<tool id="gd_specify_restriction_enzymes" name="Differential Cleavage" version="1.0.0">
  <description>: Select SNPs differentially cut by specified restriction enzymes</description>

  <command interpreter="python">
    specify_restriction_enzymes.py "--input=$input" "--output=$output" "--primers_loc=${GALAXY_DATA_INDEX_DIR}/gd.primers.loc"
    #if $override_metadata.choice == "0":
      "--scaffold_col=${input.metadata.scaffold}" "--pos_col=${input.metadata.pos}" "--species=${input.metadata.species}"
    #else
      "--scaffold_col=$scaf_col" "--pos_col=$pos_col" "--species=$species"
    #end if
    "--enzyme_list=$enzymes"
  </command>

  <inputs>
    <param format="tabular" name="input" type="data" label="SNP dataset"/>
    <conditional name="override_metadata">
      <param name="choice" type="select" format="integer" label="Choose columns" help="Datasets in gd_snp format have the columns in the metadata, all others need the columns chosen." >
        <option value="0" selected="true">No, get columns from metadata</option>
        <option value="1" >Yes, choose columns</option>
      </param>
      <when value="0" />
      <when value="1">
        <param name="scaf_col" type="data_column" data_ref="input" numerical="false" label="Column with scaffold"/>
        <param name="pos_col" type="data_column" data_ref="input" numerical="true" label="Column with position"/>
        <param name="species" type="select" label="Choose species">
          <options from_file="gd.species.txt">
            <column name="name" index="1"/>
            <column name="value" index="0"/>
          </options>
        </param>
      </when>
    </conditional>

    <param name="enzymes" type="select" display="checkboxes" multiple="true" label="Choose enzymes">
        <options from_file="gd.restriction_enzymes.txt">
            <column name="name" index="0"/>
            <column name="value" index="1"/>
        </options>
    </param>
  </inputs>

  <outputs>
    <data format="gd_snp" name="output" metadata_source="input"/>
  </outputs>

  <tests>
    <test>
      <param name="input" value="test_out/select_snps/select_snps.gd_snp" ftype="gd_snp" />
      <param name="choice" value="0" />
      <param name="enzymes" value="Bsp1286I,HaeII,RsaI" />
      <output name="output" file="test_out/specify_restriction_enzymes/specify_restriction_enzymes.gd_snp" />
    </test>
  </tests>

  <help>

**Dataset formats**

The input and output datasets are in tabular_ format.
The input dataset must contain columns for scaffold or chromosome and position.
(`Dataset missing?`_)

.. _tabular: ./static/formatHelp.html#tab
.. _Dataset missing?: ./static/formatHelp.html

-----

**What it does**

It selects the SNPs that are differentially cut by at least one of the
specified restriction enzymes. The enzymes are required to cut the amplified
segment (for the specified PCR primers) only at the SNP.

-----

**Example**

- input (gd_snp format)::

    chr2_75111355_75112576    314  A  C  L  F  chr2   75111676  C  F  15  4  53   2   9  48   Y  96   0.369  0.355  0.396  0
    chr8_93901796_93905612   2471  A  C  A  A  chr8   93904264  A  A  8   0  51   10  2  14   Y  961  0.016  0.534  0.114  2
    chr10_7434473_7435447    524   T  C  S  S  chr10  7435005   T  S  11  5  90   14  0  69   Y  626  0.066  0.406  0.727  0
    chr14_80021455_80022064  138   G  A  H  H  chr14  80021593  G  H  14  0  69   9   6  124  Y  377  0.118  0.997  0.195  1
    chr15_64470252_64471048  89    G  A  Y  Y  chr15  64470341  G  Y  5   6  109  14  0  69   Y  312  0.247  0.998  0.393  0
    chr18_48070585_48071386  514   C  T  E  K  chr18  48071100  T  K  7   7  46   14  0  69   Y  2    0.200  0.032  0.163  0
    chr18_50154905_50155664  304   A  G  Y  C  chr18  50155208  A  Y  4   2  17   5   1  22   Y  8    0.022  0.996  0.128  0
    chr18_57379354_57380496  315   C  T  V  V  chr18  57379669  G  V  11  0  60   9   6  62   Y  726  0.118  0.048  0.014  1
    chr19_14240610_14242055  232   C  T  A  V  chr19  14240840  C  A  18  8  56   15  5  42   Y  73   0.003  0.153  0.835  0
    chr19_39866997_39874915  3117  C  T  P  P  chr19  39870110  C  P  3   7  65   14  2  32   Y  6    0.321  0.911  0.462  4
    etc.

- output::

    chr8_93901796_93905612   2471  A  C  A  A  chr8   93904264  A  A  8   0  51   10  2  14   Y  961  0.016  0.534  0.114  2
    chr14_80021455_80022064  138   G  A  H  H  chr14  80021593  G  H  14  0  69   9   6  124  Y  377  0.118  0.997  0.195  1
    chr18_57379354_57380496  315   C  T  V  V  chr18  57379669  G  V  11  0  60   9   6  62   Y  726  0.118  0.048  0.014  1
    chr19_39866997_39874915  3117  C  T  P  P  chr19  39870110  C  P  3   7  65   14  2  32   Y  6    0.321  0.911  0.462  4
    etc.

  </help>
</tool>