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comparison select_compound.xml @ 1:843adfe71ce2 draft

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planemo upload commit a1f4dd8eb560c649391ada1a6bb9505893a35272-dirty
author anmoljh
date Sun, 03 Jun 2018 01:35:07 -0400
parents 639d350de274
children 1de0e9f0367d
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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>