Mercurial > repos > jfb > kinatest_scoring_function

comparison scoring function/KinatestScoring.xml @ 11:7dff31e9a48f draft

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author jfb
date Mon, 29 Apr 2019 11:58:54 -0400
parents 1816bf5d1735
children 6897a83b9096
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10:1816bf5d1735 11:7dff31e9a48f
5 </requirements> 5 </requirements>
6 <command><![CDATA[ 6 <command><![CDATA[
7 ln -s '$__tool_directory__/screener.csv' screener.csv && 7 ln -s '$__tool_directory__/screener.csv' screener.csv &&
8 ln -s '$FisherTable' Fisher-Char.csv && 8 ln -s '$FisherTable' Fisher-Char.csv &&
9 ln -s '$CharacterizationTable' Fisher-Table.csv && 9 ln -s '$CharacterizationTable' Fisher-Table.csv &&
10 Rscript '$__tool_directory__/KinatestFisherScoring.R' ${outGroup} ${Msix} ${Mfive} ${Mfour} ${Mthree} ${Mtwo} ${Mone} ${Dzero} ${Pone} ${Ptwo} ${Pthree} ${Pfour} ${Pfive} ${Psix} 10 Rscript '$__tool_directory__/KinatestFisherScoring.R' $outGroup $Ms $Mfi $Mfo $Mth $Mtw $Mo $Dz $Po $Ptw $Pth $Pfo $Pfi $Ps
11 ]]></command> 11 ]]></command>
12 <inputs> 12 <inputs>
13 <param format="csv" name="FisherTable" type="data" label="Fisher Odds Table output"/> 13 <param format="csv" name="FisherTable" type="data" label="Fisher Odds Table output"/>
14 <param format="csv" name="CharacterizationTable" type="data" label="Characterization Table Output"/> 14 <param format="csv" name="CharacterizationTable" type="data" label="Characterization Table Output"/>
15 <param name="Msix" type="text" value="ACD" label="Amino Acid(s) in -6 Position"/> 15 <param name="Ms" type="text" value="ACD" label="Amino Acid(s) in -6 Position"/>
16 <param name="Mfive" type="text" value="EFG" label="Amino Acid(s) in -5 Position"/> 16 <param name="Mfi" type="text" value="EFG" label="Amino Acid(s) in -5 Position"/>
17 <param name="Mfour" type="text" value="HIK" label="Amino Acid(s) in -4 Position"/> 17 <param name="Mfo" type="text" value="HIK" label="Amino Acid(s) in -4 Position"/>
18 <param name="Mthree" type="text" value="LMN" label="Amino Acid(s) in -3 Position"/> 18 <param name="Mth" type="text" value="LMN" label="Amino Acid(s) in -3 Position"/>
19 <param name="Mtwo" type="text" value="PQR" label="Amino Acid(s) in -2 Position"/> 19 <param name="Mtw" type="text" value="PQR" label="Amino Acid(s) in -2 Position"/>
20 <param name="Mone" type="text" value="STV" label="Amino Acid(s) in -1 Position"/> 20 <param name="Mo" type="text" value="STV" label="Amino Acid(s) in -1 Position"/>
21 <param name="Dzero" type="text" value="Y" label="Amino Acid(s) in Central Position"/> 21 <param name="Dz" type="text" value="Y" label="Amino Acid(s) in Central Position"/>
22 <param name="Pone" type="text" value="VTS" label="Amino Acid(s) in +1 Position"/> 22 <param name="Po" type="text" value="VTS" label="Amino Acid(s) in +1 Position"/>
23 <param name="Ptwo" type="text" value="RQP" label="Amino Acid(s) in +2 Position"/> 23 <param name="Ptw" type="text" value="RQP" label="Amino Acid(s) in +2 Position"/>
24 <param name="Pthree" type="text" value="NML" label="Amino Acid(s) in +3 Position"/> 24 <param name="Pth" type="text" value="NML" label="Amino Acid(s) in +3 Position"/>
25 <param name="Pfour" type="text" value="KIH" label="Amino Acid(s) in +4 Position"/> 25 <param name="Pfo" type="text" value="KIH" label="Amino Acid(s) in +4 Position"/>
26 <param name="Pfive" type="text" value="GFE" label="Amino Acid(s) in +5 Position"/> 26 <param name="Pfi" type="text" value="GFE" label="Amino Acid(s) in +5 Position"/>
27 <param name="Psix" type="text" value="DCA" label="Amino Acid(s) in +6 Position"/> 27 <param name="Ps" type="text" value="DCA" label="Amino Acid(s) in +6 Position"/>
28 <param name="outGroup" type="text" value="kinase" label="Kinase Name"/> 28 <param name="outGroup" type="text" value="kinase" label="Kinase Name"/>
29 </inputs> 29 </inputs>
30 <outputs> 30 <outputs>
31 <data format="csv" name="PeptidesWithScores" from_work_dir="output.csv" label="${outGroup}_Substrates and Scores"/> 31 <data format="csv" name="PeptidesWithScores" from_work_dir="output.csv" label="${outGroup}_Substrates and Scores"/>
32 </outputs> 32 </outputs>