Mercurial > repos > bgruening > hicexplorer_hiccorrelate

comparison hicCorrelate.xml @ 4:c153ea23aca8 draft

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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
author iuc
date Sat, 16 Dec 2017 16:34:28 -0500
parents ae2d7e2dfeef
children c1f9dc3b2238
comparison
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3:f7e53fd4a0be 4:c153ea23aca8
98 <output name="outFileNameScatter" file="hicCorrelate_scatter_result1.png" ftype="png" compare="sim_size"/> 98 <output name="outFileNameScatter" file="hicCorrelate_scatter_result1.png" ftype="png" compare="sim_size"/>
99 </test> 99 </test>
100 </tests> 100 </tests>
101 <help><![CDATA[ 101 <help><![CDATA[
102 102
103 **What it does** 103 Matrix correlation
104 ==================
104 105
105 Computes pairwise correlations between Hi-C matrices data. 106 Computes pairwise correlations between Hi-C contact matrices.
106 The correlation is computed taking the values from each pair of matrices and discarding values that are zero in both matrices. 107 The correlation is computed taking the values from each pair of matrices and discarding values that are zero in both matrices.
107 108
109 Input
110 -----
111
112 Parameters
113 __________
114 - Two contact matrices which are used for the correlation.
115 - Choice if pearson or spearman correlation should be used.
116 - log scale for the values
117 - Correlate full matrix or only specific chromosomes
118 - Correlate only within a given range.
119 - colormap to use: Colormap_
120
121 Output
122 ------
123
124 Pearson correlation
125 ___________________
126
127 |pearson| |pearson_scatter|
128
129 .. |pearson| image:: $PATH_TO_IMAGES/hicCorrelate_pearson.png
130 :width: 45%
131
132 .. |pearson_scatter| image:: $PATH_TO_IMAGES/hicCorrelate_pearson_scatter.png
133 :width: 45%
134
135 Scatter plot
136
137 Spearman correlation
138 _____________________
139
140 |spearman| |spearman_scatter|
141
142 .. |spearman| image:: $PATH_TO_IMAGES/hicCorrelate_spearman.png
143 :width: 45 %
144
145 .. |spearman_scatter| image:: $PATH_TO_IMAGES/hicCorrelate_spearman_scatter.png
146 :width: 45 %
147
148 For more information about HiCExplorer please consider our documentation on readthedocs.io_.
149
150 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
151 .. _Colormap: https://matplotlib.org/examples/color/colormaps_reference.html
108 152
109 ]]></help> 153 ]]></help>
110 <expand macro="citations" /> 154 <expand macro="citations" />
111 </tool> 155 </tool>