Mercurial > repos > bgruening > hicexplorer_hicsummatrices

comparison hicSumMatrices.xml @ 5:b9f41afc3312 draft

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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
author bgruening
date Sat, 30 Dec 2017 09:36:36 -0500
parents d387dacb6867
children e0df60f3b0d5
comparison
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4:d387dacb6867 5:b9f41afc3312
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements" /> 7 <expand macro="requirements" />
8 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
9 9
10 #for $counter, $m in enumerate($matrices): 10 #for $counter, $m in enumerate($matrix_h5_cooler_multiple):
11 ln -s '$m' ${counter}.npz.h5 && 11 ln -s '$m' ${counter}_matrix &&
12 #end for 12 #end for
13 #set $m = '" "'.join([ '%s_matrix' % $counter for $counter, $matrix in enumerate($matrix_h5_cooler_multiple) ])
13 14
14 #set $m = '" "'.join([ '%s.npz.h5' % $counter for $counter, $matrix in enumerate($matrices) ])
15 hicSumMatrices 15 hicSumMatrices
16 --matrices "$m" 16 --matrices "$m"
17 --outFileName ./out.npz.h5 17 #if $outputFormat == 'h5'
18 --outFileName matrix.h5
19 #elif $outputFormat == 'cool'
20 --outFileName matrix.cool
21 #end if
18 ]]> 22 ]]>
19 </command> 23 </command>
20 <inputs> 24 <inputs>
21 <param argument="--matrices" type="data" format="h5" multiple="True" 25 <expand macro='matrix_h5_cooler_multiple_macro'/>
22 label="Matrices to combine" help="Needs to have the same shape"/> 26
27 <param name='outputFormat' type='select' label="Output file format">
28 <option value='h5'>HiCExplorer format</option>
29 <option value="cool">cool</option>
30 </param>
23 </inputs> 31 </inputs>
24 <outputs> 32 <outputs>
25 <data name="outFileName" from_work_dir="out.npz.h5" format="h5"/> 33 <data name="outFileName_h5" from_work_dir="matrix.h5" format="h5">
34 <filter>outputFormat == 'h5'</filter>
35 </data>
36 <data name="outFileName_cool" from_work_dir="matrix.cool" format="cool">
37 <filter>outputFormat == 'cool'</filter>
38 </data>
26 </outputs> 39 </outputs>
27 <tests> 40 <tests>
28 <test> 41 <test>
29 <param name="matrices" value="hicCorrectMatrix_result1.npz.h5,hicCorrectMatrix_result1.npz.h5"/> 42 <param name="matrix_h5_cooler_multiple" value="hicCorrectMatrix_result1.npz.h5,hicCorrectMatrix_result1.npz.h5"/>
30 <output name="outFileName" file="hicSumMatrices_result1.npz.h5" ftype="h5" compare="sim_size" delta="70000"/> 43 <!-- <param name="matrices" value="hicCorrectMatrix_result1.npz.h5,hicCorrectMatrix_result1.npz.h5"/> -->
44 <param name='outputFormat' value='h5'/>
45 <output name="outFileName_h5" file="hicSumMatrices_result1.npz.h5" ftype="h5" compare="sim_size" delta="70000"/>
31 </test> 46 </test>
32 </tests> 47 </tests>
33 <help><![CDATA[ 48 <help><![CDATA[
34 Summation of matrices 49 Summation of matrices
35 ===================== 50 =====================
36 51
37 ``hicSumMatrix`` is combining two (or more) contact matrices of the same size to one. 52 ``hicSumMatrix`` is combining two (or more) contact matrices of the same size to one.
38 This is useful if replicates of an Hi-C experiment should be merged into one contact matrix to 53 This is useful if replicates of an Hi-C experiment should be merged into one contact matrix to
39 increase the power of the data. It is the nature of Hi-C that real contact cannot be distinguished 54 increase the power of the data. It is the nature of Hi-C that real contact cannot be distinguished
40 from noise, especially with a low contact count. The more contacts are given, the more likely it is 55 from noise, especially with a low contact count. The more contacts are given, the more likely it is
41 that a high number of contacts are real contact or contain at least a high amount. Therefore it is 56 that a high number of contacts are real contact or contain at least a high amount. Therefore it is
42 a common way to merge replicates of Hi-C experiments to increase the validity of the experiment. 57 a common way to merge replicates of Hi-C experiments to increase the validity of the experiment.
43 58
44 Input 59 Input
45 ----- 60 -----
46 61
47 Parameters 62 Parameters