Mercurial > repos > jjohnson > encyclopedia_searchtolib

comparison encyclopedia_searchtolib.xml @ 5:b9c8e02d1405 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 880d327a6dce00616a0b0b58bcabcea7b58358cc"
author jjohnson
date Wed, 19 Aug 2020 08:40:05 -0400
parents 54f4d8c5fbe0
children 7efddaece152
comparison
equal deleted inserted replaced
4:54f4d8c5fbe0 5:b9c8e02d1405
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 -Xmx20g
16 #if not $l 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@
21 @TARGET_FASTA@ 21 @TARGET_FASTA@
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 -Xmx12g -libexport
33 #if not $l 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@
38 @TARGET_FASTA@ 38 @TARGET_FASTA@
112 <action name="column_names" type="metadata" default="Protein,NumPeptides,PeptideSequences" /> 112 <action name="column_names" type="metadata" default="Protein,NumPeptides,PeptideSequences" />
113 </actions> 113 </actions>
114 </data> 114 </data>
115 --> 115 -->
116 </outputs> 116 </outputs>
117 <tests>
118 <test>
119 <param name="scan_inputs" ftype="mzml" value="BCS_hela_narrow_3_1.mzML,BCS_hela_narrow_3_2.mzML"/>
120 <param name="library" ftype="dlib" value="small_pan_human_library.dlib"/>
121 <param name="fasta" ftype="fasta" value="uniprot_human.fasta"/>
122 <param name="select_outputs" value="log,elib,features,results"/>
123 <output name="results" ftype="tabular">
124 <assert_contents>
125 <has_text text="QDSAAVGFDYK"/>
126 </assert_contents>
127 </output>
128 </test>
129 </tests>
117 <help><![CDATA[ 130 <help><![CDATA[
118 131
119 **SearchToLIB** 132 **SearchToLIB**
120 133
121 @ENCYCLOPEDIA_WIKI@ 134 @ENCYCLOPEDIA_WIKI@