Mercurial > repos > jjohnson > encyclopedia_quantify
comparison encyclopedia_quantify.xml @ 3:aa52f0eadc85 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 96a023cccea27c30ff61caf271a3c79b92db1873"
author | jjohnson |
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date | Tue, 07 Jul 2020 11:56:28 -0400 |
parents | acf6acfc8632 |
children | bd937e4efa04 |
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2:174886084dc5 | 3:aa52f0eadc85 |
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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} - ${on_string}: Retention Time Plots"> | |
87 <filter>l and 'rt_plots' in select_outputs</filter> | |
88 <discover_datasets pattern="(?P<designation>.+\.pdf)" ext="pdf" directory="inputs"/> | |
89 </collection> | |
90 <collection name="rt_tables" type="list" label="${tool.name} - ${on_string}: Retention Time Tables"> | |
91 <filter>l and 'rt_tables' in select_outputs</filter> | |
92 <discover_datasets pattern="(?P<designation>.+\.rt_fit\.txt)" ext="tabular" directory="inputs"/> | |
93 </collection> | |
94 --> | |
95 <data name="peptides" format="tabular" label="${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> |