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comparison bmsb.xml @ 3:f622abc513d6 draft

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Uploaded
author greg
date Thu, 11 Aug 2016 11:15:15 -0400
parents e6809bb0bcf8
children f5e63e70a754
comparison
equal deleted inserted replaced
2:5cc7d287decd 3:f622abc513d6
1 <?xml version="."?> 1 <?xml version="."?>
2 <tool id="bmsb" name="BMSB" version="1.0.0"> 2 <tool id="bmsb" name="BMSB" version="1.0.0">
3 <description></description> 3 <description></description>
4 <requirements> 4 <requirements>
5 <requirement type="package" version="1.0">bmsb</requirement> 5 <requirement type="package" version="1.3.0">r-optparse</requirement>
6 <requirement type="package" version="1.20.0">r-getopt</requirement>
7 <requirement type="package" version="0.9.19">r-jsonlite</requirement>
6 </requirements> 8 </requirements>
7 <command> 9 <command>
8 <![CDATA[ 10 <![CDATA[
9 #import json 11 #import json
10 Rscript $__tool_directory__/bmsb.R 12 Rscript $__tool_directory__/bmsb.R
11 -o "$output" 13 -o "$output"
14 #if str($output_r_logging_cond.output_r_logging) == "yes":
15 -s "true"
16 -m "$output_r_log"
17 #end if
18 #if str($output_r_logging_cond.output_r_logging) == "yes":
19 -e "true"
20 -x "$output_ex_report"
21 #end if
12 ]]> 22 ]]>
13 </command> 23 </command>
14 <inputs> 24 <inputs>
15 <param name="input" type="data" format="csv" label="CSV input" /> 25 <conditional name="output_r_logging_cond">
26 <param name="output_r_logging" type="select" label="Output R logging?" help="Generate an additional dataset consisting of R messages.">
27 <option value="yes" selected="True">Yes</option>
28 <option value="no">No</option>
29 </param>
30 <when value="no"/>
31 <when value="yes"/>
32 </conditional>
16 </inputs> 33 </inputs>
17 <outputs> 34 <outputs>
35 <data name="output_r_log" format="txt" label="${tool.name} on ${on_string}: R log">
36 <filter>output_r_logging_cond['output_r_logging'] == "yes"</filter>
37 </data>
38 <data name="output_ex_report" format="json" label="${tool.name} on ${on_string}: Experiment report">
39 <filter>output_experiment_report_cond['output_experiment_report'] == "yes"</filter>
40 </data>
18 <data name="output" format="RData"/> 41 <data name="output" format="RData"/>
19 </outputs> 42 </outputs>
20 <help> 43 <help>
21 **What it does** 44 **What it does**
22 45