diff README.rst @ 0:b67ea47730d3 draft

Version 1.0.1.

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+motif_tools
+===========
+
+Galaxy tools for various motif-finding utilities developed by Ian Donaldson.
+
+There are five tools available:
+
+ * **IUPAC scan and output each match** Returns all matches to a given IUPAC in
+   GFF format
+
+ * **IUPAC scan and output matches per seq** Counts the matches to a given IUPAC
+
+ * **Count unique seq in GFF** Gives the non-redundant count of sequences
+
+ * **TFBScluster two TFBS** Identifies clusters of two TFBS
+
+ * **TFBScluster three TFBS** Identifies clusters of three TFBS
+
+Automated installation
+======================
+
+Installation via the Galaxy Tool Shed will take of installing the tools
+and the underlying dependencies.
+
+Manual Installation
+===================
+
+To add these to Galaxy put the following lines in tool_conf.xml for each:
+tool that you want::
+
+    <tool file="motif_tools/Scan_IUPAC_output_each_match.xml" />
+    <tool file="motif_tools/Scan_IUPAC_output_matches_per_seq.xml" />
+    <tool file="motif_tools/CountUniqueIDs.xml" />
+    <tool file="motif_tools/TFBScluster_candidates_2TFBS.xml" />
+    <tool file="motif_tools/TFBScluster_candidates_3TFBS.xml" />
+
+The tools also require Perl and ``Bioperl`` to be installed.
+
+History
+=======
+
+========== =====================================================================
+=
+Version    Changes
+---------- ----------------------------------------------------------------------
+- 1.0.1    Updates to use conda dependency resolution and tidy up XML
+- 1.0.0    Initial version
+========== =====================================================================
+=
+
+Developers
+==========
+
+This tool is developed on the following GitHub repository:
+https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/tools/macs21
+
+
+Licence (MIT)
+=============
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.