view svdetect/SVDetect_import.xml @ 22:eb65c0fa5542 draft

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<tool id="svdetect_import" name="Import data">
  <description>BAM, chromosome info or sv files</description>
  <command interpreter="bash">SVDetect_import.sh -i $file_path
  #if str($type.file_type)=="bam"
  -o $outbamfile
  #elif str($type.file_type)=="len"
  -o $outlenfile
  #elif str($type.file_type)=="sv"
  -o $outsvfile
  #end if
  </command>
  <inputs>
    <param name="file_name" type="text" value="file1" label="File Name"/>
    <conditional name="type">
      <param name="file_type" type="select" label="Select the file type to import" help="BAM file (BAM) or text file (SAM, chromosome list or a SV tabulated text file)">
          <option value="bam">BAM file (.bam)</option>
          <option value="len">Chromosome info file (.len)</option>
          <option value="sv">SVDetect output file (.sv)</option>
      </param>
    <when value="bam">
      <!-- do nothing here -->
    </when>
    <when value="len">
      <!-- do nothing here -->
    </when>
     <when value="sv">
      <!-- do nothing here -->
    </when>
    </conditional>
     <param name="file_path" type="text" size="150" label="Path to file"/>
  </inputs>
  <outputs>
    <data format="bam" name="outbamfile" label="${file_name}.bam">
      <filter>type['file_type']=="bam"</filter>
    </data>
    <data format="len" name="outlenfile" label="${file_name}.len">
      <filter>type['file_type']=="len"</filter>
    </data>
    <data format="sv" name="outsvfile" label="${file_name}.sv">
      <filter>type['file_type']=="sv"</filter>
    </data>
  </outputs>
  <help>
**What it does**

This tool allows you to import quickly a BAM file, a chromosome info file or a SVDetect output file from you computer as inputs for SVDetect.


**Example of chromosome file**

Input len file::

    1  chr1  247249719
    2  chr2  242951149
    3  chr3  199501827
    4  chr4  191273063
    5  chr5  180857866
    6  chr6  170899992
    7  chr7  158821424
    8  chr8  146274826
    9  chr9  140273252
    10  chr10  135374737
    11  chr11  134452384
    12  chr12  132349534
    13  chr13  114142980
    14  chr14  106368585
    15  chr15  100338915
    16  chr16  88827254
    17  chr17  78774742
    18  chr18  76117153
    19  chr19  63811651
    20  chr20  62435964
    21  chr21  46944323
    22  chr22  49691432
    23  chrX  154913754
    24  chrY  57772954

-----

.. class:: infomark

Contact Bruno Zeitouni ([e-mail]) for any questions or concerns about the Galaxy implementation of SVDetect.
  </help>

</tool>