Mercurial > repos > jjohnson > encyclopedia_quantify

comparison encyclopedia_quantify.xml @ 6:5a5da160f667 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 14:39:14 -0400
parents 30f6b9c88ceb
children
comparison
equal deleted inserted replaced
5:30f6b9c88ceb 6:5a5da160f667
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[