIA Quantify is then run on the wide-window quantitative replicate mzML files using that chromatogram library, with the *align between files* option, to produce quantification results. 114 2. EncyclopeDIA Quantify is then run on the wide-window quantitative replicate mzML files using that chromatogram library, with the *align between files* option, to produce quantification results.
121 115
122 .. image:: SearchToLib_Workflow.png 116 .. image:: SearchToLib_Workflow.png
123 :height: 439 117 :width: 810
124 :width: 768 118 :height: 580
125 119
126 .. _Prosit: https://www.proteomicsdb.org/prosit 120 .. _Prosit: https://www.proteomicsdb.org/prosit
127 121
128 ]]></help> 122 ]]></help>
129 <expand macro="citations" /> 123 <expand macro="citations" />