Mercurial > repos > jfb > kinatest_scoring_function
comparison scoring function/KinatestScoring.xml @ 7:9243cdb86997 draft
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author | jfb |
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date | Sat, 27 Apr 2019 16:14:55 -0400 |
parents | 1d532e5664dd |
children | ff1ff59af83c |
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6:153ed20b5aab | 7:9243cdb86997 |
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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 '$__tool_directory__/KinatestFisherScoring.R' outGroup M6 M5 M4 M3 M2 M1 D0 P1 P2 P3 P4 P5 P6 | 10 Rscript '$__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="M6" 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="M5" 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="M4" 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="M3" 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="M2" 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="M1" 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="D0" 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="P1" 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="P2" 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="P3" 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="P4" 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="P5" type="text" value="GFE" label="Amino Acid(s) in +5 Position"/> | 26 <param name="Pf" type="text" value="GFE" label="Amino Acid(s) in +5 Position"/> |
27 <param name="P6" 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> |