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comparison bmsb.xml @ 31:aefd45f2fa43 draft

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author greg
date Thu, 15 Dec 2016 11:04:41 -0500
parents 53d2ac56c953
children 7418fc8f0780
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30:53d2ac56c953 31:aefd45f2fa43
1 <?xml version="."?> 1 <?xml version="."?>
2 <tool id="bmsb_model" name="Brown Marmorated Stink Bug" version="1.0.0"> 2 <tool id="bmsb_model" name="Brown Marmorated Stink Bug" version="1.0.0">
3 <description></description> 3 <description></description>
4 <requirements> 4 <requirements>
5 <requirement type="package" version="3.3.1">r-base</requirement>
6 <requirement type="package" version="1.3.0">r-optparse</requirement> 5 <requirement type="package" version="1.3.0">r-optparse</requirement>
7 </requirements> 6 </requirements>
8 <command> 7 <command>
9 <![CDATA[ 8 <![CDATA[
10 #import json 9 Rscript $__tool_directory__/BMSB.R
11 Rscript $__tool_directory__/bmsb.R 10 -adult_mort $adult_mort
12 -i "$input" 11 -adult_nymph_accum $adult_nymph_accum
13 -o "$output" 12 -egg_mort $egg_mort
14 ###if str($output_r_logging_cond.output_r_logging) == "yes": 13 -latitude $latitude
15 ## -s "true" 14 -location $location
16 ## -m "$output_r_log" 15 -max_clutch_size $max_clutch_size
17 ###end if 16 -min_clutch_size $min_clutch_size
18 ###if str($output_r_logging_cond.output_r_logging) == "yes": 17 -nymph_mort $nymph_mort
19 ## -e "true" 18 -old_nymph_accum $old_nymph_accum
20 ## -x "$output_ex_report" 19 -output $output
21 ###end if 20 -oviposition $oviposition
21 -photoperiod $photoperiod
22 -replications $replications
23 -se_plot $se_plot
24 -sim_year $sim_year
25 -start_year $start_year
26 -temperature_datasets "$temperature_datasets"
27 -young_nymph_accum $young_nymph_accum
22 ]]> 28 ]]>
23 </command> 29 </command>
24 <inputs> 30 <inputs>
25 <param name="input" type="data" format="RData" label="RData input" /> 31 <param name="location" type="select" label="Select a location">
26 <!-- 32 <option value="asheville" selected=True>Asheville</option>
27 <conditional name="output_r_logging_cond"> 33 <option value="wenatchee">Wenatchee</option>
28 <param name="output_r_logging" type="select" label="Output R logging?" help="Generate an additional dataset consisting of R messages."> 34 </param>
29 <option value="yes" selected="True">Yes</option> 35 <param name="latitude" type="float" value="35.60" label="Latitude of selected location">
30 <option value="no">No</option> 36 <param name="temperature_datasets" type="data" format="csv" multiple="true" label="Select datasets containing temperatures" help="One or more datasets can be selected"/>
31 </param> 37 <param name="start_year" type="integer" min="1990" label="Enter a starting year" />
32 <when value="no"/> 38 <param name="replications" type="integer" value="3" label="Number of replications" />
33 <when value="yes"/> 39 <param name="photoperiod" type="float" value="13.5" label="Critical photoperiod for diapause induction/termination">
34 </conditional> 40 <param name="egg_mort" type="integer" label="Adjustment rate for egg mortality" />
35 --> 41 <param name="nymph_mort" type="integer" label="Adjustment rate for nymph mortality" />
42 <param name="adult_mort" type="integer" label="Adjustment rate for adult mortality" />
43 <param name="oviposition" type="integer" label="Adjustment oviposition rate" />
44 <param name="min_clutch_size" type="integer" label="Adjustment of minimum clutch size" />
45 <param name="max_clutch_size" type="integer" label="Adjustment of maximum clutch size" />
46 <param name="young_nymph_accum" type="integer" label="Adjustment of DD accumulation (egg->young nymph)" />
47 <param name="old_nymph_accum" type="integer" label="Adjustment of DD accumulation (young nymph->old nymph)" />
48 <param name="adult_nymph_accum" type="integer" label="Adjustment of DD accumulation (old nymph->adult)" />
49 <param name="sim_year" type="integer" min="1990" label="Simulation year" />
50 <param name="se_plot" type="select" label="Plot SE?">
51 <option value="0" selected=True>No</option>
52 <option value="1">Yes</option>
53 </param>
36 </inputs> 54 </inputs>
37 <outputs> 55 <outputs>
38 <!-- 56 <data name="output" format="RData" label="${tool.name}: ${location}, ${sim_year} on ${on_string}" />
39 <data name="output_r_log" format="txt" label="${tool.name} on ${on_string}: R log">
40 <filter>output_r_logging_cond['output_r_logging'] == "yes"</filter>
41 </data>
42 <data name="output_ex_report" format="json" label="${tool.name} on ${on_string}: Experiment report">
43 <filter>output_experiment_report_cond['output_experiment_report'] == "yes"</filter>
44 </data>
45 -->
46 <data name="output" format="RData"/>
47 </outputs> 57 </outputs>
48 <help> 58 <help>
49 **What it does** 59 **What it does**
50 60
51 BMSB prototype tool. 61 BMSB prototype tool.