Mercurial > repos > jjohnson > encyclopedia_quantify
changeset 6:5a5da160f667 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit dd611a143e4e003a5fb085cdf93ae477cc5ea0b1"
| author | jjohnson |
|---|---|
| date | Wed, 26 Aug 2020 14:39:14 -0400 |
| parents | 30f6b9c88ceb |
| children | cb69090da7a4 |
| files | encyclopedia_quantify.xml |
| diffstat | 1 files changed, 7 insertions(+), 5 deletions(-) [+] |
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--- 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>