annotate cooler_balance.xml @ 0:8f71aaf6e59d draft

planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296

<tool id="cooler_balance" name="cooler_balance" version="@VERSION@+galaxy0" profile="18.01">
  <description>Copy and balance a cool file.</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <expand macro="stdio" />
  <command detect_errors="exit_code"><![CDATA[
    cp '$input' '$output' &&
    cooler balance -p \${GALAXY_SLOTS:-1} --mad-max $madmax --min-nnz $minnnz --min-count $mincount --ignore-diags $ignorediags --ignore-dist $ignoredist --tol $tol --max-iters $maxiters $cistrans -f --convergence-policy $convergencepolicy
    #if $blacklist:
      --blacklist '$blacklist'
    #end if
    '$output'
    ]]>
  </command>
  <inputs>
    <param name="input" multiple="false" type="data" format="cool" label="Select the input cool file to balance."/>
    <param argument="--mad-max" name="madmax" type="integer" value="5" label="Ignore bins from the contact matrix using the 'MAD-max' filter: bins whose log marginal sum is less than ``mad-max`` median absolute deviations below the median log marginal sum of all the bins in the same chromosome."/>
    <param argument="--min-nnz" name="minnnz" type="integer" value="10" label="Ignore bins from the contact matrix whose marginal number of nonzeros is less than this number."/>
    <param argument="--min-count" name="mincount" type="integer" value="0" label="Ignore bins from the contact matrix whose marginal count is less than this number."/>
    <param argument="--ignore-diags" name="ignorediags" type="integer" value="2" label="Number of diagonals of the contact matrix to ignore, including the main diagonal. Examples: 0 ignores nothing, 1 ignores the main diagonal, 2 ignores diagonals (-1, 0, 1), etc."/>
    <param argument="--ignore-dist" name="ignoredist" type="integer" value="0" label="Distance in bp to ignore." help="Max between distance and diags will be used."/>
    <param argument="--tol" type="float" value="1e-5" label="Threshold value of variance of the marginals for the algorithm to converge."/>
    <param argument="--max-iters" name="maxiters" type="integer" value="200" label="Maximum number of iterations to perform if convergence is not achieved.."/>
    <param name="cistrans" type="select" label="Interactions to consider to calculate weights.">
        <option value="">Genome wide </option>
        <option value="--cis-only">Cis only </option>
        <option value="--trans-only">Trans only </option>
    </param>
    <param argument="--blacklist" type="data" format="bed" optional="true" label="Path to a 3-column BED file containing genomic regions to mask out during the balancing procedure, e.g. sequence gaps or regions of poor mappability."/>
    <param argument="--name" type="text" value="weight" label="Name of column to write to." />
    <param name="convergencepolicy" type="select" label="Convergence policy: What to do with weights when balancing doesn't converge in max_iters."
           help="'store_final': Store the final result, regardless of whether the iterations converge to the specified tolerance; 'store_nan': Store a vector of NaN values to indicate that the matrix failed to converge; 'discard': Store nothing and exit gracefully; 'error': Abort with non-zero exit status.">
        <option value="store_final">store_final</option>
        <option value="store_nan">store_nan</option>
        <option value="discard">discard</option>
        <option value="error">error</option>
    </param>
  </inputs>
  
  <outputs>
    <data format="cool" name="output" label="balanced of $input.name"/>
  </outputs>
  
  <tests>
    <test>
      <param name="input" value="input.cool" ftype="cool"/>
      <param name="madmax" value="5"/>
      <param name="mincount" value="0"/>
      <param name="ignorediags" value="2"/>
      <param name="tol" value="1e-5"/>
      <param name="maxiters" value="1000"/>
      <param name="cistrans" value="--cis-only"/>
      <output name="output" file="output.cool" compare="sim_size"/>
    </test>
  </tests> 

  <help>
    **cooler balance**
    tool developped by mirnylab
    see https://github.com/mirnylab/cooler
    and https://cooler.readthedocs.io/en/latest/cli.html#cooler-balance
    
    command-line::
    
      cp $input $output
      cooler balance -p \${GALAXY_SLOTS:-1} --mad-max madmax --min-nnz minnnz --min-count mincount --ignore-diags ignorediags --ignore-dist ignoredist --tol tol --max-iters maxiters cistrans -f 
      --blacklist 'blacklist'

    
  </help>
  <expand macro="citation_cooler" />
</tool>