Mercurial > repos > bgruening > hicexplorer_hicsummatrices
comparison hicSumMatrices.xml @ 5:b9f41afc3312 draft
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 |
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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 |