Mercurial > repos > jjohnson > encyclopedia_quantify
comparison encyclopedia_quantify.xml @ 6:5a5da160f667 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit dd611a143e4e003a5fb085cdf93ae477cc5ea0b1"
author | jjohnson |
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date | Wed, 26 Aug 2020 14:39:14 -0400 |
parents | 30f6b9c88ceb |
children |
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5:30f6b9c88ceb | 6:5a5da160f667 |
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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 -i \$SCAN_FILE | 16 -i \$SCAN_FILE |
17 @FASTA_INPUT@ | 17 @FASTA_INPUT@ |
18 @TARGET_FASTA@ | 18 @TARGET_FASTA@ |
19 @LIB_INPUT@ | 19 @LIB_INPUT@ |
20 @COMMON_OPTIONS@ | 20 @COMMON_OPTIONS@ |
24 @WINDOW_OPTIONS@ | 24 @WINDOW_OPTIONS@ |
25 @MODIFICATION_OPTIONS@ | 25 @MODIFICATION_OPTIONS@ |
26 @SEARCH_OPTIONS@ | tee -a search2lib.log | 26 @SEARCH_OPTIONS@ | tee -a search2lib.log |
27 ; done && | 27 ; done && |
28 for TXT in `find inputs/*.mzML.[efw]*[ast].txt`; do TRGT=`echo \$TXT | sed 's/mzML/dia/'`; ln -s \$TXT \$TRGT; done && | 28 for TXT in `find inputs/*.mzML.[efw]*[ast].txt`; do TRGT=`echo \$TXT | sed 's/mzML/dia/'`; ln -s \$TXT \$TRGT; done && |
29 EncyclopeDIA -Djava.awt.headless=true -Xmx12g -libexport | 29 EncyclopeDIA -Djava.awt.headless=true -Xmx\$[ \${GALAXY_MEMORY_MB:-20480} / 1024 ]g -libexport |
30 @SCAN_INPUTS@ | 30 @SCAN_INPUTS@ |
31 @FASTA_INPUT@ | 31 @FASTA_INPUT@ |
32 @TARGET_FASTA@ | 32 @TARGET_FASTA@ |
33 @LIB_INPUT@ | 33 @LIB_INPUT@ |
34 -a $a | 34 -a $a |
35 -o chromatogram_library.elib | 35 -o chromatogram_library.elib |
36 && ls -l ./*.* inputs/* | 36 && ls -l ./*.* inputs/* |
37 && cat chromatogram_library.elib.peptides.txt | |
38 && cat chromatogram_library.elib.proteins.txt | |
37 | tee -a search2lib.log | 39 | tee -a search2lib.log |
38 ]]></command> | 40 ]]></command> |
39 <inputs> | 41 <inputs> |
40 <expand macro="scan_inputs"/> | 42 <expand macro="scan_inputs"/> |
41 <expand macro="lib_input" optional="false" libhelp="Use a Chromatogram elib from SearchToLib"/> | 43 <expand macro="lib_input" optional="false" libhelp="Use a Chromatogram elib from SearchToLib"/> |
106 <param name="scan_inputs" ftype="mzml" value="BCS_hela_wide_500_900_1.mzML,BCS_hela_wide_500_900_2.mzML"/> | 108 <param name="scan_inputs" ftype="mzml" value="BCS_hela_wide_500_900_1.mzML,BCS_hela_wide_500_900_2.mzML"/> |
107 <param name="library" ftype="elib" value="BCS_hela.elib"/> | 109 <param name="library" ftype="elib" value="BCS_hela.elib"/> |
108 <param name="fasta" ftype="fasta" value="uniprot_human.fasta"/> | 110 <param name="fasta" ftype="fasta" value="uniprot_human.fasta"/> |
109 <output name="results" ftype="tabular"> | 111 <output name="results" ftype="tabular"> |
110 <assert_contents> | 112 <assert_contents> |
111 <has_text text="ESYDDVSSFR"/> | 113 <has_text text="GIEQAVQSHAVAEEEAR"/> |
112 </assert_contents> | 114 </assert_contents> |
113 </output> | 115 </output> |
114 <output name="proteins" ftype="tabular"> | 116 <output name="peptides" ftype="tabular"> |
115 <assert_contents> | 117 <assert_contents> |
116 <has_text text="ESYDDVSSFR"/> | 118 <has_text text="AYPLADAHLTK"/> |
117 </assert_contents> | 119 </assert_contents> |
118 </output> | 120 </output> |
119 </test> | 121 </test> |
120 </tests> | 122 </tests> |
121 <help><![CDATA[ | 123 <help><![CDATA[ |