Mercurial > repos > bgruening > hicexplorer_hiccorrelate
comparison hicCorrelate.xml @ 18:340aa8042c7f draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
| author | iuc |
|---|---|
| date | Tue, 16 Mar 2021 15:03:46 +0000 |
| parents | e89d515c3594 |
| children | bab2fa7355d9 |
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| 17:1099d84fcc21 | 18:340aa8042c7f |
|---|---|
| 1 <tool id="hicexplorer_hiccorrelate" name="@BINARY@" version="@WRAPPER_VERSION@.0"> | 1 <tool id="hicexplorer_hiccorrelate" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> |
| 2 <description>compute pairwise correlations between multiple Hi-C contact matrices</description> | 2 <description>compute pairwise correlations between multiple Hi-C contact matrices</description> |
| 3 <macros> | 3 <macros> |
| 4 <token name="@BINARY@">hicCorrelate</token> | 4 <token name="@BINARY@">hicCorrelate</token> |
| 5 <import>macros.xml</import> | 5 <import>macros.xml</import> |
| 6 </macros> | 6 </macros> |
| 33 ]]> | 33 ]]> |
| 34 </command> | 34 </command> |
| 35 <inputs> | 35 <inputs> |
| 36 <expand macro="multiple_input_matrices" /> | 36 <expand macro="multiple_input_matrices" /> |
| 37 | 37 |
| 38 <param name="method" type="select" label="Correlation method to use" argument="--method" > | 38 <param argument="--method" type="select" label="Correlation method to use"> |
| 39 <option value="spearman">Spearman</option> | 39 <option value="spearman">Spearman</option> |
| 40 <option selected="true" value="pearson">Pearson</option> | 40 <option selected="true" value="pearson">Pearson</option> |
| 41 </param> | 41 </param> |
| 42 <param name="log1p" type="boolean" argument="--log1p" truevalue="--log1p" falsevalue="" | 42 <param argument="--log1p" type="boolean" truevalue="--log1p" falsevalue="" label="Use the log1p of the matrix values" help="If set, then the log1p of the matrix values is used. |
| 43 label="Use the log1p of the matrix values" help="If set, then the log1p of the matrix values is used. | |
| 44 This parameter has no effect for Spearman correlations | 43 This parameter has no effect for Spearman correlations |
| 45 but changes the output of Pearson correlation and, for | 44 but changes the output of Pearson correlation and, for |
| 46 the scatter plot, if set, the visualization of the | 45 the scatter plot, if set, the visualization of the |
| 47 values is easier." /> | 46 values is easier." /> |
| 48 | 47 |
| 53 <validator type="empty_field" /> | 52 <validator type="empty_field" /> |
| 54 </param> | 53 </param> |
| 55 </repeat> | 54 </repeat> |
| 56 <expand macro="colormap" /> | 55 <expand macro="colormap" /> |
| 57 </inputs> | 56 </inputs> |
| 58 <outputs> <!-- not sure if argument is specifiable for output yet, would be cool if so --> | 57 <outputs> <!-- not sure if argument is specifiable for output yet, would be cool if so --> |
| 59 <data name="outFileNameHeatmap" from_work_dir="heatmap.png" format="png" /> | 58 <data name="outFileNameHeatmap" from_work_dir="heatmap.png" format="png" /> |
| 60 <data name="outFileNameScatter" from_work_dir="scatter.png" format="png" /> | 59 <data name="outFileNameScatter" from_work_dir="scatter.png" format="png" /> |
| 61 </outputs> | 60 </outputs> |
| 62 <tests> | 61 <tests> |
| 63 <test> | 62 <test> |
| 64 <repeat name="input_files"> | 63 <repeat name="input_files"> |
| 65 <param name="matrix" value="small_test_matrix.h5" ftype="h5"/> | 64 <param name="matrix" value="small_test_matrix.h5" ftype="h5" /> |
| 66 <param name="mlabel" value="first"/> | 65 <param name="mlabel" value="first" /> |
| 67 </repeat> | 66 </repeat> |
| 68 <repeat name="input_files"> | 67 <repeat name="input_files"> |
| 69 <param name="matrix" value="small_test_matrix.h5" ftype="h5" /> | 68 <param name="matrix" value="small_test_matrix.h5" ftype="h5" /> |
| 70 <param name="mlabel" value="second"/> | 69 <param name="mlabel" value="second" /> |
| 71 </repeat> | 70 </repeat> |
| 72 <param name="log1p" value="True"/> | 71 <param name="log1p" value="True" /> |
| 73 <param name="colormap" value="jet"/> | 72 <param name="colormap" value="jet" /> |
| 74 <param name="method" value="spearman"/> | 73 <param name="method" value="spearman" /> |
| 75 <output name="outFileNameHeatmap" file="hicCorrelate_heatmap_result1.png" ftype="png" compare="sim_size"/> | 74 <output name="outFileNameHeatmap" file="hicCorrelate_heatmap_result1.png" ftype="png" compare="sim_size" /> |
| 76 <output name="outFileNameScatter" file="hicCorrelate_scatter_result1.png" ftype="png" compare="sim_size"/> | 75 <output name="outFileNameScatter" file="hicCorrelate_scatter_result1.png" ftype="png" compare="sim_size" /> |
| 77 </test> | 76 </test> |
| 78 <test> | 77 <test> |
| 79 <repeat name="input_files"> | 78 <repeat name="input_files"> |
| 80 <param name="matrix" value="small_test_matrix.h5" ftype="h5"/> | 79 <param name="matrix" value="small_test_matrix.h5" ftype="h5" /> |
| 81 <param name="mlabel" value="first"/> | 80 <param name="mlabel" value="first" /> |
| 82 </repeat> | 81 </repeat> |
| 83 <repeat name="input_files"> | 82 <repeat name="input_files"> |
| 84 <param name="matrix" value="small_test_matrix.h5" ftype="h5" /> | 83 <param name="matrix" value="small_test_matrix.h5" ftype="h5" /> |
| 85 <param name="mlabel" value="second"/> | 84 <param name="mlabel" value="second" /> |
| 86 </repeat> | 85 </repeat> |
| 87 | 86 |
| 88 <param name="log1p" value="True"/> | 87 <param name="log1p" value="True" /> |
| 89 <param name="colormap" value="jet"/> | 88 <param name="colormap" value="jet" /> |
| 90 <param name="method" value="spearman"/> | 89 <param name="method" value="spearman" /> |
| 91 <output name="outFileNameHeatmap" file="hicCorrelate_heatmap_result1.png" ftype="png" compare="sim_size"/> | 90 <output name="outFileNameHeatmap" file="hicCorrelate_heatmap_result1.png" ftype="png" compare="sim_size" /> |
| 92 <output name="outFileNameScatter" file="hicCorrelate_scatter_result1.png" ftype="png" compare="sim_size"/> | 91 <output name="outFileNameScatter" file="hicCorrelate_scatter_result1.png" ftype="png" compare="sim_size" /> |
| 93 </test> | 92 </test> |
| 94 </tests> | 93 </tests> |
| 95 <help><![CDATA[ | 94 <help><![CDATA[ |
| 96 | 95 |
| 97 Matrix correlation | 96 Matrix correlation |
| 138 For more information about HiCExplorer please consider our documentation on readthedocs.io_. | 137 For more information about HiCExplorer please consider our documentation on readthedocs.io_. |
| 139 | 138 |
| 140 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html | 139 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html |
| 141 .. _Colormap: https://matplotlib.org/examples/color/colormaps_reference.html | 140 .. _Colormap: https://matplotlib.org/examples/color/colormaps_reference.html |
| 142 | 141 |
| 143 ]]></help> | 142 ]]> </help> |
| 144 <expand macro="citations" /> | 143 <expand macro="citations" /> |
| 145 </tool> | 144 </tool> |