# HG changeset patch
# User jjohnson
# Date 1598467154 14400
# Node ID 5a5da160f6670d4d73f609da04599ad4b190a210
# Parent  30f6b9c88ceb7ec9bb803a06ea1e461182c5b732
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit dd611a143e4e003a5fb085cdf93ae477cc5ea0b1"

diff -r 30f6b9c88ceb -r 5a5da160f667 encyclopedia_quantify.xml
--- a/encyclopedia_quantify.xml	Fri Aug 21 16:11:54 2020 -0400
+++ b/encyclopedia_quantify.xml	Wed Aug 26 14:39:14 2020 -0400
@@ -12,7 +12,7 @@
         @LINK_LIB_INPUT@
         for SCAN_FILE in `ls -1 inputs/*`; do 
         echo "\$SCAN_FILE" &&
-        EncyclopeDIA -Djava.awt.headless=true -Xmx20g 
+        EncyclopeDIA -Djava.awt.headless=true -Xmx\$[ \${GALAXY_MEMORY_MB:-20480} / 1024 ]g 
         -i \$SCAN_FILE
         @FASTA_INPUT@
         @TARGET_FASTA@
@@ -26,7 +26,7 @@
         @SEARCH_OPTIONS@ | tee -a search2lib.log
         ; done && 
         for TXT in `find inputs/*.mzML.[efw]*[ast].txt`; do TRGT=`echo \$TXT | sed 's/mzML/dia/'`; ln -s \$TXT \$TRGT; done &&
-        EncyclopeDIA -Djava.awt.headless=true -Xmx12g -libexport
+        EncyclopeDIA -Djava.awt.headless=true -Xmx\$[ \${GALAXY_MEMORY_MB:-20480} / 1024 ]g -libexport
         @SCAN_INPUTS@
         @FASTA_INPUT@
         @TARGET_FASTA@
@@ -34,6 +34,8 @@
         -a $a
         -o chromatogram_library.elib
         && ls -l ./*.* inputs/*
+        && cat chromatogram_library.elib.peptides.txt
+        && cat chromatogram_library.elib.proteins.txt
         | tee -a search2lib.log
     ]]></command>
     <inputs>
@@ -108,12 +110,12 @@
             <param name="fasta" ftype="fasta" value="uniprot_human.fasta"/>
             <output name="results" ftype="tabular">
                 <assert_contents>
-                    <has_text text="ESYDDVSSFR"/>
+                    <has_text text="GIEQAVQSHAVAEEEAR"/>
                 </assert_contents>
             </output>
-            <output name="proteins" ftype="tabular">
+            <output name="peptides" ftype="tabular">
                 <assert_contents>
-                    <has_text text="ESYDDVSSFR"/>
+                    <has_text text="AYPLADAHLTK"/>
                 </assert_contents>
             </output>
         </test>