Mercurial > repos > anmoljh > candidate_compound_select
comparison select_compound.xml @ 1:843adfe71ce2 draft
planemo upload commit a1f4dd8eb560c649391ada1a6bb9505893a35272-dirty
| author | anmoljh |
|---|---|
| date | Sun, 03 Jun 2018 01:35:07 -0400 |
| parents | 639d350de274 |
| children | 1de0e9f0367d |
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| 0:639d350de274 | 1:843adfe71ce2 |
|---|---|
| 1 <?xml version="1.0"?> | 1 <?xml version="1.0"?> |
| 2 <tool id="select_compound" name="Compound Selector" version="1.0"> | 2 <tool id="candidate_compound_selector" name="Candidate Compound Selector" version="1.0"> |
| 3 <description>This tool selects compounds from prediction result based on score</description> | |
| 4 | 3 |
| 5 <requirements> | 4 <description>selects compounds from prediction result based on score</description> |
| 6 <requirement type="package" version="3.2.1">R</requirement> | |
| 7 </requirements> | |
| 8 | 5 |
| 9 <stdio> | 6 <requirements> |
| 10 <exit_code range="1:" /> | 7 <requirement type="package" version="3.2.1">R</requirement> |
| 11 </stdio> | 8 </requirements> |
| 12 | 9 |
| 13 <command interpreter="Rscript">select_compound.R $predictionfile $LT $GT $type $SelectedCompound </command> | 10 <stdio> |
| 11 <exit_code range="1:" /> | |
| 12 </stdio> | |
| 14 | 13 |
| 15 <inputs> | 14 <command interpreter="Rscript">select_compound.R $predictionfile $LT $GT $type $SelectedCompound </command> |
| 16 <param name="predictionfile" type="data" format="txt,tabular,csv" label="Predition Result File" help ="upload gcac prediction result file " /> | |
| 17 <param name="type" type="select" label="Active/Positive or Inactive/Negative" help ="select type of molecule"> | |
| 18 <option value="Active" selected="True">Active/Positive</option> | |
| 19 <option value="Inactive">Inactive/Negative</option> | |
| 20 </param> | |
| 21 <param name="GT" type="float" value="0.5" label="Score greater than and equal to" help ="define value above which compound selected default is 0.5" /> | |
| 22 <param name="LT" type="float" value="1.0" label="Score less than and equal to" help ="define value below which compound selected default is 1" /> | |
| 23 </inputs> | |
| 24 | 15 |
| 25 <outputs> | 16 <inputs> |
| 26 <data name="SelectedCompound" format="txt" label="Refind-${predictionfile.name}" /> | 17 <param name="predictionfile" type="data" format="txt,tabular,csv" label="Predition Result File" help ="upload gcac prediction result file" /> |
| 27 </outputs> | 18 <param name="type" type="select" label="Active/Positive or Inactive/Negative" help ="select type of molecule"> |
| 28 <tests> | 19 <option value="Active" selected="True">Active/Positive</option> |
| 29 <test> | 20 <option value="Inactive">Inactive/Negative</option> |
| 30 <param name="predictionfile" value="prediction_set_result.txt" /> | 21 </param> |
| 31 <param name="type" value="Active" /> | 22 <param name="GT" type="float" value="0.5" label="Score greater than and equal to" help ="define value above which compound selected default is 0.5" /> |
| 32 <param name="GT" value="0.5" /> | 23 <param name="LT" type="float" value="1.0" label="Score less than and equal to" help ="define value below which compound selected default is 1" /> |
| 33 <param name="LT" value="1.0" /> | 24 </inputs> |
| 34 <output name="SelectedCompound" file="selected_prediction_set_result.txt" compare="sim_size" delta="4000" /> | 25 |
| 35 </test> | 26 <outputs> |
| 36 </tests> | 27 <data name="SelectedCompound" format="txt" label="Refind-${predictionfile.name}" /> |
| 37 <help></help> | 28 </outputs> |
| 29 <tests> | |
| 30 <test> | |
| 31 <param name="predictionfile" value="prediction_set_result.txt" /> | |
| 32 <param name="type" value="Active" /> | |
| 33 <param name="GT" value="0.5" /> | |
| 34 <param name="LT" value="1.0" /> | |
| 35 <output name="SelectedCompound" file="selected_prediction_set_result.txt" compare="sim_size" delta="4000" /> | |
| 36 </test> | |
| 37 </tests> | |
| 38 <help></help> | |
| 38 </tool> | 39 </tool> |