Mercurial > repos > jjohnson > encyclopedia_searchtolib

comparison encyclopedia_searchtolib.xml @ 4:54f4d8c5fbe0 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 96a023cccea27c30ff61caf271a3c79b92db1873"
author jjohnson
date Tue, 07 Jul 2020 11:57:09 -0400
parents a74d446c8f5f
children b9c8e02d1405
comparison
equal deleted inserted replaced
3:899fc684202e 4:54f4d8c5fbe0
2 <description>Build a Chromatogram Library from Data-Independent Acquisition (DIA) MS/MS Data</description> 2 <description>Build a Chromatogram Library from Data-Independent Acquisition (DIA) MS/MS Data</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="aggressive"><![CDATA[
8 @CMD_IMPORTS@ 8 @CMD_IMPORTS@
9 @LINK_SCAN_INPUTS@ 9 @LINK_SCAN_INPUTS@
10 @LINK_FASTA_INPUT@ 10 @LINK_FASTA_INPUT@
11 @LINK_TARGET_FASTA@ 11 @LINK_TARGET_FASTA@
12 @LINK_LIB_INPUT@ 12 @LINK_LIB_INPUT@
26 @PEAK_OPTIONS@ 26 @PEAK_OPTIONS@
27 @WINDOW_OPTIONS@ 27 @WINDOW_OPTIONS@
28 @MODIFICATION_OPTIONS@ 28 @MODIFICATION_OPTIONS@
29 @SEARCH_OPTIONS@ | tee -a search2lib.log 29 @SEARCH_OPTIONS@ | tee -a search2lib.log
30 ; done && 30 ; done &&
31 for TXT in `find inputs/*.mzML.[efw]*[ast].txt`; do TRGT=`echo \$TXT | sed 's/mzML/dia/'`; ln -s \$TXT \$TRGT; done &&
31 EncyclopeDIA -Djava.awt.headless=true -Xmx12g -libexport 32 EncyclopeDIA -Djava.awt.headless=true -Xmx12g -libexport
32 #if not $l 33 #if not $l
33 -pecan 34 -pecan
34 #end if 35 #end if
35 @SCAN_INPUTS@ 36 @SCAN_INPUTS@
36 @FASTA_INPUT@ 37 @FASTA_INPUT@
37 @TARGET_FASTA@ 38 @TARGET_FASTA@
38 @LIB_INPUT@ 39 @LIB_INPUT@
39 -a $a 40 -a $a
40 -o chromatogram_library.elib 41 -o chromatogram_library.elib
42 && ls -l ./*.* inputs/*
41 | tee -a search2lib.log 43 | tee -a search2lib.log
42 ]]></command> 44 ]]></command>
43 <inputs> 45 <inputs>
44 <expand macro="scan_inputs"/> 46 <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"/> 47 <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"/>
52 <option value="elib" selected="true">elib</option> 54 <option value="elib" selected="true">elib</option>
53 <option value="features" selected="false">concatenated_features.txt</option> 55 <option value="features" selected="false">concatenated_features.txt</option>
54 <option value="results" selected="false">concatenated_results.txt</option> 56 <option value="results" selected="false">concatenated_results.txt</option>
55 <option value="decoy" selected="false">concatenated_decoy.txt</option> 57 <option value="decoy" selected="false">concatenated_decoy.txt</option>
56 <!-- 58 <!--
59 <option value="rt_plots" selected="false">Retention Time Plots</option>
60 <option value="rt_tables" selected="false">Retention Time Tables</option>
57 <option value="peptides" selected="false">peptides.txt (requires align between files)</option> 61 <option value="peptides" selected="false">peptides.txt (requires align between files)</option>
58 <option value="proteins" selected="false">proteins.txt (requires align between files)</option> 62 <option value="proteins" selected="false">proteins.txt (requires align between files)</option>
59 --> 63 -->
60 </param> 64 </param>
61 </inputs> 65 </inputs>
83 <actions> 87 <actions>
84 <action name="column_names" type="metadata" default="PSMId,score,q-value,posterior_error_prob,peptide,proteinIds" /> 88 <action name="column_names" type="metadata" default="PSMId,score,q-value,posterior_error_prob,peptide,proteinIds" />
85 </actions> 89 </actions>
86 </data> 90 </data>
87 <!-- 91 <!--
88 <data name="peptides" format="tabular" label="${tool.name} ${on_string} peptides.txt" from_work_dir="chromatogram_library.peptides.txt"> 92 <collection name="rt_plots" type="list" label="${tool.name} - ${on_string}: Retention Time Plots">
93 <filter>l and 'rt_plots' in select_outputs</filter>
94 <discover_datasets pattern="(?P&lt;designation&gt;.+\.pdf)" ext="pdf" directory="inputs"/>
95 </collection>
96 <collection name="rt_tables" type="list" label="${tool.name} - ${on_string}: Retention Time Tables">
97 <filter>l and 'rt_tables' in select_outputs</filter>
98 <discover_datasets pattern="(?P&lt;designation&gt;.+\.rt_fit\.txt)" ext="tabular" directory="inputs"/>
99 </collection>
100 -->
101
102 <!--
103 <data name="peptides" format="tabular" label="${tool.name} ${on_string} peptides.txt" from_work_dir="chromatogram_library.elib.peptides.txt">
89 <filter>a and 'peptides' in select_outputs</filter> 104 <filter>a and 'peptides' in select_outputs</filter>
90 <actions> 105 <actions>
91 <action name="column_names" type="metadata" default="Peptide,Protein,numFragments" /> 106 <action name="column_names" type="metadata" default="Peptide,Protein,numFragments" />
92 </actions> 107 </actions>
93 </data> 108 </data>
94 <data name="proteins" format="tabular" label="${tool.name} ${on_string} proteins.txt" from_work_dir="chromatogram_library.proteins.txt"> 109 <data name="proteins" format="tabular" label="${tool.name} ${on_string} proteins.txt" from_work_dir="chromatogram_library.elib.proteins.txt">
95 <filter>a and 'proteins' in select_outputs</filter> 110 <filter>a and 'proteins' in select_outputs</filter>
96 <actions> 111 <actions>
97 <action name="column_names" type="metadata" default="Protein,NumPeptides,PeptideSequences" /> 112 <action name="column_names" type="metadata" default="Protein,NumPeptides,PeptideSequences" />
98 </actions> 113 </actions>
99 </data> 114 </data>