comparison pileup_parser.xml @ 2:85bedbea8a12 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/pileup_parser commit ab627176cd4f6efe6d1fe4b85baa679aaa651eb1

1:1670f0565000

<tool id="pileup_parser" name="Filter pileup" version="1.0.2">>
  <description>on coverage and SNPs</description>
  <command interpreter="perl">
    #if   $pileup_type.type_select == "six"    #pileup_parser.pl $input "3" "5" "6" "4" $qv_cutoff $cvrg_cutoff $snps_only $interval "2" $out_file1 $diff $qc_base
    #elif $pileup_type.type_select == "ten"    #pileup_parser.pl $input "3" "9" "10" "8" $qv_cutoff $cvrg_cutoff $snps_only $interval "2" $out_file1 $diff $qc_base
    #elif $pileup_type.type_select == "manual" #pileup_parser.pl $input $pileup_type.ref_base_column $pileup_type.read_bases_column $pileup_type.read_qv_column $pileup_type.cvrg_column $qv_cutoff $cvrg_cutoff $snps_only $interval $pileup_type.coord_column $out_file1 $diff $qc_base
    #end if#

    </param>
    <param name="qc_base" label="Print quality and base string?" type="select" help="See &quot;Example 4&quot; below for explanation">
        <option value="No">No</option>
        <option value="Yes" selected="true">Yes</option>
    </param>
        
  </inputs>
  <outputs>
    <data format="tabular" name="out_file1">
        <change_format>
            <when input="interval" value="Yes" format="interval" />

      <param name="input" value="pileup_parser.10col.pileup"/>
      <output name="out_file1" file="pileup_parser.10col.20-3-yes-yes.pileup.out"/>
      <param name="type_select" value="ten"/>
      <param name="qv_cutoff" value="20" />
      <param name="cvrg_cutoff" value="3" />
      <param name="snps_only" value="Yes"/>q
      <param name="interval" value="Yes" />
       <param name="diff" value="No" />
      <param name="qc_base" value="Yes" />
    </test>
    <test>

      <param name="coord_column" value="2"/>
      <param name="qv_cutoff" value="20" />
      <param name="cvrg_cutoff" value="3" />
      <param name="snps_only" value="Yes"/>
      <param name="interval" value="Yes" />
       <param name="diff" value="No" />
      <param name="qc_base" value="Yes" />
    </test>
        <test>
      <param name="input" value="pileup_parser.10col.pileup"/>
      <output name="out_file1" file="pileup_parser.10col.20-3-yes-yes-yes-yes.pileup.out"/>
      <param name="type_select" value="manual"/>
      <param name="ref_base_column" value="3"/>
      <param name="read_bases_column" value="9"/>

      <param name="coord_column" value="2"/>
      <param name="qv_cutoff" value="20" />
      <param name="cvrg_cutoff" value="3" />
      <param name="snps_only" value="Yes"/>
      <param name="interval" value="Yes" />
       <param name="diff" value="Yes" />
      <param name="qc_base" value="Yes" />
    </test>
    <test>
      <param name="input" value="pileup_parser.10col.pileup"/>
      <output name="out_file1" file="pileup_parser.10col.20-3-yes-yes-yes-no.pileup.out"/>

      <param name="coord_column" value="2"/>
      <param name="qv_cutoff" value="20" />
      <param name="cvrg_cutoff" value="3" />
      <param name="snps_only" value="Yes"/>
      <param name="interval" value="Yes" />
       <param name="diff" value="Yes" />
      <param name="qc_base" value="No" />
    </test>


 </tests>
<help>

**What it does**

Allows one to find sequence variants and/or sites covered by a specified number of reads with bases above a set quality threshold. The tool works on six and ten column pileup formats produced with *samtools pileup* command. However, it also allows you to specify columns in the input file manually. The tool assumes the following:

.. _SAMTools: http://samtools.sourceforge.net/pileup.shtml

**Six column pileup**::

    1    2  3  4        5        6
 ---------------------------------   
 chrM  412  A  2       .,       II
 chrM  413  G  4     ..t,     IIIH
 chrM  414  C  4     ..Ta     III2
 chrM  415  C  4     TTTt     III7
   
where::

  Column Definition
 ------- ----------------------------
       1 Chromosome
       2 Position (1-based)
       3 Reference base at that position
       4 Coverage (# reads aligning over that position)
       5 Bases within reads
       6 Quality values (phred33 scale, see Galaxy wiki for more)
       
**Ten column pileup**

The `ten-column`__ pileup incorporates additional consensus information generated with the *-c* option of the *samtools pileup* command::

- Number of **A** variants
- Number of **C** variants
- Number of **G** variants
- Number of **T** variants
- Number of read bases covering this position, where quality is equal to or higher than the value set by **Do not consider read bases with  quality lower than** option. 

Optionally, if **Print total number of differences?** is set to **Yes**, the tool will append the sixth column with the total number of deviants (see below).

2. If **Convert coordinates to intervals?** is set to **Yes**, the tool replaces the position column (typically the second column) with a pair of tab-delimited start/end values.

you will get::

 chrM  413  G  4  ..t,  IIIH  0  0  2  1  3
 chrM  414  C  4  ..Ta  III2  1  1  0  1  3
 chrM  415  C  4  TTTt  III7  0  0  0  4  4
 
where::

  Column Definition
 ------- ----------------------------
       1 Chromosome

       9 Number of G variants
      10 Number of T variants
      11 Quality adjusted coverage:
      12 Number of read bases (i.e., # of reads) with quality above the set threshold
      13 Total number of deviants (if Convert coordinates to intervals? is set to yes)
         
if **Print total number of differences?** is set to **Yes**, you will get::

 chrM  413  G  4  ..t,  IIIH  0  0  2  1  3  1
 chrM  414  C  4  ..Ta  III2  1  2  0  1  3  2
 chrM  415  C  4  TTTt  III7  0  0  0  4  4  0 
 
Note the additional column 13, that contains the number of deviant reads (e.g., there are two deviants, T and a, for position 414).

 
Finally, if **Convert coordinates to intervals?** is set to **Yes**, you will get one additional column with the end coordinate::
 
 chrM  412 413  G  4  ..t,  III2  0  0  2  1  3
 chrM  414 415  C  4  ..Ta  III2  1  2  0  1  3
 chrM  414 415  C  4  TTTt  III7  0  0  0  4  4
 
where::

  Column Definition
 ------- ----------------------------
       1 Chromosome

      11 Number of T variants
      12 Quality adjusted coverage
      13 Total number of deviants (if Convert coordinates to intervals? is set to yes)


Note that in this case the coordinates of SNPs were converted to intervals, where the start coordinate is 0-based and the end coordinate in 1-based using the UCSC Table Browser convention. 
 
Although three positions have variants in the original file (413, 414, and 415), only 413 and 415 are reported because the quality values associated with these two SNPs are above the threshold of 20. In the case of 414 the **a** allele has a quality value of 17 ( ord("2")-33 ), and is therefore not reported. Note that five columns have been added to each of the reported lines::

  chrM  413  G  4  ..t,  IIIH  0  0  2  1  3
  
Here, there is one variant, **t**. Because the fourth column represents **T** counts, it is incremented by 1. The last column shows that at this position, three reads have bases above the quality threshold of 20.

-----

**Example 1**: Just variants

 chrM  412  A  2       .,       II
 chrM  413  G  4     ..t,     III2
 chrM  414  C  4     ..Ta     III2
 chrM  415  C  4     TTTt     III7
 
To call all variants (with no restriction by coverage) with quality above phred value of 20, we will need to set the parameters as follows:

.. image:: pileup_parser_help1.png 

Running the tool with these parameters will return::

 chrM  413  G  4  ..t,  IIIH  0  0  0  1  3
 chrM  414  C  4  ..Ta  III2  0  2  0  1  3
 chrM  415  C  4  TTTt  III7  0  0  0  4  4
 
**Note** that position 414 is not reported because the *a* variant has associated quality value of 17 (because ord('2')-33 = 17) and is below the phred threshold of 20 set by the **Count variants with quality above this value** parameter.

-----

**Example 2**: Report everything

In addition to calling variants, it is often useful to know the quality adjusted coverage. Running the tool with these parameters:

.. image:: pileup_parser_help2.png 

will report everything from the original file::

 chrM  412  A  2  .,    II    2  0  0  0  2
 chrM  413  G  4  ..t,  III2  0  0  2  1  3
 chrM  414  C  4  ..Ta  III2  0  2  0  1  3
 chrM  415  C  4  TTTt  III7  0  0  0  4  4
 
Here, you can see that although the total coverage at position 414 is 4 (column 4), the quality adjusted coverage is 3 (last column). This is because only three out of four reads have bases with quality above the set threshold of 20 (the actual qualities are III2 or, after conversion,  40, 40, 40, 17).

One can use the last column of this dataset to filter out (using Galaxy's **Filter** tool) positions where quality adjusted coverage (last column) is below a set threshold.

------

 chrM  412  A  2  .,    II    2  0  0  0  2  0
 chrM  413  G  4  ..t,  III2  0  0  2  1  3  1
 chrM  414  C  4  ..Ta  III2  0  2  0  1  3  1
 chrM  415  C  4  TTTt  III7  0  0  0  4  4  0
 
 
-----

**Example 4**: Report everything, print total number of differences, and ignore qualities and read bases

Setting **Print quality and base string?** to **Yes** as shown here:

 chrM  412  A  2  2  0  0  0  2  0
 chrM  413  G  4  0  0  2  1  3  1
 chrM  414  C  4  0  2  0  1  3  1
 chrM  415  C  4  0  0  0  4  4  0



 
</help>
</tool>

2:85bedbea8a12

<tool id="pileup_parser" name="Filter pileup" version="1.0.2">
  <description>on coverage and SNPs</description>
  <requirements>
        <requirement type="package" version="5.22.0">perl</requirement>
   </requirements>
  <command interpreter="perl">
    #if   $pileup_type.type_select == "six"    #pileup_parser.pl $input "3" "5" "6" "4" $qv_cutoff $cvrg_cutoff $snps_only $interval "2" $out_file1 $diff $qc_base
    #elif $pileup_type.type_select == "ten"    #pileup_parser.pl $input "3" "9" "10" "8" $qv_cutoff $cvrg_cutoff $snps_only $interval "2" $out_file1 $diff $qc_base
    #elif $pileup_type.type_select == "manual" #pileup_parser.pl $input $pileup_type.ref_base_column $pileup_type.read_bases_column $pileup_type.read_qv_column $pileup_type.cvrg_column $qv_cutoff $cvrg_cutoff $snps_only $interval $pileup_type.coord_column $out_file1 $diff $qc_base
    #end if#

    </param>
    <param name="qc_base" label="Print quality and base string?" type="select" help="See &quot;Example 4&quot; below for explanation">
        <option value="No">No</option>
        <option value="Yes" selected="true">Yes</option>
    </param>
  </inputs>
  <outputs>
    <data format="tabular" name="out_file1">
        <change_format>
            <when input="interval" value="Yes" format="interval" />

      <param name="input" value="pileup_parser.10col.pileup"/>
      <output name="out_file1" file="pileup_parser.10col.20-3-yes-yes.pileup.out"/>
      <param name="type_select" value="ten"/>
      <param name="qv_cutoff" value="20" />
      <param name="cvrg_cutoff" value="3" />
      <param name="snps_only" value="Yes"/>
      <param name="interval" value="Yes" />
       <param name="diff" value="No" />
      <param name="qc_base" value="Yes" />
    </test>
    <test>

      <param name="coord_column" value="2"/>
      <param name="qv_cutoff" value="20" />
      <param name="cvrg_cutoff" value="3" />
      <param name="snps_only" value="Yes"/>
      <param name="interval" value="Yes" />
      <param name="diff" value="No" />
      <param name="qc_base" value="Yes" />
    </test>
    <test>
      <param name="input" value="pileup_parser.10col.pileup"/>
      <output name="out_file1" file="pileup_parser.10col.20-3-yes-yes-yes-yes.pileup.out"/>
      <param name="type_select" value="manual"/>
      <param name="ref_base_column" value="3"/>
      <param name="read_bases_column" value="9"/>

      <param name="coord_column" value="2"/>
      <param name="qv_cutoff" value="20" />
      <param name="cvrg_cutoff" value="3" />
      <param name="snps_only" value="Yes"/>
      <param name="interval" value="Yes" />
      <param name="diff" value="Yes" />
      <param name="qc_base" value="Yes" />
    </test>
    <test>
      <param name="input" value="pileup_parser.10col.pileup"/>
      <output name="out_file1" file="pileup_parser.10col.20-3-yes-yes-yes-no.pileup.out"/>

      <param name="coord_column" value="2"/>
      <param name="qv_cutoff" value="20" />
      <param name="cvrg_cutoff" value="3" />
      <param name="snps_only" value="Yes"/>
      <param name="interval" value="Yes" />
      <param name="diff" value="Yes" />
      <param name="qc_base" value="No" />
    </test>
</tests>
<help>

**What it does**

Allows one to find sequence variants and/or sites covered by a specified number of reads with bases above a set quality threshold. The tool works on six and ten column pileup formats produced with *samtools pileup* command. However, it also allows you to specify columns in the input file manually. The tool assumes the following:

.. _SAMTools: http://samtools.sourceforge.net/pileup.shtml

**Six column pileup**::

    1    2  3  4        5        6
 ---------------------------------
 chrM  412  A  2       .,       II
 chrM  413  G  4     ..t,     IIIH
 chrM  414  C  4     ..Ta     III2
 chrM  415  C  4     TTTt     III7

where::

  Column Definition
 ------- ----------------------------
       1 Chromosome
       2 Position (1-based)
       3 Reference base at that position
       4 Coverage (# reads aligning over that position)
       5 Bases within reads
       6 Quality values (phred33 scale, see Galaxy wiki for more)

**Ten column pileup**

The `ten-column`__ pileup incorporates additional consensus information generated with the *-c* option of the *samtools pileup* command::

- Number of **A** variants
- Number of **C** variants
- Number of **G** variants
- Number of **T** variants
- Number of read bases covering this position, where quality is equal to or higher than the value set by **Do not consider read bases with  quality lower than** option.

Optionally, if **Print total number of differences?** is set to **Yes**, the tool will append the sixth column with the total number of deviants (see below).

2. If **Convert coordinates to intervals?** is set to **Yes**, the tool replaces the position column (typically the second column) with a pair of tab-delimited start/end values.

you will get::

 chrM  413  G  4  ..t,  IIIH  0  0  2  1  3
 chrM  414  C  4  ..Ta  III2  1  1  0  1  3
 chrM  415  C  4  TTTt  III7  0  0  0  4  4

where::

  Column Definition
 ------- ----------------------------
       1 Chromosome

       9 Number of G variants
      10 Number of T variants
      11 Quality adjusted coverage:
      12 Number of read bases (i.e., # of reads) with quality above the set threshold
      13 Total number of deviants (if Convert coordinates to intervals? is set to yes)

if **Print total number of differences?** is set to **Yes**, you will get::

 chrM  413  G  4  ..t,  IIIH  0  0  2  1  3  1
 chrM  414  C  4  ..Ta  III2  1  2  0  1  3  2
 chrM  415  C  4  TTTt  III7  0  0  0  4  4  0

Note the additional column 13, that contains the number of deviant reads (e.g., there are two deviants, T and a, for position 414).

Finally, if **Convert coordinates to intervals?** is set to **Yes**, you will get one additional column with the end coordinate::

 chrM  412 413  G  4  ..t,  III2  0  0  2  1  3
 chrM  414 415  C  4  ..Ta  III2  1  2  0  1  3
 chrM  414 415  C  4  TTTt  III7  0  0  0  4  4

where::

  Column Definition
 ------- ----------------------------
       1 Chromosome

      11 Number of T variants
      12 Quality adjusted coverage
      13 Total number of deviants (if Convert coordinates to intervals? is set to yes)


Note that in this case the coordinates of SNPs were converted to intervals, where the start coordinate is 0-based and the end coordinate in 1-based using the UCSC Table Browser convention.

Although three positions have variants in the original file (413, 414, and 415), only 413 and 415 are reported because the quality values associated with these two SNPs are above the threshold of 20. In the case of 414 the **a** allele has a quality value of 17 ( ord("2")-33 ), and is therefore not reported. Note that five columns have been added to each of the reported lines::

  chrM  413  G  4  ..t,  IIIH  0  0  2  1  3

Here, there is one variant, **t**. Because the fourth column represents **T** counts, it is incremented by 1. The last column shows that at this position, three reads have bases above the quality threshold of 20.

-----

**Example 1**: Just variants

 chrM  412  A  2       .,       II
 chrM  413  G  4     ..t,     III2
 chrM  414  C  4     ..Ta     III2
 chrM  415  C  4     TTTt     III7

To call all variants (with no restriction by coverage) with quality above phred value of 20, we will need to set the parameters as follows:

.. image:: pileup_parser_help1.png

Running the tool with these parameters will return::

 chrM  413  G  4  ..t,  IIIH  0  0  0  1  3
 chrM  414  C  4  ..Ta  III2  0  2  0  1  3
 chrM  415  C  4  TTTt  III7  0  0  0  4  4

**Note** that position 414 is not reported because the *a* variant has associated quality value of 17 (because ord('2')-33 = 17) and is below the phred threshold of 20 set by the **Count variants with quality above this value** parameter.

-----

**Example 2**: Report everything

In addition to calling variants, it is often useful to know the quality adjusted coverage. Running the tool with these parameters:

.. image:: pileup_parser_help2.png

will report everything from the original file::

 chrM  412  A  2  .,    II    2  0  0  0  2
 chrM  413  G  4  ..t,  III2  0  0  2  1  3
 chrM  414  C  4  ..Ta  III2  0  2  0  1  3
 chrM  415  C  4  TTTt  III7  0  0  0  4  4

Here, you can see that although the total coverage at position 414 is 4 (column 4), the quality adjusted coverage is 3 (last column). This is because only three out of four reads have bases with quality above the set threshold of 20 (the actual qualities are III2 or, after conversion,  40, 40, 40, 17).

One can use the last column of this dataset to filter out (using Galaxy's **Filter** tool) positions where quality adjusted coverage (last column) is below a set threshold.

------

 chrM  412  A  2  .,    II    2  0  0  0  2  0
 chrM  413  G  4  ..t,  III2  0  0  2  1  3  1
 chrM  414  C  4  ..Ta  III2  0  2  0  1  3  1
 chrM  415  C  4  TTTt  III7  0  0  0  4  4  0

-----

**Example 4**: Report everything, print total number of differences, and ignore qualities and read bases

Setting **Print quality and base string?** to **Yes** as shown here:

 chrM  412  A  2  2  0  0  0  2  0
 chrM  413  G  4  0  0  2  1  3  1
 chrM  414  C  4  0  2  0  1  3  1
 chrM  415  C  4  0  0  0  4  4  0
</help>
<citations>
</citations>
</tool>