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comparison encyclopedia_encyclopedia.xml @ 0:d0ea7589e95f draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
author galaxyp
date Mon, 14 Sep 2020 17:05:37 +0000
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children d263296cd73e
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-1:000000000000 0:d0ea7589e95f
1 <tool id="encyclopedia_encyclopedia" name="EncyclopeDIA" version="@VERSION@.0">
2 <description>Library Searching Directly from Data-Independent Acquisition (DIA) MS/MS Data</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <command detect_errors="aggressive"><![CDATA[
8 @CMD_IMPORTS@
9 @LINK_SCAN_INPUT@
10 @LINK_FASTA_INPUT@
11 @LINK_LIB_INPUT@
12 EncyclopeDIA -Djava.awt.headless=true -Duser.language=en-US -Duser.region=US
13 -Xmx\$[ \${GALAXY_MEMORY_MB:-20480} / 1024 ]g
14 -numberOfThreadsUsed "\${GALAXY_SLOTS:-4}"
15 @SCAN_INPUT@
16 @FASTA_INPUT@
17 @LIB_INPUT@
18 @COMMON_OPTIONS@
19 @MASS_LIBRARY_TOLERANCE@
20 @PERCOLATOR_OPTIONS@
21 @PEAK_OPTIONS@
22 @WINDOW_OPTIONS@
23 @MODIFICATION_OPTIONS@
24 -o gxpedia
25 ]]></command>
26 <inputs>
27 <expand macro="scan_input"/>
28 <expand macro="fasta_input"/>
29 <expand macro="lib_input" optional="false" libhelp="Chromatogram elib from SearchToLib on pooled samples"/>
30 <expand macro="options_section"/>
31 <param name="select_outputs" type="select" label="Select outputs" multiple="true">
32 <option value="log" selected="true">log</option>
33 <option value="elib" selected="true">elib</option>
34 <option value="first_delta_rt_pdf" selected="false">Initial Delta Retention Time Plot</option>
35 <option value="first_rt_fit_pdf" selected="false">Initial Fitted Retention Time Plot</option>
36 <option value="first_rt_fit_txt" selected="false">Initial Fitted Retention Time Table</option>
37 <option value="final_delta_rt_pdf" selected="false">Final Delta Retention Time Plot</option>
38 <option value="final_rt_fit_pdf" selected="false">Final Fitted Retention Time Plot</option>
39 <option value="final_rt_fit_txt" selected="false">Final Fitted Retention Time Table</option>
40 <option value="features" selected="false">features</option>
41 <option value="encyclopedia" selected="true">encyclopedia results</option>
42 <option value="encyclopedia_decoy" selected="false">encyclopedia decoy results</option>
43 </param>
44 </inputs>
45 <outputs>
46 <data name="log" format="txt" label="${tool.name} ${on_string} log" from_work_dir="gxpedia.log">
47 <filter>'log' in select_outputs</filter>
48 </data>
49 <data name="elib" format="elib" label="${tool.name} ${on_string} elib" from_work_dir="gxpedia.elib">
50 <filter>'elib' in select_outputs</filter>
51 </data>
52 <data name="first_delta_rt_pdf" format="pdf" label="${tool.name} ${on_string} encyclopedia.txt.first.delta_rt.pdf" from_work_dir="gxpedia.encyclopedia.txt.first.delta_rt.pdf">
53 <filter>'first_delta_rt_pdf' in select_outputs</filter>
54 </data>
55 <data name="first_rt_fit_pdf" format="pdf" label="${tool.name} ${on_string} encyclopedia.txt.first.rt_fit.pdf" from_work_dir="gxpedia.encyclopedia.txt.first.rt_fit.pdf">
56 <filter>'first_rt_fit_pdf' in select_outputs</filter>
57 </data>
58 <data name="first_rt_fit_txt" format="tabular" label="${tool.name} ${on_string} encyclopedia.txt.first.rt_fit.txt" from_work_dir="gxpedia.encyclopedia.txt.first.rt_fit.txt">
59 <filter>'first_rt_fit_txt' in select_outputs</filter>
60 <actions>
61 <action name="column_names" type="metadata" default="library,actual,warpToActual,delta,fitProb,isDecoy,sequence" />
62 </actions>
63 </data>
64 <data name="final_delta_rt_pdf" format="pdf" label="${tool.name} ${on_string} encyclopedia.txt.final.delta_rt.pdf" from_work_dir="gxpedia.encyclopedia.txt.final.delta_rt.pdf">
65 <filter>'final_delta_rt_pdf' in select_outputs</filter>
66 </data>
67 <data name="final_rt_fit_pdf" format="pdf" label="${tool.name} ${on_string} encyclopedia.txt.final.rt_fit.pdf" from_work_dir="gxpedia.encyclopedia.txt.final.rt_fit.pdf">
68 <filter>'final_rt_fit_pdf' in select_outputs</filter>
69 </data>
70 <data name="final_rt_fit_txt" format="tabular" label="${tool.name} ${on_string} encyclopedia.txt.final.rt_fit.txt" from_work_dir="gxpedia.encyclopedia.txt.final.rt_fit.txt">
71 <filter>'final_rt_fit_txt' in select_outputs</filter>
72 <actions>
73 <action name="column_names" type="metadata" default="library,actual,warpToActual,delta,fitProb,isDecoy,sequence" />
74 </actions>
75 </data>
76 <data name="features" format="tabular" label="${tool.name} ${on_string} features.txt" from_work_dir="gxpedia.features.txt">
77 <filter>'features' in select_outputs</filter>
78 <actions>
79 <action name="column_names" type="metadata" default="id,TD,ScanNr,topN,deltaCN,primary,xCorrLib,xCorrModel,LogDotProduct,logWeightedDotProduct,sumOfSquaredErrors,weightedSumOfSquaredErrors,numberOfMatchingPeaks,numberOfMatchingPeaksAboveThreshold,averageAbsFragmentDeltaMass,averageFragmentDeltaMasses,isotopeDotProduct,averageAbsParentDeltaMass,averageParentDeltaMass,eValue,deltaRT,pepLength,charge2,charge3,precursorMz,RTinMin,sequence,protein" />
80 </actions>
81 </data>
82 <data name="encyclopedia" format="tabular" label="${tool.name} ${on_string} encyclopedia.txt" from_work_dir="gxpedia.encyclopedia.txt">
83 <filter>'encyclopedia' in select_outputs</filter>
84 <actions>
85 <action name="column_names" type="metadata" default="PSMId,score,q-value,posterior_error_prob,peptide,proteinIds" />
86 </actions>
87 </data>
88 <data name="encyclopedia_decoy" format="tabular" label="${tool.name} ${on_string} encyclopedia.decoy.txt" from_work_dir="gxpedia.encyclopedia.decoy.txt">
89 <filter>'encyclopedia_decoy' in select_outputs</filter>
90 <actions>
91 <action name="column_names" type="metadata" default="PSMId,score,q-value,posterior_error_prob,peptide,proteinIds" />
92 </actions>
93 </data>
94 </outputs>
95 <tests>
96 <test>
97 <param name="scan_input" ftype="mzml" value="BCS_hela_wide_500_900_1.mzML"/>
98 <param name="library" ftype="elib" value="BCS_hela.elib"/>
99 <param name="fasta" ftype="fasta" value="uniprot_human.fasta"/>
100 <param name="select_outputs" value="log,features,encyclopedia"/>
101 <output name="features" ftype="tabular">
102 <assert_contents>
103 <has_text text="ESYDDVSSFR"/>
104 </assert_contents>
105 </output>
106 <output name="encyclopedia" ftype="tabular">
107 <assert_contents>
108 <has_text text="ESYDDVSSFR"/>
109 </assert_contents>
110 </output>
111 </test>
112 </tests>
113
114 <help><![CDATA[
115 **EncyclopeDIA**
116
117 @ENCYCLOPEDIA_WIKI@
118
119 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.
120
121
122 **Inputs**
123
124 - A spectrum file in mzML format
125 - A chromatogram library that can be generated by SearchToLib
126 - A protein data base in fasta format
127
128
129 @MSCONVERT_HELP@
130
131 **Outputs**
132
133 - A log file
134 - A Chromatogram Library (.elib)
135 - The identified features in tabular format
136 Feature values of scans that are used by percolator to determine matches.
137 - The identified Peptide Spectral Match results in tabular format
138 Columns: PSMId, score, q-value, posterior_error_prob, peptide, proteinIds
139 - The identified peptides in tabular format
140 Per peptide: the normalized intensity for each scan file.
141 Columns: Peptide, Protein, numFragments, intensity_in_file1, intensity_in_file2, ...
142 - The identified proteins in tabular format
143 Per protein: the normalized intensity for each scan file.
144 Columns: Protein, NumPeptides, PeptideSequences, intensity_in_file1, intensity_in_file2, ...
145
146 ]]></help>
147 <expand macro="citations" />
148 </tool>