view viz.xml @ 15:6db3bd727fde draft

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<tool id="viz_tool" name="Viz_tool: After Deseq2" version="0.1.0">
  <description>for each sequence in a file</description>
  <requirements>
    <requirement type="package" version="1.7">fpdf</requirement>
    <requirement type="package" version="3.7.4">python</requirement>
    <requirement type="package" version="1.17.3">numpy</requirement>
    <requirement type="package" version="3.1.2">matplotlib</requirement>
    <requirement type="package" version="1.0.3">pandas</requirement>
  </requirements>
  <command>
    #if $stats.choice == "1":
      python $__tool_directory__/viz_ultra.py -in $input_file -p_value "$stats.pvalue" -fc $log2fc -top $top_mirna -tool_dir $__tool_directory__ -statistic "$stats.choice" -diff_tool "$tool"
    #else:
      python $__tool_directory__/viz_ultra.py -in $input_file -p_value "$stats.padj" -fc $log2fc -top $top_mirna -tool_dir $__tool_directory__ -statistic "$stats.choice" -diff_tool "$tool"
    #end if
  </command>
  <inputs>
    <param name="tool" type="select" label="File comes from" help="Choose the tool which generates the input file.">
      <option value="1" selected="true">Deseq2</option>
      <option value="2">EdgeR</option>
    </param>
    <param name="input_file" type="data" format="tabular" label="Input file" help="File from Deseq2 or EdgeR"/>
    <param name="top_mirna" type="select" label="Choose the top differentially miRNAs of the analysis" help="Choose the number of top differentially expressed miRNAs.">
      <option value="10" selected="true">Top 10</option>
      <option value="20">Top 20</option>
      <option value="30">Top 30</option>
      <option value="40">Top 40</option>
      <option value="50">Top 50</option>
    </param>
    <conditional name="stats">
     <param name="choice" type="select" label="Choose p-value or p-adj" help="asdadadasd">
      <option value="1" selected="true">Pvalue</option>
      <option value="2">Padj</option>
     </param>
     <when value="1">
      <param name="pvalue" type="float" min="0" max="1" value="0.05" label="P-value (max value)" help="p-value threshold" />
     </when>
     <when value="2">
      <param name="padj" type="float" min="0" max="1" value="0.05" label="P-adjustment (max value)" help="p-adjustment threshold" />
     </when>
    </conditional>
    <param name="log2fc" type="float" min="0" max="10" value="1" label="Log2FC (Absolute value)" help="Log2FC threshold" />
  </inputs>
  <outputs>
    <!--data name="TOP_temp" format="png" label="TOP_$top_mirna Differentially Expressed miRNAs" from_work_dir="$__tool_directory__/tem.png" /-->
    <!--data name="TOP_non" format="png" label="TOP_$top_mirna Differentially Expressed miRNAs" from_work_dir="$__tool_directory__/non.png" /-->
    <data name="Scatter" format="png" label="Scatter Differentially Expressed miRNAs" from_work_dir="$__tool_directory__/a3.png" />
    <data name="File" format="pdf" label="PDF" from_work_dir="$__tool_directory__/report2.pdf" />
    <data name="File1" format="txt" label="txt" from_work_dir="$__tool_directory__/demo.txt" />
  </outputs>
  <help>

  </help>
</tool>