# HG changeset patch
# User jjohnson
# Date 1599764643 0
# Node ID dedfeaab569dfd2f0939114a56ef998fc447fceb
# Parent  7003adde566812c326f7f93b1bb40e9295fa4d47
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit dd611a143e4e003a5fb085cdf93ae477cc5ea0b1-dirty"

diff -r 7003adde5668 -r dedfeaab569d macros.xml
--- a/macros.xml	Fri Aug 21 16:14:27 2020 -0400
+++ b/macros.xml	Thu Sep 10 19:04:03 2020 +0000
@@ -102,8 +102,12 @@
     </token>
 
     <xml name="target_fasta">
-        <param name="target_fasta" argument="-t" type="data" format="fasta" label="Target fasta database" optional="true"/> 
-        <param argument="-tp" type="boolean" truevalue="true" falsevalue="false" checked="false" label="target FASTA file contains peptides"/>
+        <param name="target_fasta" argument="-t" type="data" format="fasta" label="Target fasta database" optional="true"> 
+            <help>Optional - Only analyze this subset of the background fasta proteome</help>
+        </param>
+        <param argument="-tp" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Target FASTA file contains peptides">
+            <help>Rather than full proteins</help>
+        </param>
     </xml>
     <token name="@LINK_TARGET_FASTA@"><![CDATA[
     #if $target_fasta
diff -r 7003adde5668 -r dedfeaab569d test-data/BCS_hela.elib
Binary file test-data/BCS_hela.elib has changed
diff -r 7003adde5668 -r dedfeaab569d test-data/BCS_hela_narrow_3_1.mzML
--- a/test-data/BCS_hela_narrow_3_1.mzML	Fri Aug 21 16:14:27 2020 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,113576 +0,0 @@
-<?xml version="1.0" encoding="utf-8"?>
-<indexedmzML xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.2_idx.xsd">
-  <mzML xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.0.xsd" id="2018may16_hela_window_size_test_BCS_hela_narrow_3" version="1.1.0">
-    <cvList count="2">
-      <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.0.1" URI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"/>
-      <cv id="UO" fullName="Unit Ontology" version="12:10:2011" URI="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo"/>
-    </cvList>
-    <fileDescription>
-      <fileContent>
-        <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value=""/>
-        <cvParam cvRef="MS" accession="MS:1000580" name="MSn spectrum" value=""/>
-      </fileContent>
-      <sourceFileList count="2">
-        <sourceFile id="RAW1" name="2018may16_hela_window_size_test_BCS_hela_narrow_3.raw" location="file:///Z:\CCMSConversion\intermediate_files\ba2eb07be92c401a9cfe511c1fad9661_input">
-          <cvParam cvRef="MS" accession="MS:1000768" name="Thermo nativeID format" value=""/>
-          <cvParam cvRef="MS" accession="MS:1000563" name="Thermo RAW format" value=""/>
-          <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="20fed88a444214bb781488329e5c14b4259015ca"/>
-        </sourceFile>
-        <sourceFile id="_x0032_018may16_hela_window_size_test_BCS_hela_narrow_3.mzML" name="2018may16_hela_window_size_test_BCS_hela_narrow_3.mzML" location="file:///">
-          <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="9ddcb1a1fb98de10fe72c7eb4998bfd0b8859bf6"/>
-        </sourceFile>
-      </sourceFileList>
-    </fileDescription>
-    <referenceableParamGroupList count="1">
-      <referenceableParamGroup id="CommonInstrumentParams">
-        <cvParam cvRef="MS" accession="MS:1001911" name="Q Exactive" value=""/>
-        <cvParam cvRef="MS" accession="MS:1000529" name="instrument serial number" value="Exactive Series slot #1"/>
-      </referenceableParamGroup>
-    </referenceableParamGroupList>
-    <softwareList count="3">
-      <software id="Xcalibur" version="2.8-280502/2.8.1.2806">
-        <cvParam cvRef="MS" accession="MS:1000532" name="Xcalibur" value=""/>
-      </software>
-      <software id="pwiz" version="3.0.9172">
-        <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>
-      </software>
-      <software id="pwiz_3.0.9987" version="3.0.9987">
-        <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>
-      </software>
-    </softwareList>
-    <instrumentConfigurationList count="1">
-      <instrumentConfiguration id="IC1">
-        <referenceableParamGroupRef ref="CommonInstrumentParams"/>
-        <componentList count="4">
-          <source order="1">
-            <cvParam cvRef="MS" accession="MS:1000398" name="nanoelectrospray" value=""/>
-            <cvParam cvRef="MS" accession="MS:1000485" name="nanospray inlet" value=""/>
-          </source>
-          <analyzer order="2">
-            <cvParam cvRef="MS" accession="MS:1000081" name="quadrupole" value=""/>
-          </analyzer>
-          <analyzer order="3">
-            <cvParam cvRef="MS" accession="MS:1000484" name="orbitrap" value=""/>
-          </analyzer>
-          <detector order="4">
-            <cvParam cvRef="MS" accession="MS:1000624" name="inductive detector" value=""/>
-          </detector>
-        </componentList>
-        <softwareRef ref="Xcalibur"/>
-      </instrumentConfiguration>
-    </instrumentConfigurationList>
-    <dataProcessingList count="2">
-      <dataProcessing id="pwiz_Reader_Thermo_conversion">
-        <processingMethod order="0" softwareRef="pwiz">
-          <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value=""/>
-        </processingMethod>
-        <processingMethod order="1" softwareRef="pwiz">
-          <cvParam cvRef="MS" accession="MS:1000035" name="peak picking" value=""/>
-          <userParam name="Thermo/Xcalibur peak picking"/>
-        </processingMethod>
-      </dataProcessing>
-      <dataProcessing id="pwiz_Reader_conversion">
-        <processingMethod order="0" softwareRef="pwiz_3.0.9987">
-          <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value=""/>
-        </processingMethod>
-      </dataProcessing>
-    </dataProcessingList>
-    <run id="_x0032_018may16_hela_window_size_test_BCS_hela_narrow_3" defaultInstrumentConfigurationRef="IC1" startTimeStamp="2018-05-18T06:16:23Z" defaultSourceFileRef="RAW1">
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-        <spectrum index="0" id="controllerType=0 controllerNumber=1 scan=26629" defaultArrayLength="1895">
-          <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value=""/>
-          <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="1"/>
-          <cvParam cvRef="MS" accession="MS:1000130" name="positive scan" value=""/>
-          <cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum" value=""/>
-          <cvParam cvRef="MS" accession="MS:1000504" name="base peak m/z" value="435.2587732" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
-          <cvParam cvRef="MS" accession="MS:1000505" name="base peak intensity" value="1.1119594e08" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of detector counts"/>
-          <cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="1.0921969e09"/>
-          <cvParam cvRef="MS" accession="MS:1000528" name="lowest observed m/z" value="400.734130859375" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
-          <cvParam cvRef="MS" accession="MS:1000527" name="highest observed m/z" value="1350.546142578125" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
-          <scanList count="1">
-            <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value=""/>
-            <scan>
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-              <cvParam cvRef="MS" accession="MS:1000512" name="filter string" value="FTMS + p NSI Full lock ms [400.0000-1600.0000]"/>
-              <cvParam cvRef="MS" accession="MS:1000616" name="preset scan configuration" value="1"/>
-              <cvParam cvRef="MS" accession="MS:1000927" name="ion injection time" value="3.606225829571" unitCvRef="UO" unitAccession="UO:0000028" unitName="millisecond"/>
-              <scanWindowList count="1">
-                <scanWindow>
-                  <cvParam cvRef="MS" accession="MS:1000501" name="scan window lower limit" value="400.0" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
-                  <cvParam cvRef="MS" accession="MS:1000500" name="scan window upper limit" value="1600.0" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
-                </scanWindow>
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-              <cvParam cvRef="MS" accession="MS:1000523" name="64-bit float" value=""/>
-              <cvParam cvRef="MS" accession="MS:1000574" name="zlib compression" value=""/>
-              <cvParam cvRef="MS" accession="MS:1000514" name="m/z array" value="" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
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