Mercurial > repos > jjohnson > encyclopedia_searchtolib
comparison encyclopedia_searchtolib.xml @ 7:29309591ca3e draft
"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@ |