diff encyclopedia_walnut.xml @ 0:ce1a157a41bd draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/encyclopedia_walnut.xml	Mon Sep 14 17:06:23 2020 +0000
@@ -0,0 +1,113 @@
+<tool id="encyclopedia_walnut" name="Walnut" version="@VERSION@.0">
+    <description>PeCAn-based Peptide Detection Directly from Data-Independent Acquisition (DIA) MS/MS Data</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="aggressive"><![CDATA[
+        @CMD_IMPORTS@
+        @LINK_SCAN_INPUT@
+        @LINK_FASTA_INPUT@
+        @LINK_TARGET_FASTA@
+        EncyclopeDIA -Djava.awt.headless=true -Duser.language=en-US -Duser.region=US
+            -Xmx\$[ \${GALAXY_MEMORY_MB:-20480} / 1024 ]g -walnut
+            -numberOfThreadsUsed "\${GALAXY_SLOTS:-4}"
+        @SCAN_INPUT@
+        @FASTA_INPUT@
+        @TARGET_FASTA@
+        @COMMON_OPTIONS@
+        @MASS_LIBRARY_TOLERANCE@
+        @PERCOLATOR_OPTIONS@
+        @PEAK_OPTIONS@
+        @WINDOW_OPTIONS@
+        @MODIFICATION_OPTIONS@
+        @SEARCH_OPTIONS@
+        -o gxpedia
+    ]]></command>
+    <inputs>
+        <expand macro="scan_input"/>
+        <expand macro="fasta_input"/>
+        <expand macro="target_fasta"/>
+        <expand macro="options_section"/>
+        <param name="select_outputs" type="select" label="Select outputs" multiple="true">
+            <option value="log" selected="true">log</option>
+            <option value="elib" selected="true">elib</option>
+            <option value="features" selected="false">features.txt</option>
+            <option value="pecan" selected="true">pecan.txt</option>
+            <option value="pecan_decoy" selected="false">pecan.decoy.txt</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="log" format="txt" label="${tool.name} ${on_string} log" from_work_dir="gxpedia.log">
+            <filter>'log' in select_outputs</filter>
+        </data>
+        <data name="elib" format="elib" label="${tool.name} ${on_string} elib" from_work_dir="gxpedia.elib">
+            <filter>'elib' in select_outputs</filter>
+        </data>
+        <data name="features" format="tabular" label="${tool.name} ${on_string} features.txt" from_work_dir="gxpedia.features.txt">
+            <filter>'features' in select_outputs</filter>
+            <actions>
+                <action name="column_names" type="metadata" default="id,TD,ScanNr,topN,rank,peakZScore,peakCalibratedScore,deltaSn,avgIdotp,midIdotp,peakScore,peakWeightedScore,NCI,CIMassErrMean,CIMassErrVar,precursorMassErrMean,precursorMassErrVar,peakSimilarity,sampledTimes,midTime,spectraNorm,pepLength,charge2,charge3,precursorMz,sequence,protein" />
+            </actions>
+        </data>
+        <data name="pecan" format="tabular" label="${tool.name} ${on_string} pecan.txt" from_work_dir="gxpedia.pecan.txt">
+            <filter>'pecan' in select_outputs</filter>
+            <actions>
+                <action name="column_names" type="metadata" default="PSMId,score,q-value,posterior_error_prob,peptide,proteinIds" />
+            </actions>
+        </data>
+        <data name="pecan_decoy" format="tabular" label="${tool.name} ${on_string} pecan.decoy.txt" from_work_dir="gxpedia.pecan.decoy.txt">
+            <filter>'pecan_decoy' in select_outputs</filter>
+            <actions>
+                <action name="column_names" type="metadata" default="PSMId,score,q-value,posterior_error_prob,peptide,proteinIds" />
+            </actions>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="scan_input" ftype="mzml" value="BCS_hela_narrow_3_1.mzML"/>
+            <param name="fasta" ftype="fasta" value="uniprot_tiny_human.fasta"/>
+            <param name="select_outputs" value="log,features,pecan"/>
+            <output name="features" ftype="tabular">
+                <assert_contents>
+                    <has_text text="LHYNEGLNIK"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+**Walnut**
+
+@ENCYCLOPEDIA_WIKI@
+
+Walnut is a FASTA database search engine for Data-Independent Acquisition (DIA) MS/MS data.
+Walnut uses PeCAn-style scoring to extract peptide fragmentation chromatograms from MZML files, assign peaks, and calculate various peak features. These features are interpreted by Percolator to identify peptides.
+
+
+
+**Inputs**
+
+  - A spectrum file in mzML format
+  - A protein data base in fasta format
+
+@MSCONVERT_HELP@
+
+**Outputs**
+
+  - A log file
+  - A Chromatogram Library (.elib)
+  - The identified features in tabular format
+    Feature values of scans that are used by percolator to determine matches.
+  - The identified Peptide Spectral Match results in tabular format
+    Columns: PSMId, score, q-value, posterior_error_prob, peptide, proteinIds
+  - The identified peptides in tabular format
+    Per peptide: the normalized intensity for each scan file.
+    Columns: Peptide, Protein, numFragments, intensity_in_file1, intensity_in_file2, ...
+  - The identified proteins in tabular format
+    Per protein: the normalized intensity for each scan file.
+    Columns: Protein, NumPeptides, PeptideSequences, intensity_in_file1, intensity_in_file2, ...
+
+
+    ]]></help>
+    <expand macro="citations" />
+</tool>