annotate tools/metag_tools/mapping_to_ucsc.xml @ 0:9071e359b9a3

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<tool id="mapToUCSC" name="Format mapping data" version="1.0.0">
  <description> as UCSC custom track</description>
  <command interpreter="python">
  	mapping_to_ucsc.py 
  	$out_file1
  	$input
  	$chr_col
  	$coord_col
  	$track.track_type
  	#if $track.track_type == "coverage" or $track.track_type == "both"
  	$track.coverage_col
    "${track.cname}"
    "${track.cdescription}"
    "${track.ccolor}"
    "${track.cvisibility}"
    #end if
    #if $track.track_type == "snp" or $track.track_type == "both"
    "${track.sdescription}"
    "${track.svisibility}"
     $track.col2
    #end if
  </command>
  <inputs>
    <param format="tabular" name="input" type="data" label="Select mapping data"/>
    <param name="chr_col" type="data_column" data_ref="input" label="Column for reference chromosome" />
    <param name="coord_col" type="data_column" data_ref="input" numerical="True" label="Numerical column for reference co-ordinate" />
    <conditional name="track">
      <param name="track_type" type="select" label="Display">
    	<option value="snp" selected="true">SNPs</option>
        <option value="coverage">Read coverage</option>
    	<option value="both">Both</option>
      </param>
      <when value = "coverage">
      <param name="coverage_col" type="data_column" data_ref="input" numerical="True" label="Numerical column for read coverage" />
      <param name="cname" type="text" size="15" value="User Track" label="Coverage track name">
        <validator type="length" max="15"/>
      </param>
      <param name="cdescription" type="text" value="User Supplied Coverage Track (from Galaxy)" label="Coverage track description">
        <validator type="length" max="60" size="15"/>
      </param>
      <param label="Coverage track Color" name="ccolor" type="select">
            <option selected="yes" value="0-0-0">Black</option>
            <option value="255-0-0">Red</option>
            <option value="0-255-0">Green</option>
            <option value="0-0-255">Blue</option>
            <option value="255-0-255">Magenta</option>
            <option value="0-255-255">Cyan</option>
            <option value="255-215-0">Gold</option>
            <option value="160-32-240">Purple</option>
            <option value="255-140-0">Orange</option>
            <option value="255-20-147">Pink</option>
            <option value="92-51-23">Dark Chocolate</option>
            <option value="85-107-47">Olive green</option>
      </param>
      <param label="Coverage track Visibility" name="cvisibility" type="select">
            <option selected="yes" value="1">Dense</option>
            <option value="2">Full</option>
            <option value="3">Pack</option>
            <option value="4">Squish</option>
            <option value="0">Hide</option>
      </param>
      </when>
      
      <when value = "snp">
      <!-- 
      <param name="col1" type="data_column" data_ref="input" label="Column containing the reference nucleotide" />
       -->
      <param name="col2" type="data_column" data_ref="input" label="Column containing the read nucleotide" />
      <!-- 
      <param name="sname" type="text" size="15" value="User Track-2" label="SNP track name">
        <validator type="length" max="15"/>
      </param>
       -->
      <param name="sdescription" type="text" value="User Supplied Track (from Galaxy)" label="SNP track description">
        <validator type="length" max="60" size="15"/>
      </param>
      <param label="SNP track Visibility" name="svisibility" type="select">
            <option selected="yes" value="1">Dense</option>
            <option value="2">Full</option>
            <option value="3">Pack</option>
            <option value="4">Squish</option>
            <option value="0">Hide</option>
      </param>
      </when>
      
      <when value = "both">
      <param name="coverage_col" type="data_column" data_ref="input" numerical="True" label="Numerical column for read coverage" />
      <param name="cname" type="text" size="15" value="User Track" label="Coverage track name">
        <validator type="length" max="15"/>
      </param>
      <param name="cdescription" type="text" size="15" value="User Supplied Track (from Galaxy)" label="Coverage track description">
        <validator type="length" max="60"/>
      </param>
      <param label="Coverage track Color" name="ccolor" type="select">
            <option selected="yes" value="0-0-0">Black</option>
            <option value="255-0-0">Red</option>
            <option value="0-255-0">Green</option>
            <option value="0-0-255">Blue</option>
            <option value="255-0-255">Magenta</option>
            <option value="0-255-255">Cyan</option>
            <option value="255-215-0">Gold</option>
            <option value="160-32-240">Purple</option>
            <option value="255-140-0">Orange</option>
            <option value="255-20-147">Pink</option>
            <option value="92-51-23">Dark Chocolate</option>
            <option value="85-107-47">Olive green</option>
      </param>
      <param label="Coverage track Visibility" name="cvisibility" type="select">
            <option selected="yes" value="1">Dense</option>
            <option value="2">Full</option>
            <option value="3">Pack</option>
            <option value="4">Squish</option>
            <option value="0">Hide</option>
      </param>
      <!-- 
      <param name="col1" type="data_column" data_ref="input" label="Column containing the reference nucleotide" />
       -->
      <param name="col2" type="data_column" data_ref="input" label="Column containing the read nucleotide" />
      <!-- 
      <param name="sname" type="text" size="15" value="User Track-2" label="SNP track name">
        <validator type="length" max="15"/>
      </param>
       -->
      <param name="sdescription" type="text" size="15" value="User Supplied Track (from Galaxy)" label="SNP track description">
        <validator type="length" max="60"/>
      </param>
      <param label="SNP track Visibility" name="svisibility" type="select">
            <option selected="yes" value="1">Dense</option>
            <option value="2">Full</option>
            <option value="3">Pack</option>
            <option value="4">Squish</option>
            <option value="0">Hide</option>
      </param>
      </when>
    </conditional>
  </inputs>
  <outputs>
    <data format="customtrack" name="out_file1"/>
  </outputs>

  
 <help> 

.. class:: infomark

**What it does**

This tool turns mapping data generated by short read mappers into a format that can be displayed in the UCSC genome browser as a custom track. 

-----

.. class:: warningmark

**Note**

This tool requires the mapping data to contain at least the following information: 

chromosome, genome coordinate, read nucleotide (if option to display is SNPs), read coverage (if option to display is Read coverage). 

-----

**Example**

For the following Mapping data::

   #chr g_start read_id          read_coord g_nt read_nt qual read_coverage
   chrM    1   1:29:1672:1127/1    11        G    G       40  134
   chrM    1   1:32:93:933/1       4         G    A       40  134
   chrM    1   1:34:116:2032/1     11        G    A       40  134
   chrM    1   1:39:207:964/1      1         G    G       40  134
   chrM    2   1:3:359:848/1       1         G    C       40  234
   chrM    2   1:40:1435:1013/1    1         G    G       40  234
   chrM    3   1:40:730:972/1      9         G    G       40  334
   chrM    4   1:42:1712:921/2     31        G    T       35  434
   chrM    4   1:44:1649:493/1     4         G    G       40  434

running this tool to display both SNPs and Read coverage will return the following tracks, containing aggregated data per genome co-ordinate::

   track type=wiggle_0 name="Coverage Track" description="User Supplied Track (from Galaxy)" color=0,0,0 visibility=1
   variableStep chrom=chrM
   1   134
   2   234
   3   334
   4   434
   track type=wiggle_0 name="Track A" description="User Supplied SNP Track (from Galaxy)" color=255,0,0 visibility=1
   variableStep chrom=chrM
   1   2
   track type=wiggle_0 name="Track T" description="User Supplied SNP Track (from Galaxy)" color=0,255,0 visibility=1
   variableStep chrom=chrM
   4   1
   track type=wiggle_0 name="Track G" description="User Supplied SNP Track (from Galaxy)" color=0,0,255 visibility=1
   variableStep chrom=chrM
   1   2
   2   1
   3   1
   4   1
   track type=wiggle_0 name="Track C" description="User Supplied SNP Track (from Galaxy)" color=255,0,255 visibility=1
   variableStep chrom=chrM
   2   1
   
  </help>  
</tool>