Mercurial > repos > jjohnson > encyclopedia_quantify

annotate encyclopedia_quantify.xml @ 4:bd937e4efa04 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 880d327a6dce00616a0b0b58bcabcea7b58358cc"
author jjohnson
date Wed, 19 Aug 2020 08:38:25 -0400
parents aa52f0eadc85
children 30f6b9c88ceb
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
1 <tool id="encyclopedia_quantify" name="EncyclopeDIA Quantify" version="@VERSION@.0">
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
2 <description>samples from Data-Independent Acquisition (DIA) MS/MS Data</description>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
3 <macros>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
4 <import>macros.xml</import>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
5 </macros>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
6 <expand macro="requirements" />
3
aa52f0eadc85 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 96a023cccea27c30ff61caf271a3c79b92db1873"
jjohnson
parents: 1
diff changeset
7 <command detect_errors="aggressive"><![CDATA[
0
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
8 @CMD_IMPORTS@
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
9 @LINK_SCAN_INPUTS@
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
10 @LINK_FASTA_INPUT@
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
11 @LINK_TARGET_FASTA@
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
12 @LINK_LIB_INPUT@
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
13 for SCAN_FILE in `ls -1 inputs/*`; do
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
14 echo "\$SCAN_FILE" &&
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
15 EncyclopeDIA -Djava.awt.headless=true -Xmx20g
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
16 -i \$SCAN_FILE
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
17 @FASTA_INPUT@
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
18 @TARGET_FASTA@
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
19 @LIB_INPUT@
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
20 @COMMON_OPTIONS@
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
21 @MASS_LIBRARY_TOLERANCE@
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
22 @PERCOLATOR_OPTIONS@
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
23 @PEAK_OPTIONS@
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
24 @WINDOW_OPTIONS@
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
25 @MODIFICATION_OPTIONS@
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
26 @SEARCH_OPTIONS@ | tee -a search2lib.log
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
27 ; done &&
3
aa52f0eadc85 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 96a023cccea27c30ff61caf271a3c79b92db1873"
jjohnson
parents: 1
diff changeset
28 for TXT in `find inputs/*.mzML.[efw]*[ast].txt`; do TRGT=`echo \$TXT | sed 's/mzML/dia/'`; ln -s \$TXT \$TRGT; done &&
0
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
29 EncyclopeDIA -Djava.awt.headless=true -Xmx12g -libexport
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
30 @SCAN_INPUTS@
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
31 @FASTA_INPUT@
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
32 @TARGET_FASTA@
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
33 @LIB_INPUT@
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
34 -a $a
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
35 -o chromatogram_library.elib
3
aa52f0eadc85 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 96a023cccea27c30ff61caf271a3c79b92db1873"
jjohnson
parents: 1
diff changeset
36 && ls -l ./*.* inputs/*
0
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
37 | tee -a search2lib.log
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
38 ]]></command>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
39 <inputs>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
40 <expand macro="scan_inputs"/>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
41 <expand macro="lib_input" optional="false" libhelp="Use a Chromatogram elib from SearchToLib"/>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
42 <expand macro="fasta_input"/>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
43 <expand macro="target_fasta"/>
1
acf6acfc8632 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 0
diff changeset
44 <expand macro="options_section"/>
0
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
45 <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"/>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
46 <param name="select_outputs" type="select" label="Select outputs" multiple="true">
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
47 <option value="log" selected="true">log</option>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
48 <option value="elib" selected="true">elib</option>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
49 <option value="features" selected="true">concatenated_features.txt</option>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
50 <option value="results" selected="true">concatenated_results.txt</option>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
51 <option value="decoy" selected="false">concatenated_decoy.txt</option>
3
aa52f0eadc85 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 96a023cccea27c30ff61caf271a3c79b92db1873"
jjohnson
parents: 1
diff changeset
52 <!--
aa52f0eadc85 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 96a023cccea27c30ff61caf271a3c79b92db1873"
jjohnson
parents: 1
diff changeset
53 <option value="rt_plots" selected="false">Retention Time Plots</option>
aa52f0eadc85 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 96a023cccea27c30ff61caf271a3c79b92db1873"
jjohnson
parents: 1
diff changeset
54 <option value="rt_tables" selected="false">Retention Time Tables</option>
aa52f0eadc85 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 96a023cccea27c30ff61caf271a3c79b92db1873"
jjohnson
parents: 1
diff changeset
55 -->
0
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
56 <option value="peptides" selected="true">peptides.txt (requires align between files)</option>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
57 <option value="proteins" selected="true">proteins.txt (requires align between files)</option>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
58 </param>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
59 </inputs>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
60 <outputs>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
61 <data name="log" format="txt" label="${tool.name} ${on_string} log" from_work_dir="search2lib.log">
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
62 <filter>'log' in select_outputs</filter>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
63 </data>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
64 <data name="elib" format="elib" label="${tool.name} ${on_string} elib" from_work_dir="chromatogram_library.elib">
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
65 <filter>'elib' in select_outputs</filter>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
66 </data>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
67 <data name="features" format="tabular" label="${tool.name} ${on_string} concatenated_features.txt" from_work_dir="inputs/chromatogram_library_concatenated_features.txt">
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
68 <filter>'features' in select_outputs</filter>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
69 <actions>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
70 <action name="column_names" type="metadata" default="id,TD,ScanNr,topN,rank,peakZScore,peakCalibratedScore,deltaSn,avgIdotp,midIdotp,peakScore,peakWeightedScore,NCI,CIMassErrMean,CIMassErrVar,precursorMassErrMean,precursorMassErrVar,peakSimilarity,sampledTimes,midTime,spectraNorm,pepLength,charge2,charge3,precursorMz,sequence,protein" />
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
71 </actions>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
72 </data>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
73 <data name="results" format="tabular" label="${tool.name} ${on_string} concatenated_results.txt" from_work_dir="inputs/chromatogram_library_concatenated_results.txt">
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
74 <filter>'results' in select_outputs</filter>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
75 <actions>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
76 <action name="column_names" type="metadata" default="PSMId,score,q-value,posterior_error_prob,peptide,proteinIds" />
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
77 </actions>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
78 </data>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
79 <data name="decoy" format="tabular" label="${tool.name} ${on_string} concatenated_decoy.txt" from_work_dir="inputs/chromatogram_library_concatenated_decoy.txt">
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
80 <filter>'decoy' in select_outputs</filter>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
81 <actions>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
82 <action name="column_names" type="metadata" default="PSMId,score,q-value,posterior_error_prob,peptide,proteinIds" />
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
83 </actions>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
84 </data>
3
aa52f0eadc85 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 96a023cccea27c30ff61caf271a3c79b92db1873"
jjohnson
parents: 1
diff changeset
85 <!--
aa52f0eadc85 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 96a023cccea27c30ff61caf271a3c79b92db1873"
jjohnson
parents: 1
diff changeset
86 <collection name="rt_plots" type="list" label="${tool.name} - ${on_string}: Retention Time Plots">
aa52f0eadc85 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 96a023cccea27c30ff61caf271a3c79b92db1873"
jjohnson
parents: 1
diff changeset
87 <filter>l and 'rt_plots' in select_outputs</filter>
aa52f0eadc85 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 96a023cccea27c30ff61caf271a3c79b92db1873"
jjohnson
parents: 1
diff changeset
88 <discover_datasets pattern="(?P&lt;designation&gt;.+\.pdf)" ext="pdf" directory="inputs"/>
aa52f0eadc85 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 96a023cccea27c30ff61caf271a3c79b92db1873"
jjohnson
parents: 1
diff changeset
89 </collection>
aa52f0eadc85 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 96a023cccea27c30ff61caf271a3c79b92db1873"
jjohnson
parents: 1
diff changeset
90 <collection name="rt_tables" type="list" label="${tool.name} - ${on_string}: Retention Time Tables">
aa52f0eadc85 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 96a023cccea27c30ff61caf271a3c79b92db1873"
jjohnson
parents: 1
diff changeset
91 <filter>l and 'rt_tables' in select_outputs</filter>
aa52f0eadc85 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 96a023cccea27c30ff61caf271a3c79b92db1873"
jjohnson
parents: 1
diff changeset
92 <discover_datasets pattern="(?P&lt;designation&gt;.+\.rt_fit\.txt)" ext="tabular" directory="inputs"/>
aa52f0eadc85 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 96a023cccea27c30ff61caf271a3c79b92db1873"
jjohnson
parents: 1
diff changeset
93 </collection>
aa52f0eadc85 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 96a023cccea27c30ff61caf271a3c79b92db1873"
jjohnson
parents: 1
diff changeset
94 -->
aa52f0eadc85 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 96a023cccea27c30ff61caf271a3c79b92db1873"
jjohnson
parents: 1
diff changeset
95 <data name="peptides" format="tabular" label="${tool.name} ${on_string} peptides.txt" from_work_dir="chromatogram_library.elib.peptides.txt">
0
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
96 <filter>a and 'peptides' in select_outputs</filter>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
97 <actions>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
98 <action name="column_names" type="metadata" default="Peptide,Protein,numFragments" />
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
99 </actions>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
100 </data>
3
aa52f0eadc85 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 96a023cccea27c30ff61caf271a3c79b92db1873"
jjohnson
parents: 1
diff changeset
101 <data name="proteins" format="tabular" label="${tool.name} ${on_string} proteins.txt" from_work_dir="chromatogram_library.elib.proteins.txt">
0
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
102 <filter>a and 'proteins' in select_outputs</filter>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
103 <actions>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
104 <action name="column_names" type="metadata" default="Protein,NumPeptides,PeptideSequences" />
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
105 </actions>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
106 </data>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
107 </outputs>
4
bd937e4efa04 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 880d327a6dce00616a0b0b58bcabcea7b58358cc"
jjohnson
parents: 3
diff changeset
108 <tests>
bd937e4efa04 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 880d327a6dce00616a0b0b58bcabcea7b58358cc"
jjohnson
parents: 3
diff changeset
109 <test>
bd937e4efa04 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 880d327a6dce00616a0b0b58bcabcea7b58358cc"
jjohnson
parents: 3
diff changeset
110 <param name="scan_inputs" ftype="mzml" value="BCS_hela_wide_500_900_1.mzML,BCS_hela_wide_500_900_2.mzML"/>
bd937e4efa04 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 880d327a6dce00616a0b0b58bcabcea7b58358cc"
jjohnson
parents: 3
diff changeset
111 <param name="library" ftype="elib" value="BCS_hela.elib"/>
bd937e4efa04 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 880d327a6dce00616a0b0b58bcabcea7b58358cc"
jjohnson
parents: 3
diff changeset
112 <param name="fasta" ftype="fasta" value="uniprot_human.fasta"/>
bd937e4efa04 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 880d327a6dce00616a0b0b58bcabcea7b58358cc"
jjohnson
parents: 3
diff changeset
113 <output name="results" ftype="tabular">
bd937e4efa04 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 880d327a6dce00616a0b0b58bcabcea7b58358cc"
jjohnson
parents: 3
diff changeset
114 <assert_contents>
bd937e4efa04 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 880d327a6dce00616a0b0b58bcabcea7b58358cc"
jjohnson
parents: 3
diff changeset
115 <has_text text="ESYDDVSSFR"/>
bd937e4efa04 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 880d327a6dce00616a0b0b58bcabcea7b58358cc"
jjohnson
parents: 3
diff changeset
116 </assert_contents>
bd937e4efa04 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 880d327a6dce00616a0b0b58bcabcea7b58358cc"
jjohnson
parents: 3
diff changeset
117 </output>
bd937e4efa04 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 880d327a6dce00616a0b0b58bcabcea7b58358cc"
jjohnson
parents: 3
diff changeset
118 <output name="proteins" ftype="tabular">
bd937e4efa04 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 880d327a6dce00616a0b0b58bcabcea7b58358cc"
jjohnson
parents: 3
diff changeset
119 <assert_contents>
bd937e4efa04 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 880d327a6dce00616a0b0b58bcabcea7b58358cc"
jjohnson
parents: 3
diff changeset
120 <has_text text="ESYDDVSSFR"/>
bd937e4efa04 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 880d327a6dce00616a0b0b58bcabcea7b58358cc"
jjohnson
parents: 3
diff changeset
121 </assert_contents>
bd937e4efa04 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 880d327a6dce00616a0b0b58bcabcea7b58358cc"
jjohnson
parents: 3
diff changeset
122 </output>
bd937e4efa04 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 880d327a6dce00616a0b0b58bcabcea7b58358cc"
jjohnson
parents: 3
diff changeset
123 </test>
bd937e4efa04 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 880d327a6dce00616a0b0b58bcabcea7b58358cc"
jjohnson
parents: 3
diff changeset
124 </tests>
0
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
125 <help><![CDATA[
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
126
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
127 **EncyclopeDIA Quantify**
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
128
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
129 @ENCYCLOPEDIA_WIKI@
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
130
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
131 EncyclopeDIA Quantify retention-time aligns peptides from the chromatogram library and produces quantitation results.
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
132
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
133 @MSCONVERT_HELP@
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
134
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
135 **Typical DIA SearchToLib Workflow**
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
136
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
137 Two sets of Mass Spec MS/MS DIA data are collected for the experiment. In addition to collecting wide-window DIA experiments on each quantitative replicate, a pool containing peptides from every condition is measured using several staggered narrow-window DIA experiments.
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
138
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
139 1. SearchToLib is first run with the pooled narrow-window mzML files to create a combined DIA elib chromatogram library.
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
140 If a Spectral library argument is provided, for example from **Prosit**, SearchToLIB uses EncyclopeDIA to search each input spectrum mzML file.
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
141 Otherwise, SearchToLIB uses Walnut, a FASTA database search engine for DIA data that uses PECAN-style scoring.
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
142
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
143
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
144 * Prosit_ generates a predicted spectrum library of fragmentation patterns and retention times for every +2H and +3H tryptic peptide in a FASTA database, with up to one missed cleavage.
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
145
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
146
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
147 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.
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
148
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
149 .. image:: SearchToLib_Workflow.png
1
acf6acfc8632 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 0
diff changeset
150 :width: 810
acf6acfc8632 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 0
diff changeset
151 :height: 580
0
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
152
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
153 .. _Prosit: https://www.proteomicsdb.org/prosit
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
154
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
155 ]]></help>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
156 <expand macro="citations" />
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
157 </tool>