Mercurial > repos > bgruening > hicexplorer_hiccompartmentspolarization
comparison hicCompartmentalization.xml @ 8:3a6a5381db36 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
| author | iuc |
|---|---|
| date | Wed, 18 Oct 2023 10:51:18 +0000 |
| parents | bd6e26c47853 |
| children |
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| 7:bd6e26c47853 | 8:3a6a5381db36 |
|---|---|
| 22 #set $offset = ' '.join([ '%s' % int($value) for $value in $offset_array ]) | 22 #set $offset = ' '.join([ '%s' % int($value) for $value in $offset_array ]) |
| 23 --offset $offset | 23 --offset $offset |
| 24 #end if | 24 #end if |
| 25 --outliers $outliers | 25 --outliers $outliers |
| 26 --outputFileName plot.$image_file_format | 26 --outputFileName plot.$image_file_format |
| 27 #if $matrix: | |
| 28 --outputMatrix output_matrix.npz | |
| 29 #end if | |
| 27 && mv plot.$image_file_format plot | 30 && mv plot.$image_file_format plot |
| 28 ]]> | 31 ]]> |
| 29 </command> | 32 </command> |
| 30 <inputs> | 33 <inputs> |
| 31 <expand macro="matrix_h5_cooler_multiple_macro" /> | 34 <expand macro="matrix_h5_cooler_multiple_macro" /> |
| 32 <param name='pca' type="data" format="bedgraph" label="Eigenvector file" help='A PCA vector as a bedgraph file with no header. In case of several matrices with | 35 <param name="pca" type="data" format="bedgraph" label="Eigenvector file" help="A PCA vector as a bedgraph file with no header. In case of several matrices with |
| 33 different conditions, ie. control treatment, the PCA of control can be | 36 different conditions, ie. control treatment, the PCA of control can be |
| 34 used. Note that only one PCA can be provided.' /> | 37 used. Note that only one PCA can be provided." /> |
| 35 <param name='quantile' type="integer" value="30" label="Quantile" help='The number of to be used quantiles.' /> | 38 <param name="quantile" type="integer" value="30" label="Quantile" help="The number of to be used quantiles." /> |
| 36 <param name='outliers' type="float" value="0.0" label="Outliers" help='The number of outliers to be removed.' /> | 39 <param name="outliers" type="float" value="0.0" label="Outliers" help="The number of outliers to be removed." /> |
| 37 <param name="set_offset_value" type="text" optional='True' value="" label="Offset values"> | 40 <param name="set_offset_value" type="text" optional="True" value="" label="Offset values"> |
| 38 <validator type="expression" message="Only numeric characters and the a space as seperator are allowed.">value.replace(' ', '').isnumeric()</validator> | 41 <validator type="expression" message="Only numeric characters and the a space as seperator are allowed.">value.replace(' ', '').isnumeric()</validator> |
| 39 </param> | 42 </param> |
| 40 | 43 |
| 41 <param name="image_file_format" type="select" label="Image output format"> | 44 <param name="image_file_format" type="select" label="Image output format"> |
| 42 <option value="png" selected="True">png</option> | 45 <option value="png" selected="True">png</option> |
| 43 <option value="svg">svg</option> | 46 <option value="svg">svg</option> |
| 44 <option value="pdf">pdf</option> | 47 <option value="pdf">pdf</option> |
| 45 </param> | 48 </param> |
| 49 <param name="matrix" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Output matrix?"/> | |
| 46 </inputs> | 50 </inputs> |
| 47 <outputs> | 51 <outputs> |
| 48 <data name="outFileName" format="png" from_work_dir="plot" label="${tool.name} [${on_string}]: Plot"> | 52 <data name="outFileName" format="png" from_work_dir="plot" label="${tool.name} [${on_string}]: Plot"> |
| 49 <change_format> | 53 <change_format> |
| 50 <when input="image_file_format" value="svg" format="svg" /> | 54 <when input="image_file_format" value="svg" format="svg" /> |
| 51 <when input="image_file_format" value="pdf" format="pdf" /> | 55 <when input="image_file_format" value="pdf" format="pdf" /> |
| 52 </change_format> | 56 </change_format> |
| 53 </data> | 57 </data> |
| 54 <data name='output_matrix' from_work_dir='output_matrix.npz' format='binary' label='Output .npz file includes all the generated matrices'> | 58 <data name="output_matrix" from_work_dir="output_matrix.npz" format="npz" label="Output .npz file includes all the generated matrices"> |
| 55 <filter>outputMatrix == '--outputMatrix output_matrix.npz'</filter> | 59 <filter>matrix</filter> |
| 56 </data> | 60 </data> |
| 57 </outputs> | 61 </outputs> |
| 58 <tests> | 62 <tests> |
| 59 <test> | 63 <test expect_num_outputs="1"> |
| 60 <param name="matrix_h5_cooler_multiple" value="hicTransform/obs_exp_norm.h5" /> | 64 <param name="matrix_h5_cooler_multiple" value="hicTransform/obs_exp_norm.h5" /> |
| 61 <param name="pca" value="hicCompartmentsPolarization/pca1.bedgraph" ftype="bedgraph" /> | 65 <param name="pca" value="hicCompartmentsPolarization/pca1.bedgraph" ftype="bedgraph" /> |
| 62 <output name="outFileName" file="hicCompartmentsPolarization/compartmentsPolarizationRatio.png" ftype="png" compare="sim_size" /> | 66 <output name="outFileName" file="hicCompartmentsPolarization/compartmentsPolarizationRatio.png" ftype="png" compare="sim_size" /> |
| 63 </test> | 67 </test> |
| 64 <test> | 68 <test expect_num_outputs="1"> |
| 65 <param name="matrix_h5_cooler_multiple" value="hicTransform/obs_exp_norm.h5" /> | 69 <param name="matrix_h5_cooler_multiple" value="hicTransform/obs_exp_norm.h5" /> |
| 66 <param name="pca" value="hicCompartmentsPolarization/pca1.bedgraph" ftype="bedgraph" /> | 70 <param name="pca" value="hicCompartmentsPolarization/pca1.bedgraph" ftype="bedgraph" /> |
| 67 <param name="quantile" value='30' /> | 71 <param name="quantile" value="30" /> |
| 68 <output name="outFileName" file="hicCompartmentsPolarization/compartmentsPolarizationRatio.png" ftype="png" compare="sim_size" /> | 72 <output name="outFileName" file="hicCompartmentsPolarization/compartmentsPolarizationRatio.png" ftype="png" compare="sim_size" /> |
| 69 </test> | 73 </test> |
| 70 <test> | 74 <test expect_num_outputs="1"> |
| 71 <param name="matrix_h5_cooler_multiple" value="hicTransform/obs_exp_norm.h5" /> | 75 <param name="matrix_h5_cooler_multiple" value="hicTransform/obs_exp_norm.h5" /> |
| 72 <param name="pca" value="hicCompartmentsPolarization/pca1.bedgraph" ftype="bedgraph" /> | 76 <param name="pca" value="hicCompartmentsPolarization/pca1.bedgraph" ftype="bedgraph" /> |
| 73 <param name="outliers" value='1.0' /> | 77 <param name="outliers" value="1.0" /> |
| 74 <output name="outFileName" file="hicCompartmentsPolarization/compartmentsPolarizationRatio.png" ftype="png" compare="sim_size" /> | 78 <output name="outFileName" file="hicCompartmentsPolarization/compartmentsPolarizationRatio.png" ftype="png" compare="sim_size" /> |
| 79 </test> | |
| 80 <test expect_num_outputs="2"> | |
| 81 <param name="matrix_h5_cooler_multiple" value="hicTransform/obs_exp_norm.h5" /> | |
| 82 <param name="pca" value="hicCompartmentsPolarization/pca1.bedgraph" ftype="bedgraph" /> | |
| 83 <param name="matrix" value="True" /> | |
| 84 <output name="outFileName" file="hicCompartmentsPolarization/compartmentsPolarizationRatio.png" ftype="png" compare="sim_size" /> | |
| 85 <output name="output_matrix" file="hicCompartmentsPolarization/output_matrix.npz" ftype="npz" compare="sim_size"/> | |
| 75 </test> | 86 </test> |
| 76 </tests> | 87 </tests> |
| 77 <help><![CDATA[ | 88 <help><![CDATA[ |
| 78 | 89 |
| 79 Comparmentalization | 90 Comparmentalization |