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1 <tool id="MaREA RAS Generator" name="Expression2RAS" version="1.0.2">
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2 <description>- Reaction Activity Scores computation</description>
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3 <macros>
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4 <import>marea_macros.xml</import>
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5 </macros>
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6 <requirements>
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7 <requirement type="package" version="0.23.0">pandas</requirement>
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8 <requirement type="package" version="1.1.0">scipy</requirement>
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9 <requirement type="package" version="0.10.1">cobra</requirement>
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10 <requirement type="package" version="4.2.1">lxml</requirement>
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11 <requirement type="package" version="0.8.1">svglib</requirement>
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12 <requirement type="package" version="3.4.0">reportlab</requirement>
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13 </requirements>
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14 <command detect_errors="exit_code">
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15 <![CDATA[
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16 python $__tool_directory__/ras_generator.py
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17 --rules_selector $cond_rule.rules_selector
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18 --input $input
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19 --none $none
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20 --tool_dir $__tool_directory__
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21 --out_log $log
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22 --ras_output $ras_output
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23 ]]>
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24 </command>
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25 <inputs>
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26 <conditional name="cond_rule">
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27 <expand macro="options"/>
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28 <when value="HMRcore">
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29 </when>
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30 <when value="Recon">
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31 </when>
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32 <when value="Custom">
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33 <param name="Custom_rules" type="data" format="tabular, csv, tsv, xml" label="Custom rules" />
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34 <conditional name="cond_map">
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35 <param name="yes_no" type="select" label="Custom map? (optional)">
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36 <option value="no" selected="true">no</option>
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37 <option value="yes">yes</option>
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38 </param>
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39 <when value="yes">
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40 <param name="Custom_map" argument="--custom_map" type="data" format="xml, svg" label="custom-map.svg"/>
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41 </when>
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42 <when value="no">
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43 </when>
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44 </conditional>
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45 </when>
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46 </conditional>
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47 <param name="input" argument="--input" type="data" format="tabular, csv, tsv" label="Gene Expression dataset:" />
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48 <param name="name" argument="--name" type="text" label="Dataset's name:" value="Dataset" help="Default: Dataset" />
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49 <param name="none" argument="--none" type="boolean" truevalue="true" falsevalue="false" checked="true" label="(A and NaN) solved as (A)?" />
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50 </inputs>
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51
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52 <outputs>
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53 <data format="txt" name="log" label="Expression2RAS - $name - Log" />
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54 <data format="tabular" name="ras_output" label="$name RAS"/>
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55 </outputs>
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56
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57 <help>
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58 <![CDATA[
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59
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60 What it does
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61 -------------
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62 ]]>
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63 </help>
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64 <expand macro="citations" />
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65 </tool>
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