Mercurial > repos > glogobyte > mirviz
comparison viz.xml @ 6:5e57bcdc731c draft
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| author | glogobyte |
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| date | Wed, 13 Oct 2021 11:19:32 +0000 |
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| 5:4d59ac081282 | 6:5e57bcdc731c |
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| 1 <tool id="mirViz" name="mirViz: Vizualizations and reports" version="0.1.0"> | |
| 2 <requirements> | |
| 3 <requirement type="package" version="1.7">fpdf</requirement> | |
| 4 <requirement type="package" version="3.7.4">python</requirement> | |
| 5 <requirement type="package" version="1.17.3">numpy</requirement> | |
| 6 <requirement type="package" version="3.1.2">matplotlib</requirement> | |
| 7 <requirement type="package" version="1.0.3">pandas</requirement> | |
| 8 </requirements> | |
| 9 <command> | |
| 10 #if $opt.stats.choice == "1": | |
| 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" | |
| 12 #elif $opt.stats.choice == "2": | |
| 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" | |
| 14 #else: | |
| 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" | |
| 16 #end if | |
| 17 </command> | |
| 18 <inputs> | |
| 19 <conditional name="opt"> | |
| 20 <param name="tool" type="select" label="Input file source:" help="Choose the tool which generates the input file."> | |
| 21 <option value="1" selected="true">Deseq2</option> | |
| 22 <option value="2">EdgeR</option> | |
| 23 </param> | |
| 24 <when value="1"> | |
| 25 <param name="input_file" type="data" format="tabular" label="Input file" help="File from Deseq2"/> | |
| 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."> | |
| 27 <option value="10" selected="true">Top 10</option> | |
| 28 <option value="20">Top 20</option> | |
| 29 <option value="30">Top 30</option> | |
| 30 <option value="40">Top 40</option> | |
| 31 <option value="50">Top 50</option> | |
| 32 </param> | |
| 33 <conditional name="stats"> | |
| 34 <param name="choice" type="select" label="Filter by p-value, p-adj or Base mean"> | |
| 35 <option value="1" selected="true">p-value</option> | |
| 36 <option value="2">P-adj</option> | |
| 37 <option value="3">Base mean</option> | |
| 38 </param> | |
| 39 <when value="1"> | |
| 40 <param name="pvalue" type="float" min="0" max="1" value="0.05" label="P-value (max value)" help="p-value threshold" /> | |
| 41 </when> | |
| 42 <when value="2"> | |
| 43 <param name="padj" type="float" min="0" max="1" value="0.05" label="P-adjustment (max value)" help="p-adjustment threshold" /> | |
| 44 </when> | |
| 45 <when value="3"> | |
| 46 <param name="Basemean" type="integer" value="0" min="0" label="Base mean (min value)" help="Base mean threshold" /> | |
| 47 </when> | |
| 48 </conditional> | |
| 49 <param name="log2fc" type="float" min="0" max="10" value="1" label="Log2FC (Absolute value)" help="Log2FC threshold" /> | |
| 50 </when> | |
| 51 <when value="2"> | |
| 52 <param name="input_file" type="data" format="tabular" label="Input file" help="File from EdgeR"/> | |
| 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."> | |
| 54 <option value="10" selected="true">Top 10</option> | |
| 55 <option value="20">Top 20</option> | |
| 56 <option value="30">Top 30</option> | |
| 57 <option value="40">Top 40</option> | |
| 58 <option value="50">Top 50</option> | |
| 59 </param> | |
| 60 <conditional name="stats"> | |
| 61 <param name="choice" type="select" label="Filter by p-value or p-adj"> | |
| 62 <option value="1" selected="true">p-value</option> | |
| 63 <option value="2">P-adj</option> | |
| 64 </param> | |
| 65 <when value="1"> | |
| 66 <param name="pvalue" type="float" min="0" max="1" value="0.05" label="P-value (max value)" help="p-value threshold" /> | |
| 67 </when> | |
| 68 <when value="2"> | |
| 69 <param name="padj" type="float" min="0" max="1" value="0.05" label="P-adjustment (max value)" help="p-adjustment threshold" /> | |
| 70 </when> | |
| 71 </conditional> | |
| 72 <param name="log2fc" type="float" min="0" max="10" value="1" label="Log2FC (Absolute value)" help="Log2FC threshold" /> | |
| 73 </when> | |
| 74 </conditional> | |
| 75 </inputs> | |
| 76 <outputs> | |
| 77 <data name="File" format="pdf" label="Differential expression of miRNAs and isoforms" from_work_dir="$__tool_directory__/report2.pdf" /> | |
| 78 </outputs> | |
| 79 <help> | |
| 80 | |
| 81 </help> | |
| 82 </tool> |