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1 <tool id="MaREA_cluester" name="MaREA cluster analysis">
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2 <description>of Reaction Activity Scores</description>
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3 <requirements>
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4 <requirement type="package">pandas</requirement>
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5 <requirement type="package">scikit-learn</requirement>
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6 <requirement type="package">scipy</requirement>
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7 <requirement type="package">matplotlib</requirement>
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8 <requirement type="package">cobrapy</requirement>
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9 <requirement type="package">python-libsbml</requirement>
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10 </requirements>
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11 <command>
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12 <![CDATA[
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13 python $__tool_directory__/marea_cluster.py
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14 --rules_selector $cond_rule.rules_selector
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15 #if $cond_rule.rules_selector == 'Custom':
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16 --custom ${cond_rule.Custom_rules}
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17 #end if
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18 --cond_hier $cond_hier.hier
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19 #if $cond_hier.hier == 'yes':
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20 --linkage ${cond_hier.linkage}
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21 --dendro $dendrogram
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22 #end if
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23 --k_max $k_max
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24 --k_min $k_min
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25 --data $input
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26 --name $name
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27 --none $None
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28 --tool_dir $__tool_directory__
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29 --out_log $log
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30 --elbow $elbow
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31 ]]>
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32 </command>
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33 <inputs>
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34 <conditional name="cond_rule">
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35 <param name="rules_selector" type="select" label="Gene-Protein-Reaction rules:">
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36 <option value="HMRcore" selected="true">HMRcore rules</option>
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37 <option value="Recon">Recon 2.2 rules</option>
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38 <option value="Custom">Custom rules</option>
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39 </param>
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40 <when value="Custom">
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41 <param name="Custom_rules" type="data" format="tabular, csv, tsv, xml" label="Custom rules"/>
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42 </when>
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43 </conditional>
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44 <param name="input" type="data" format="tabular, csv, tsv" label="RNAseq of all samples"/>
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45 <param name="name" type="text" label="Output name prefix" value = "dataset"/>
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46 <param name="k_min" type="integer" size="20" value="3" min="2" max="30" label="min number of clusters (k) to be tested (k-means)"/>
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47 <param name="k_max" type="integer" size="20" value="3" min="2" max="30" label="max number of clusters (k) to be tested (k-means)"/>
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48 <param name="None" type="boolean" truevalue="true" falsevalue="false" checked="true" label="(A and NaN) solved as (A)?" help="if NO is selected (A and NaN) is solved as (NaN)"/>
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49 <conditional name="cond_hier">
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50 <param name="hier" type="select" label="Produce dendrogram (hierarchical clustering):">
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51 <option value="no" selected="true">no</option>
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52 <option value="yes">yes</option>
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53 </param>
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54 <when value="yes">
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55 <param name="linkage" type="select" label="Linkage type:">
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56 <option value="single" selected="true">Single: minimum distance between all observations of two sets</option>
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57 <option value="complete">Complete: maximum distance between all observations of two sets</option>
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58 <option value="average">Average: average distance between all observations of two sets</option>
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59 </param>
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60 </when>
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61 </conditional>
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62 </inputs>
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63 <outputs>
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64 <data format="txt" name="log" label="Log"/>
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65 <data format="pdf" name="dendrogram" label="$name dendrogram">
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66 <filter>cond_hier['hier'] == 'yes'</filter>
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67 </data>
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68 <data format="pdf" name="elbow" label="$name elbow evaluation method"/>
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69 <collection name="cluster_out" type="list" label="Clusters $k_min - $k_max">
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70 <discover_datasets pattern="__name_and_ext__" directory="cluster_out"/>
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71 </collection>
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72 </outputs>
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73 <help>
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74
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75 .. class:: warningmark
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76
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77 This tool expects input datasets consisting of tab-delimited columns.
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78
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79 .. class:: infomark
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80
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81 **TIP:** If your data is not TAB delimited, use *Text Manipulation > Convert delimiters to TAB*
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82
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83 </help>
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84 </tool>
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