Mercurial > repos > bgruening > hicexplorer_hicplotdistvscounts
comparison hicPlotDistVsCounts.xml @ 4:ed96f2fd7e3f draft
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
author | iuc |
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date | Sat, 16 Dec 2017 16:31:27 -0500 |
parents | 9b664f43a90e |
children | 819bd2c44d4a |
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74 </repeat> | 74 </repeat> |
75 <output name="plotFile" file="hicPlotDistVsCounts_result2.png" ftype="png" compare="sim_size" delta="40000"/> | 75 <output name="plotFile" file="hicPlotDistVsCounts_result2.png" ftype="png" compare="sim_size" delta="40000"/> |
76 </test> | 76 </test> |
77 </tests> | 77 </tests> |
78 <help><![CDATA[ | 78 <help><![CDATA[ |
79 Relation of genomic distance and number of contacts | |
80 ======================================================== | |
79 | 81 |
80 **What it does** | 82 | This program makes a distance vs. Hi-C counts plots. It can use several matrix files to compare |
81 | 83 | them. If the ``--perchr`` option is given, each chromosome is plotted independently. In the case |
82 This program makes a distance vs. Hi-C counts plots. It can use several matrix files to compare | 84 | of more than one matrix, multiple plots are created, one per chromosome. When plotting multiple |
83 them. If the `--perchr` option is given, each chromosome is plotted independently. In the case | 85 | matrices denser matrices are scaled down to match the sum of the smaller matrix. |
84 of more than one matrix, multiple plots are created, one per chromosome. When plotting multiple | 86 | |
85 matrices denser matrices are scaled down to match the sum of the smaller matrix. | 87 | For more information about HiCExplorer please consider our documentation on readthedocs.io_ |
86 | 88 |
87 | 89 |
90 Input | |
91 ----- | |
92 | |
93 Parameters | |
94 __________ | |
95 - contact matrix | |
96 - skip diagonal | |
97 - per chromosome | |
98 - max depth | |
99 - plot size | |
100 - chromosome(s) to exclude | |
101 | |
102 Output | |
103 ------- | |
104 Output if all data in the contact matrix is considered: | |
105 | |
106 .. image:: $PATH_TO_IMAGES/hicPlotDistVsCounts_result1.png | |
107 :width: 70% | |
108 | |
109 Output if the distance vs. Hi-C contact counts is computed and plotted per chromosome: | |
110 | |
111 .. image:: $PATH_TO_IMAGES/hicPlotDistVsCounts_result2.png | |
112 :width: 80% | |
113 | |
114 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html | |
88 ]]></help> | 115 ]]></help> |
89 <expand macro="citations" /> | 116 <expand macro="citations" /> |
90 </tool> | 117 </tool> |
91 | 118 |