Mercurial > repos > lldelisle > cooler_balance
view cooler_balance.xml @ 2:8f9fe0667b89 draft
planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 060279258b63713bcfa4f67c0a3cee75d32a7266
author | lldelisle |
---|---|
date | Tue, 12 Sep 2023 08:23:56 +0000 |
parents | 8f71aaf6e59d |
children |
line wrap: on
line source
<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>