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1 <tool id="plotheatmap" name="plotHeatmap" version="1.0">
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2 <description>Plot heatmap</description>
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3 <stdio>
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4 <exit_code range="1:" />
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5 </stdio>
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6 <command>
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7 <![CDATA[
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8 $__tool_directory__/tools/script.R $main.count_matrix $main.stats_matrix $main.log_fc $main.log_cpm $main.pvalue $main.fdr $heatmap.cluster_row $heatmap.cluster_col $heatmap.hclust_method $plotparm.col_marg $plotparm.row_marg $plotparm.pdf_width $plotparm.pdf_height > $rscript_log 2> $rerror_log
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9
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10 ]]>
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11 </command>
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12 <inputs>
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13 <section name="main" title="Main parameters" expanded="True">
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14 <param name="count_matrix" type="data" format="data" label=""/>
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15 <param name="stats_matrix" type="data" format="data" label=""/>
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16 <param name="log_fc" type="float" value="0.5" label=""/>
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17 <param name="log_cpm" type="float" value="0.5" label=""/>
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18 <param name="pvalue" type="float" value="0.5" label=""/>
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19 <param name="fdr" type="float" value="0.5" label=""/>
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20 </section>
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21
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22 <section name="heatmap" title="Heatmap parameters">
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23 <param name="cluster_row" type="select" label="Determines if the row dendrogram should be reordered">
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24 <option value="No" >No </option>
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25 <option value="Yes" selected="true" >Yes </option>
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26 </param>
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27 <param name="cluster_col" type="select" label="Determines if the column dendrogram should be reordered">
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28 <option value="No" selected="true">No </option>
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29 <option value="Yes" >Yes </option>
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30 </param>
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31
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32 <param name="hclust_method" type="select" label="Hierarchical clustering method">
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33 <option value="ward.D" >ward.D </option>
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34 <option value="ward.D2" >ward.D2 </option>
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35 <option value="single" >single </option>
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36 <option value="complete" >complete </option>
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37 <option value="average" selected="true">average </option>
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38 <option value="mcquitty" >mcquitty </option>
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39 <option value="median" >median </option>
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40 <option value="centroid" >centroid </option>
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41 </param>
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42 </section>
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43
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44
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45 <section name="plotparm" title="Plot parameters">
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46 <param name="col_marg" type="float" value="7" label="Margins or column names"/>
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47 <param name="row_marg" type="float" value="8" label="Margins or row names"/>
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48 <param name="pdf_width" type="float" value="7" label="Width of the graphics region in inches" />
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49 <param name="pdf_height" type="float" value="7" label="Height of the graphics region in inches" />
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50 </section>
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51
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52
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53
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54 </inputs>
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55 <outputs>
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56 <data format="pdf" name="haetamappdf" from_work_dir="heatmap.pdf" >
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57 <filter>(outftype == 'pdf')</filter>
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58 </data>
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59 <data name="rscript_log" format="data" />
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60 <data name="rerror_log" format="data" />
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61 </outputs>
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62 <tests>
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63
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64 <test>
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65 <param name="count_matrix" value="count.matrix"/>
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66 <param name="stats_matrix" value="stats.data"/>
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67 <param name="log_fc" value="1"/>
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68 <param name="log_cpm" value="2"/>
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69 <param name="pvalue" value="0.05"/>
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70 <param name="fdr" value="0.1"/>
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71 <output name="haetamappdf" file="heatmap.pdf" ftype="pdf" compare="sim_size" />
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72 <output name="rscript_log" file="rscript.log"/>
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73 <output name="rerror_log" file="rerror.log"/>
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74
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75 </test>
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76
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77 </tests>
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78 <help>
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79 <![CDATA[
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80
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81 ]]>
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82 </help>
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83 <citations>
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84 </citations>
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85 </tool> |
