comparison dpmix.xml @ 27:8997f2ca8c7a

Update to Miller Lab devshed revision bae0d3306d3b

26:91e835060ad2

<tool id="gd_dpmix" name="Admixture" version="1.1.0">
  <description>: Map genomic intervals resembling specified ancestral populations</description>

  <command interpreter="python">
    dpmix.py "$input"
    #if $input_type.choice == '0'
      "gd_snp" "$input_type.data_source"
    #else if $input_type.choice == '1'
      "gd_genotype" "1"
    #end if
    "$switch_penalty" "$ap1_input" "$ap2_input" "$p_input" "$output" "$output2" "$output2.files_path" "$input.dataset.metadata.dbkey" "$input.dataset.metadata.ref" "$GALAXY_DATA_INDEX_DIR" "gd.heterochromatic.loc"
    #for $individual, $individual_col in zip($input.dataset.metadata.individual_names, $input.dataset.metadata.individual_columns)
      #set $arg = '%s:%s' % ($individual_col, $individual)
      "$arg"
    #end for
  </command>

  <inputs>
    <conditional name="input_type">
      <param name="choice" type="select" format="integer" label="Input format">

          <validator type="unspecified_build" message="This dataset does not have a reference species and cannot be used with this tool" />
        </param>
      </when>
    </conditional>

    <param name="ap1_input" type="data" format="gd_indivs" label="Ancestral population 1 individuals" />
    <param name="ap2_input" type="data" format="gd_indivs" label="Ancestral population 2 individuals" />
    <param name="p_input" type="data" format="gd_indivs" label="Potentially admixed individuals" />

    <param name="switch_penalty" type="float" min="0" value="10" label="Genotype switch penalty" help="Note: Depends on the density of SNPs.  For instance, with 50,000 SNPs in a vertebrate genome, 1.0 might be appropriate, with millions of SNPs, a value between 10 and 100 might be reasonable."/>
  </inputs>

  <outputs>
    <data name="output" format="tabular" />
    <data name="output2" format="html" />

-----

**What it does**

The user specifies two "ancestral" populations (i.e., sources for
chromosomes) and a set of potentially admixed individuals, and chooses
between the sequence coverage or the estimated genotypes to measure
the similarity of genomic intervals in admixed individuals to the two
classes of ancestral chromosomes.  The user also picks a "genotype switch penalty",
typically between 10 and 100.  For each potentially admixed individual,
the program divides the genome into three "genotypes": (0) homozygous
for the first ancestral population (i.e., both chromosomes from that
population), (1) heterozygous, or (2) homozygous for the second ancestral
population.  Parts of a chromosome that are labeled as "heterochromatic"
are given the non-genotype "3".  Smaller values of the switch penalty
(corresponding to more ancient admixture events) generally lead to the
reconstruction of more frequent changes between genotypes.

There are two output datasets generated.  A tabular dataset with chromosome,
start, stop, and pairs of columns containing the "genotypes" from above
and label from the admixed individual.  The second dataset is a composite
dataset with general information from the run and a link to a pdf which
graphically shows the ancestral population along each of the chromosomes.
The second link is to a text file with summary information of the 
"genotypes" over the whole genome.

  </help>
</tool>

27:8997f2ca8c7a

<tool id="gd_dpmix" name="Admixture" version="1.1.0">
  <description>: Map genomic intervals resembling specified source populations</description>

  <command interpreter="python">
    #import json
    #import base64
    #import zlib
    #set $ind_names = $input.dataset.metadata.individual_names
    #set $ind_colms = $input.dataset.metadata.individual_columns
    #set $ind_dict = dict(zip($ind_names, $ind_colms))
    #set $ind_json = json.dumps($ind_dict, separators=(',',':'))
    #set $ind_comp = zlib.compress($ind_json, 9)
    #set $ind_arg = base64.b64encode($ind_comp)
    dpmix.py '$input'
    #if $input_type.choice == '0'
      'gd_snp' '$input_type.data_source'
    #else if $input_type.choice == '1'
      'gd_genotype' '1'
    #end if
    #if $third_pop.choice == '0'
      #set $ap3_arg = '/dev/null'
      #set $ap3_name_arg = ''
    #else if $third_pop.choice == '1'
      #set $ap3_arg = $third_pop.ap3_input
      #set $ap3_name_arg = $third_pop.ap3_input.name
    #end if
    #if $user_het.choice == '0'
      #set $het_arg = 'use_installed'
    #else if $user_het.choice == '1'
      #set $het_arg = $user_het.het_file
    #else if $user_het.choice == '2'
      #set $het_arg = 'use_none'
    #end if
    '$switch_penalty' '$ap1_input' '$ap1_input.name' '$ap2_input' '$ap2_input.name' '$ap3_arg' '$ap3_name_arg' '$p_input' '$output' '$output2' '$output2.files_path' '$input.dataset.metadata.dbkey' '$input.dataset.metadata.ref' '$GALAXY_DATA_INDEX_DIR' 'gd.heterochromatic.loc' '$ind_arg' '$het_arg' '1'
  </command>

  <inputs>
    <conditional name="input_type">
      <param name="choice" type="select" format="integer" label="Input format">

          <validator type="unspecified_build" message="This dataset does not have a reference species and cannot be used with this tool" />
        </param>
      </when>
    </conditional>

    <param name="ap1_input" type="data" format="gd_indivs" label="Source population 1 individuals" />
    <param name="ap2_input" type="data" format="gd_indivs" label="Source population 2 individuals" />

    <conditional name="third_pop">
      <param name="choice" type="select" format="integer" label="Include third source population">
        <option value="0" selected="true">no</option>
        <option value="1">yes</option>
      </param>
      <when value="0" />
      <when value="1">
        <param name="ap3_input" type="data" format="gd_indivs" label="Source population 3 individuals" />
      </when>
    </conditional>

    <param name="p_input" type="data" format="gd_indivs" label="Potentially admixed individuals" />

    <param name="switch_penalty" type="float" min="0" value="10" label="Genotype switch penalty" help="Note: Depends on the density of SNPs.  For instance, with 50,000 SNPs in a vertebrate genome, 1.0 might be appropriate, with millions of SNPs, a value between 10 and 100 might be reasonable."/>

    <conditional name="user_het">
      <param name="choice" type="select" format="integer" label="Heterochromatin info">
        <option value="0" selected="true">use installed</option>
        <option value="1">use your own</option>
        <option value="2">use none</option>
      </param>
      <when value="0" />
      <when value="1">
        <param name="het_file" type="data" format="txt" label="Heterochromatin dataset" />
      </when>
    </conditional>

    <!--
    <param name="add_logs" type="select" format="integer" label="Probabilities">
      <option value="1" selected="true">add logs of probabilities</option>
      <option value="0">add probabilities</option>
    </param>
    -->

  </inputs>

  <outputs>
    <data name="output" format="tabular" />
    <data name="output2" format="html" />

-----

**What it does**

The user specifies two or three source populations (i.e., sources
for chromosomes) and a set of potentially admixed individuals, and
chooses between the sequence coverage or the estimated genotypes to
measure the similarity of genomic intervals in admixed individuals to
the three classes of source chromosomes.  The user also specifies a
"switch penalty", controlling the strength of evidence needed to switch
between source populations as the the program scans along a chromosome.
Choice of picksan appropriate value depends on the number of SNPs and, to
a lesser extent, on the time since the admixture events.  With several
million SNPs genome-wide, reasonable values might fall between 10
and 100.  If there are 3 source populatons, then for each potentially
admixed individual the program divides the genome into six "genotypes":

1. homozygous for the first source population (i.e., both chromosomes from that population),
2. homozygous for the second source population,
3. homozygous for the third source population,
4. heterozygous for the first and second populations (i.e., one chromosome from each),
5. heterozygous for the first and third populations, or
6. heterozygous for the second and third populations.

Parts of a reference chromosome that are labeled as "heterochromatic"
are given the "non-genotype" 0.  With two source populations, only
"genotypes" 1, 2 and 3 are possible, where 3 now means heterozygous in
the two source populations.

There are two output datasets generated.  A tabular dataset with chromosome,
start, stop, and pairs of columns containing the "genotypes" from above
and label from the admixed individual.  The second dataset is a composite
dataset with general information from the run and a link to a pdf which
graphically shows the source population along each of the chromosomes.
The second link is to a text file with summary information of the 
"genotypes" over the whole genome.
  </help>
</tool>