comparison hicCorrelate.xml @ 18:340aa8042c7f draft default tip

"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
comparison
equal deleted inserted replaced
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>