Mercurial > repos > jjohnson > encyclopedia_quantify

comparison encyclopedia_quantify.xml @ 3:aa52f0eadc85 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 11:56:28 -0400
parents acf6acfc8632
children bd937e4efa04
comparison
equal deleted inserted replaced
2:174886084dc5 3:aa52f0eadc85
2 <description>samples from Data-Independent Acquisition (DIA) MS/MS Data</description> 2 <description>samples 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@
23 @PEAK_OPTIONS@ 23 @PEAK_OPTIONS@
24 @WINDOW_OPTIONS@ 24 @WINDOW_OPTIONS@
25 @MODIFICATION_OPTIONS@ 25 @MODIFICATION_OPTIONS@
26 @SEARCH_OPTIONS@ | tee -a search2lib.log 26 @SEARCH_OPTIONS@ | tee -a search2lib.log
27 ; done && 27 ; done &&
28 for TXT in `find inputs/*.mzML.[efw]*[ast].txt`; do TRGT=`echo \$TXT | sed 's/mzML/dia/'`; ln -s \$TXT \$TRGT; done &&
28 EncyclopeDIA -Djava.awt.headless=true -Xmx12g -libexport 29 EncyclopeDIA -Djava.awt.headless=true -Xmx12g -libexport
29 @SCAN_INPUTS@ 30 @SCAN_INPUTS@
30 @FASTA_INPUT@ 31 @FASTA_INPUT@
31 @TARGET_FASTA@ 32 @TARGET_FASTA@
32 @LIB_INPUT@ 33 @LIB_INPUT@
33 -a $a 34 -a $a
34 -o chromatogram_library.elib 35 -o chromatogram_library.elib
36 && ls -l ./*.* inputs/*
35 | tee -a search2lib.log 37 | tee -a search2lib.log
36 ]]></command> 38 ]]></command>
37 <inputs> 39 <inputs>
38 <expand macro="scan_inputs"/> 40 <expand macro="scan_inputs"/>
39 <expand macro="lib_input" optional="false" libhelp="Use a Chromatogram elib from SearchToLib"/> 41 <expand macro="lib_input" optional="false" libhelp="Use a Chromatogram elib from SearchToLib"/>
45 <option value="log" selected="true">log</option> 47 <option value="log" selected="true">log</option>
46 <option value="elib" selected="true">elib</option> 48 <option value="elib" selected="true">elib</option>
47 <option value="features" selected="true">concatenated_features.txt</option> 49 <option value="features" selected="true">concatenated_features.txt</option>
48 <option value="results" selected="true">concatenated_results.txt</option> 50 <option value="results" selected="true">concatenated_results.txt</option>
49 <option value="decoy" selected="false">concatenated_decoy.txt</option> 51 <option value="decoy" selected="false">concatenated_decoy.txt</option>
52 <!--
53 <option value="rt_plots" selected="false">Retention Time Plots</option>
54 <option value="rt_tables" selected="false">Retention Time Tables</option>
55 -->
50 <option value="peptides" selected="true">peptides.txt (requires align between files)</option> 56 <option value="peptides" selected="true">peptides.txt (requires align between files)</option>
51 <option value="proteins" selected="true">proteins.txt (requires align between files)</option> 57 <option value="proteins" selected="true">proteins.txt (requires align between files)</option>
52 </param> 58 </param>
53 </inputs> 59 </inputs>
54 <outputs> 60 <outputs>
74 <filter>'decoy' in select_outputs</filter> 80 <filter>'decoy' in select_outputs</filter>
75 <actions> 81 <actions>
76 <action name="column_names" type="metadata" default="PSMId,score,q-value,posterior_error_prob,peptide,proteinIds" /> 82 <action name="column_names" type="metadata" default="PSMId,score,q-value,posterior_error_prob,peptide,proteinIds" />
77 </actions> 83 </actions>
78 </data> 84 </data>
79 <data name="peptides" format="tabular" label="${tool.name} ${on_string} peptides.txt" from_work_dir="chromatogram_library.peptides.txt"> 85 <!--
86 <collection name="rt_plots" type="list" label="${tool.name} - ${on_string}: Retention Time Plots">
87 <filter>l and 'rt_plots' in select_outputs</filter>
88 <discover_datasets pattern="(?P&lt;designation&gt;.+\.pdf)" ext="pdf" directory="inputs"/>
89 </collection>
90 <collection name="rt_tables" type="list" label="${tool.name} - ${on_string}: Retention Time Tables">
91 <filter>l and 'rt_tables' in select_outputs</filter>
92 <discover_datasets pattern="(?P&lt;designation&gt;.+\.rt_fit\.txt)" ext="tabular" directory="inputs"/>
93 </collection>
94 -->
95 <data name="peptides" format="tabular" label="${tool.name} ${on_string} peptides.txt" from_work_dir="chromatogram_library.elib.peptides.txt">
80 <filter>a and 'peptides' in select_outputs</filter> 96 <filter>a and 'peptides' in select_outputs</filter>
81 <actions> 97 <actions>
82 <action name="column_names" type="metadata" default="Peptide,Protein,numFragments" /> 98 <action name="column_names" type="metadata" default="Peptide,Protein,numFragments" />
83 </actions> 99 </actions>
84 </data> 100 </data>
85 <data name="proteins" format="tabular" label="${tool.name} ${on_string} proteins.txt" from_work_dir="chromatogram_library.proteins.txt"> 101 <data name="proteins" format="tabular" label="${tool.name} ${on_string} proteins.txt" from_work_dir="chromatogram_library.elib.proteins.txt">
86 <filter>a and 'proteins' in select_outputs</filter> 102 <filter>a and 'proteins' in select_outputs</filter>
87 <actions> 103 <actions>
88 <action name="column_names" type="metadata" default="Protein,NumPeptides,PeptideSequences" /> 104 <action name="column_names" type="metadata" default="Protein,NumPeptides,PeptideSequences" />
89 </actions> 105 </actions>
90 </data> 106 </data>