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planemo upload for repository https://github.com/bxlab/galaxy_tools/tools/hifive commit 00f5bb3bc367ca8dfddc094b24463af613eaccc6-dirty
author sauria
date Fri, 01 Dec 2017 12:24:14 -0500
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1 =============================
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2 Galaxy wrapper for HiFive
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3 =============================
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5 This wrapper allows use of the hifive package, a set of tools for handling HiC
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6 and 5C data, on Galaxy. This includes managing data from mapped reads, either
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7 in bam, mat, or raw formats. All stages use hdf5 dictionaries for fast access
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8 and minimal memory and storage usage.
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10 This toolset includes methods for normalizing data from either HiC or 5C
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11 experiments at the fragment-end, or fragment level resolution, respectively.
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12 Once normalized, data can be used for plotting, binning, or other statistical
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13 tests within the package very quickly.
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15 Original documentation can be found `here <http://bxlab-hifive.readthedocs.org/en/latest/>`_.
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17 Automated Installation
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18 ======================
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20 Galaxy should be able to automatically install the dependencies, i.e. the
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21 ``h5py`` and ``hifive`` tool depedency packages.
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23 Manual Installation
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24 ===================
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26 For those not using Galaxy's automated installation from the Tool Shed, put
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27 the XML and Python files in the ``tools/hifive/`` folder and add the
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28 XML files to your ``tool_conf.xml`` as normal. For example, use::
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30 <section name="HiFive" id="hifive_tools">
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31 <tool file="hifive.xml" />
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32 </section>
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35 ================
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36 Wrapper Licence
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37 ================
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39 Permission is hereby granted, free of charge, to any person obtaining a copy
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40 of this software and associated documentation files (the "Software"), to deal
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41 in the Software without restriction, including without limitation the rights
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42 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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43 copies of the Software, and to permit persons to whom the Software is
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44 furnished to do so, subject to the following conditions:
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46 The above copyright notice and this permission notice shall be included in
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47 all copies or substantial portions of the Software.
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49 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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50 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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51 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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52 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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53 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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54 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
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55 THE SOFTWARE.