comparison QDNAseq-plot.xml @ 27:f89205f51e27 draft default tip

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26:069289631381

  <!-- change to /full/path/to/Rscript if required (eg /ccagc/lib/R/R-3.1.0/bin/Rscript) -->
  <command interpreter="Rscript"> 
    QDNAseq-plot.R 
    $cfg
  </command>

  <stdio>
    <!-- Anything higher than 0 means the R script didnt finish (correctly) -->
    <!-- Because different R packages deal with err/warn differently unable to waterproof this -->
    <exit_code range="1:" level="fatal" description="R script finished too early, check log" />

        <param name="plotAll" type="hidden" value="" />
      </when>
      
    </conditional> 
    -->
    <param name="sample_index" type="integer" required="True" value="1" label="Sample-index (integer)" help="The RDS input object can contain data from multiple individuals, this number tells the script which one to plot. Plotting multiple at the same time is not supported." />

    <!-- ==================== -->
    <!-- Optional advanced options -->
    <!-- ==================== -->
    <conditional name="advanced">

## -----
"${jobName}" -> outputName
"${outputPng}" -> outputPngPath
"${rdsFile}" -> rdsFilePath
as.integer( "${sample_index}" ) -> SAMPLE_INDEX

## -----
## extra options
## -----
as.integer( "${advanced.plot_width}" ) -> PLOT_WIDTH

27:f89205f51e27

  <!-- change to /full/path/to/Rscript if required (eg /ccagc/lib/R/R-3.1.0/bin/Rscript) -->
  <command interpreter="Rscript"> 
    QDNAseq-plot.R 
    $cfg
  </command>

  <version_command interpreter="Rscript">QDNAseq-version.R</version_command>

  <stdio>
    <!-- Anything higher than 0 means the R script didnt finish (correctly) -->
    <!-- Because different R packages deal with err/warn differently unable to waterproof this -->
    <exit_code range="1:" level="fatal" description="R script finished too early, check log" />

        <param name="plotAll" type="hidden" value="" />
      </when>
      
    </conditional> 
    -->
    <param name="sample_index" type="integer" required="True" value="1" label="Sample-index (integer)" help="The RDS input object can contain data from multiple samples, this index tells the script which one to plot. Plotting multiple samples at the same time is not supported." />

    <conditional name="subset_selection">
      <param name="what_to_plot" type="select" label="What to plot" help="Instead of plotting everything in the object you can also select certain chromosomes or set a genomic region">
        <option value="everything">Everything</option>
        <option value="chromosomes">Selected chromosomes</option>
        <option value="region">Genomic region</option>
      </param>
      <when value="everything">
        <!-- ==================== -->
        <param name="chr_name" type="hidden" value="NA" />
        <param name="chr_start" type="hidden" value="NA" />
        <param name="chr_end" type="hidden" value="NA" />
        <param name="chromosomes" type="hidden" value="NA" />
      </when>
      <when value="chromosomes">
        <!-- ==================== -->
        <param name="chromosomes" type="select" multiple="true" optional="false" label="Select chromosomes to plot" help="To zoom in on a particular chromosome you can select one or more here">
          <option value="1">1</option><option value="2">2</option>
          <option value="3">3</option><option value="4">4</option>
          <option value="5">5</option><option value="6">6</option>
          <option value="7">7</option><option value="8">8</option>
          <option value="9">9</option><option value="10">10</option>
          <option value="11">11</option><option value="12">12</option>
          <option value="13">13</option><option value="14">14</option>
          <option value="15">15</option><option value="16">16</option>
          <option value="17">17</option><option value="18">18</option>
          <option value="19">19</option><option value="20">20</option>
          <option value="21">21</option><option value="22">22</option>
          <!--<option value="X" selected="true">X</option>-->
          <!--<option value="Y" selected="true">Y</option>-->
        </param>
        <param name="chr_name" type="hidden" value="NA" />
        <param name="chr_start" type="hidden" value="NA" />
        <param name="chr_end" type="hidden" value="NA" />
      </when>
      <when value="region">
        <!-- ==================== -->
        <!--
        <param name="genomic_region" type="text" optional="false" label="Genomic region" help="Supply a genomic region in format chr1:12345-23456" value="chr1:12345-23456" size="30">
          <validator type="regex" message="No whitespace characters allowed">^[^\s\\]*$</validator>
          <validator type="regex" message="String is not of correct format">^chr\d+\:\d+\-\d+$</validator>
        </param>
        -->
        <param name="chr_name" size="2" type="integer" optional="false" value="" label="Chromosome" />
        <param name="chr_start" size="15" type="integer" optional="false" value="" label="Start position on chromosome" />
        <param name="chr_end" size="15" type="integer" optional="false" value="" label="End position on chromosome" />
        <param name="chromosomes" type="hidden" value="NA" />
      </when>

    </conditional>

    <!-- ==================== -->
    <!-- Optional advanced options -->
    <!-- ==================== -->
    <conditional name="advanced">

## -----
"${jobName}" -> outputName
"${outputPng}" -> outputPngPath
"${rdsFile}" -> rdsFilePath
as.integer( "${sample_index}" ) -> SAMPLE_INDEX
"${subset_selection.what_to_plot}" -> whatToPlot
"${subset_selection.chromosomes}" -> chromosomesToPlotString
as.integer( "${subset_selection.chr_name}" ) -> chrName
as.integer( "${subset_selection.chr_start}" ) -> chrStart
as.integer( "${subset_selection.chr_end}" ) -> chrEnd

## -----
## extra options
## -----
as.integer( "${advanced.plot_width}" ) -> PLOT_WIDTH