Mercurial > repos > anmoljh > candidate_compound_select

annotate select_compound.xml @ 1:3bd5537cc516 draft default tip

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author anmoljh
date Wed, 25 Oct 2017 04:39:07 -0400
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1 <?xml version="1.0"?>
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2 <tool id="select_compound" name="Select Compounds based of score" version="1.0">
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3 <description>This tool selects compounds from prediction result based on given score</description>
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4
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5 <requirements>
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6 <requirement type="package" version="3.2.1">R</requirement>
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7 </requirements>
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8
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9 <stdio>
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10 <exit_code range="1:" />
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11 </stdio>
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12
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13 <command interpreter="Rscript">select_compound.R $predictionfile $LT $GT $type $SelectedCompound </command>
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15 <inputs>
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16 <param name="predictionfile" type="data" format="txt,tabular,csv" label="Predition Result File" help ="upload gcac prediction result file " />
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17 <param name="type" type="select" label="Active/Positive or Inactive/Negative" help ="select type of molecule">
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18 <option value="Active" selected="True">Active/Positive</option>
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19 <option value="Inactive">Inactive/Negative</option>
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20 </param>
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21 <param name="GT" type="float" value="0.5" label="Score greater than and equal to" help ="define value above which compound selected default is 0.5" />
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22 <param name="LT" type="float" value="1.0" label="Score less than and equal to" help ="define value below which compound selected default is 1" />
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23 </inputs>
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24
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25 <outputs>
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26 <data name="SelectedCompound" format="txt" label="Refind-${predictionfile.name}" />
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27 </outputs>
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28 <tests>
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29 <test>
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30 <param name="predictionfile" value="prediction_set_result.txt" />
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31 <param name="type" value="Active" />
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32 <param name="GT" value="0.5" />
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33 <param name="LT" value="1.0" />
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34 <output name="SelectedCompound" file="selected_prediction_set_result.txt" compare="sim_size" delta="4000" />
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35 </test>
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36 </tests>
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37 <help></help>
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38 </tool>