Galaxy tool for summarizing fastqc information

summarize_fastqc.xml

<tool name="Summarize FastQC" id="summarizeFastQCMetrics" version="0.0.1">
  <description>summarizes data from FastQC</description>
  <command>

    #def pairfunc($theList)
    #set $left = []
    #set $right = []
    #for $file1, $file2 in $theList
        #$left.append(str($file1))
        #$right.append(str($file2))
    #end for
    #return $left, $right
    #end def
        
    #def singlefunc($theList)
    #set $single = []
    #for $file in $theList
      #$single.append(str($file))
    #end for
    #return $single  
    #end def
    
    #set $single = []
    #set $left = []
    #set $right = []
    #if str( $single_vs_paired.single_vs_paired_selector ) == "list_of_paired_files"
      #set $l, $r = $pairfunc($single_vs_paired.paired_fastqc_results)
      #set $left += $l
      #set $right += $r
    #elif str( $single_vs_paired.single_vs_paired_selector ) == "list_of_files"
      #set $single += $singlefunc($single_vs_paired.list_fastqc_results)
    #elif str( $single_vs_paired.single_vs_paired_selector ) == "single_files"
      #set $single += $singlefunc($single_vs_paired.single_fastqc_results)
    #else
      exit 1
    #end if

    #set $files = ",".join($left + $right + $single)
    summarizeFastQCMetrics.rb $files > $outFile
  </command>
  
  <inputs>
    <conditional name="single_vs_paired">
      <param name="single_vs_paired_selector" type="select" label="What type of FastQC results do you have?">
	<option value="list_of_paired_files">Paired TXT results from FastQC on paired-end fastq files</option>
	<option value="list_of_files">List of TXT results from FastQC.</option>
	<option value="single_files">TXT results from FastQC on single fastq files.</option>
      </param>
      <when value="list_of_paired_files">
	<param name="paired_fastqc_results" type="data_collection" collection_type="list:paired" format="txt" label="Paired list of FastQC results" help="When you've run FastQC on a list of paired end fastq files." />
      </when>
      <when value="list_of_files">
	<param name="list_fastqc_results" type="data_collection" collection_type="list" format="txt" label="List of FastQC results" help="When you've run FastQC on a list of fastq files." />
      </when>
      <when value="single_files">
	<param name="single_fastqc_results" type="data" format="txt" multiple="true" label="FastQC results on single fastq files." help="When you've run FastQC on single fastq files" />
      </when>
    </conditional>
 
  </inputs>
  <outputs>
    <data name="outFile" format="tabular" label="${tool.name} on ${on_string}: Tabular summary of FastQC"/>
  </outputs>
  <tests>
    <test>
    </test>
  </tests>
  
  <stdio>
    <exit_code range="1:"  level="fatal"/>
  </stdio>
  
  <help>

.. class:: infomark

**Purpose**

Merges results from FastQC on fastqc files into a single matrix.


  </help>
</tool>