Mercurial > repos > jjohnson > encyclopedia_searchtolib

comparison encyclopedia_searchtolib.xml @ 7:29309591ca3e draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit dd611a143e4e003a5fb085cdf93ae477cc5ea0b1"
author jjohnson
date Wed, 26 Aug 2020 14:45:18 -0400
parents 7efddaece152
children
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6:7efddaece152 7:29309591ca3e
10 @LINK_FASTA_INPUT@ 10 @LINK_FASTA_INPUT@
11 @LINK_TARGET_FASTA@ 11 @LINK_TARGET_FASTA@
12 @LINK_LIB_INPUT@ 12 @LINK_LIB_INPUT@
13 for SCAN_FILE in `ls -1 inputs/*`; do 13 for SCAN_FILE in `ls -1 inputs/*`; do
14 echo "\$SCAN_FILE" && 14 echo "\$SCAN_FILE" &&
15 EncyclopeDIA -Djava.awt.headless=true -Xmx20g 15 EncyclopeDIA -Djava.awt.headless=true -Xmx\$[ \${GALAXY_MEMORY_MB:-20480} / 1024 ]g
16 #if not $library 16 #if not $library
17 -walnut 17 -walnut
18 #end if 18 #end if
19 -i \$SCAN_FILE 19 -i \$SCAN_FILE
20 @FASTA_INPUT@ 20 @FASTA_INPUT@
27 @WINDOW_OPTIONS@ 27 @WINDOW_OPTIONS@
28 @MODIFICATION_OPTIONS@ 28 @MODIFICATION_OPTIONS@
29 @SEARCH_OPTIONS@ | tee -a search2lib.log 29 @SEARCH_OPTIONS@ | tee -a search2lib.log
30 ; done && 30 ; done &&
31 for TXT in `find inputs/*.mzML.[efw]*[ast].txt`; do TRGT=`echo \$TXT | sed 's/mzML/dia/'`; ln -s \$TXT \$TRGT; done && 31 for TXT in `find inputs/*.mzML.[efw]*[ast].txt`; do TRGT=`echo \$TXT | sed 's/mzML/dia/'`; ln -s \$TXT \$TRGT; done &&
32 EncyclopeDIA -Djava.awt.headless=true -Xmx12g -libexport 32 EncyclopeDIA -Djava.awt.headless=true -Xmx\$[ \${GALAXY_MEMORY_MB:-20480} / 1024 ]g -libexport
33 #if not $library 33 #if not $library
34 -pecan 34 -pecan
35 #end if 35 #end if
36 @SCAN_INPUTS@ 36 @SCAN_INPUTS@
37 @FASTA_INPUT@ 37 @FASTA_INPUT@