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
author lldelisle
date Mon, 24 Oct 2022 15:20:46 +0000
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
lldelisle
parents:
diff changeset
1 <tool id="cooler_balance" name="cooler_balance" version="@VERSION@+galaxy0" profile="18.01">
8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
lldelisle
parents:
diff changeset
2 <description>Copy and balance a cool file.</description>
8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
lldelisle
parents:
diff changeset
3 <macros>
8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
lldelisle
parents:
diff changeset
4 <import>macros.xml</import>
8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
lldelisle
parents:
diff changeset
5 </macros>
8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
lldelisle
parents:
diff changeset
6 <expand macro="requirements" />
8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
lldelisle
parents:
diff changeset
7 <expand macro="stdio" />
8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
lldelisle
parents:
diff changeset
8 <command detect_errors="exit_code"><![CDATA[
8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
lldelisle
parents:
diff changeset
9 cp '$input' '$output' &&
8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
lldelisle
parents:
diff changeset
10 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
8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
lldelisle
parents:
diff changeset
11 #if $blacklist:
8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
lldelisle
parents:
diff changeset
12 --blacklist '$blacklist'
8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
lldelisle
parents:
diff changeset
13 #end if
8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
lldelisle
parents:
diff changeset
14 '$output'
8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
lldelisle
parents:
diff changeset
15 ]]>
8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
lldelisle
parents:
diff changeset
16 </command>
8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
lldelisle
parents:
diff changeset
17 <inputs>
8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
lldelisle
parents:
diff changeset
18 <param name="input" multiple="false" type="data" format="cool" label="Select the input cool file to balance."/>
8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
lldelisle
parents:
diff changeset
19 <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."/>
8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
lldelisle
parents:
diff changeset
20 <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."/>
8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
lldelisle
parents:
diff changeset
21 <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."/>
8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
lldelisle
parents:
diff changeset
22 <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."/>
8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
lldelisle
parents:
diff changeset
23 <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."/>
8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
lldelisle
parents:
diff changeset
24 <param argument="--tol" type="float" value="1e-5" label="Threshold value of variance of the marginals for the algorithm to converge."/>
8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
lldelisle
parents:
diff changeset
25 <param argument="--max-iters" name="maxiters" type="integer" value="200" label="Maximum number of iterations to perform if convergence is not achieved.."/>
8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
lldelisle
parents:
diff changeset
26 <param name="cistrans" type="select" label="Interactions to consider to calculate weights.">
8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
lldelisle
parents:
diff changeset
27 <option value="">Genome wide </option>
8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
lldelisle
parents:
diff changeset
28 <option value="--cis-only">Cis only </option>
8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
lldelisle
parents:
diff changeset
29 <option value="--trans-only">Trans only </option>
8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
lldelisle
parents:
diff changeset
30 </param>
8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
lldelisle
parents:
diff changeset
31 <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."/>
8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
lldelisle
parents:
diff changeset
32 <param argument="--name" type="text" value="weight" label="Name of column to write to." />
8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
lldelisle
parents:
diff changeset
33 <param name="convergencepolicy" type="select" label="Convergence policy: What to do with weights when balancing doesn't converge in max_iters."
8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
lldelisle
parents:
diff changeset
34 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.">
8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
lldelisle
parents:
diff changeset
35 <option value="store_final">store_final</option>
8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
lldelisle
parents:
diff changeset
36 <option value="store_nan">store_nan</option>
8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
lldelisle
parents:
diff changeset
37 <option value="discard">discard</option>
8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
lldelisle
parents:
diff changeset
38 <option value="error">error</option>
8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
lldelisle
parents:
diff changeset
39 </param>
8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
lldelisle
parents:
diff changeset
40 </inputs>
8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
lldelisle
parents:
diff changeset
41
8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
lldelisle
parents:
diff changeset
42 <outputs>
8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
lldelisle
parents:
diff changeset
43 <data format="cool" name="output" label="balanced of $input.name"/>
8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
lldelisle
parents:
diff changeset
44 </outputs>
8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
lldelisle
parents:
diff changeset
45
8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
lldelisle
parents:
diff changeset
46 <tests>
8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
lldelisle
parents:
diff changeset
47 <test>
8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
lldelisle
parents:
diff changeset
48 <param name="input" value="input.cool" ftype="cool"/>
8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
lldelisle
parents:
diff changeset
49 <param name="madmax" value="5"/>
8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
lldelisle
parents:
diff changeset
50 <param name="mincount" value="0"/>
8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
lldelisle
parents:
diff changeset
51 <param name="ignorediags" value="2"/>
8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
lldelisle
parents:
diff changeset
52 <param name="tol" value="1e-5"/>
8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
lldelisle
parents:
diff changeset
53 <param name="maxiters" value="1000"/>
8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
lldelisle
parents:
diff changeset
54 <param name="cistrans" value="--cis-only"/>
8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
lldelisle
parents:
diff changeset
55 <output name="output" file="output.cool" compare="sim_size"/>
8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
lldelisle
parents:
diff changeset
56 </test>
8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
lldelisle
parents:
diff changeset
57 </tests>
8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
lldelisle
parents:
diff changeset
58
8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
lldelisle
parents:
diff changeset
59 <help>
8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
lldelisle
parents:
diff changeset
60 **cooler balance**
8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
lldelisle
parents:
diff changeset
61 tool developped by mirnylab
8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
lldelisle
parents:
diff changeset
62 see https://github.com/mirnylab/cooler
8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
lldelisle
parents:
diff changeset
63 and https://cooler.readthedocs.io/en/latest/cli.html#cooler-balance
8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
lldelisle
parents:
diff changeset
64
8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
lldelisle
parents:
diff changeset
65 command-line::
8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
lldelisle
parents:
diff changeset
66
8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
lldelisle
parents:
diff changeset
67 cp $input $output
8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
lldelisle
parents:
diff changeset
68 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
8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
lldelisle
parents:
diff changeset
69 --blacklist 'blacklist'
8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
lldelisle
parents:
diff changeset
70
8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
lldelisle
parents:
diff changeset
71
8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
lldelisle
parents:
diff changeset
72 </help>
8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
lldelisle
parents:
diff changeset
73 <expand macro="citation_cooler" />
8f71aaf6e59d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
lldelisle
parents:
diff changeset
74 </tool>