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1 <tool id="mirViz" name="mirViz: Vizualizations and reports" version="0.1.0">
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2 <requirements>
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3 <requirement type="package" version="1.7">fpdf</requirement>
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4 <requirement type="package" version="3.7.4">python</requirement>
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5 <requirement type="package" version="1.17.3">numpy</requirement>
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6 <requirement type="package" version="3.1.2">matplotlib</requirement>
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7 <requirement type="package" version="1.0.3">pandas</requirement>
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8 </requirements>
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9 <command>
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10 #if $opt.stats.choice == "1":
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11 python $__tool_directory__/viz.py -in $input_file -p_value "$opt.stats.pvalue" -fc $opt.log2fc -top $opt.top_mirna -tool_dir $__tool_directory__ -statistic "$opt.stats.choice" -diff_tool "$opt.tool"
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12 #elif $opt.stats.choice == "2":
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13 python $__tool_directory__/viz.py -in $input_file -p_value "$opt.stats.padj" -fc $opt.log2fc -top $opt.top_mirna -tool_dir $__tool_directory__ -statistic "$opt.stats.choice" -diff_tool "$opt.tool"
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14 #else:
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15 python $__tool_directory__/viz.py -in $input_file -p_value "$opt.stats.Basemean" -fc $opt.log2fc -top $opt.top_mirna -tool_dir $__tool_directory__ -statistic "$opt.stats.choice" -diff_tool "$opt.tool"
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16 #end if
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17 </command>
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18 <inputs>
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19 <conditional name="opt">
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20 <param name="tool" type="select" label="Input file source:" help="Choose the tool which generates the input file.">
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21 <option value="1" selected="true">Deseq2</option>
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22 <option value="2">EdgeR</option>
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23 </param>
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24 <when value="1">
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25 <param name="input_file" type="data" format="tabular" label="Input file" help="File from Deseq2"/>
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26 <param name="top_mirna" type="select" label="Choose the number of top differentially miRNAs in the report" help="Choose the number of top differentially expressed miRNAs.">
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27 <option value="10" selected="true">Top 10</option>
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28 <option value="20">Top 20</option>
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29 <option value="30">Top 30</option>
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30 <option value="40">Top 40</option>
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31 <option value="50">Top 50</option>
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32 </param>
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33 <conditional name="stats">
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34 <param name="choice" type="select" label="Filter by p-value, p-adj or Base mean">
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35 <option value="1" selected="true">p-value</option>
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36 <option value="2">P-adj</option>
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37 <option value="3">Base mean</option>
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38 </param>
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39 <when value="1">
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40 <param name="pvalue" type="float" min="0" max="1" value="0.05" label="P-value (max value)" help="p-value threshold" />
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41 </when>
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42 <when value="2">
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43 <param name="padj" type="float" min="0" max="1" value="0.05" label="P-adjustment (max value)" help="p-adjustment threshold" />
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44 </when>
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45 <when value="3">
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46 <param name="Basemean" type="integer" value="0" min="0" label="Base mean (min value)" help="Base mean threshold" />
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47 </when>
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48 </conditional>
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49 <param name="log2fc" type="float" min="0" max="10" value="1" label="Log2FC (Absolute value)" help="Log2FC threshold" />
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50 </when>
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51 <when value="2">
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52 <param name="input_file" type="data" format="tabular" label="Input file" help="File from EdgeR"/>
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53 <param name="top_mirna" type="select" label="Choose the number of top differentially miRNAs in the report" help="Choose the number of top differentially expressed miRNAs.">
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54 <option value="10" selected="true">Top 10</option>
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55 <option value="20">Top 20</option>
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56 <option value="30">Top 30</option>
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57 <option value="40">Top 40</option>
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58 <option value="50">Top 50</option>
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59 </param>
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60 <conditional name="stats">
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61 <param name="choice" type="select" label="Filter by p-value or p-adj">
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62 <option value="1" selected="true">p-value</option>
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63 <option value="2">P-adj</option>
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64 </param>
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65 <when value="1">
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66 <param name="pvalue" type="float" min="0" max="1" value="0.05" label="P-value (max value)" help="p-value threshold" />
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67 </when>
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68 <when value="2">
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69 <param name="padj" type="float" min="0" max="1" value="0.05" label="P-adjustment (max value)" help="p-adjustment threshold" />
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70 </when>
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71 </conditional>
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72 <param name="log2fc" type="float" min="0" max="10" value="1" label="Log2FC (Absolute value)" help="Log2FC threshold" />
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73 </when>
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74 </conditional>
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75 </inputs>
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76 <outputs>
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77 <data name="File" format="pdf" label="Differential expression of miRNAs and isoforms" from_work_dir="$__tool_directory__/report2.pdf" />
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78 </outputs>
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79 <help>
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80
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81 </help>
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82 </tool>
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