# HG changeset patch
# User drosofff
# Date 1403625362 14400
# Node ID 2120acb92e0babb963efc77794770c00624b67a1
# Parent  5839bf207ee61788efa6382240f6bf66241c0227
Deleted selected files

diff -r 5839bf207ee6 -r 2120acb92e0b mississippi_gcc/annotation_collector.xml
--- a/mississippi_gcc/annotation_collector.xml	Tue Jun 24 11:40:49 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,37 +0,0 @@
-<tool id="annotation_collector" name="Collect Annotation counts" version="0.9.0">
-    <description> from matched fasta files</description>
-    <command interpreter="python">
-        annotation_collector.py
-        $out_file
-        $input1 $label1
-        #for $q in $queries
-            ${q.input2} ${q.label2}
-        #end for
-        $title
-    </command>
-    <inputs>
-       <param name="title" type="text" label="Annotation Title"/>
-       <param name="input1" type="data" label="fasta file to annotate"/>
-       <param name="label1" type="text" label="category label"/>
-        <repeat name="queries" title="Additional fasta file and label">
-            <param name="input2" type="data" label="Select" />
-            <param name="label2" type="text" label="Label" />
-        </repeat>
-    </inputs>
-    <outputs>
-        <data name="out_file" format="tabular" metadata_source="input1" label="Annotations"/>
-    </outputs>
-    <help>
-
-.. class:: warningmark
-
-**WARNING:** Be careful not to agregate datasets of different kinds (e.g., datasets must be matched fasta files). This tool does not check if the datasets being annotated are in the same format.
-
------
-
-**What it does**
-
-Generates Annotation Table from fasta files
-
-   </help>
-</tool>
\ No newline at end of file
diff -r 5839bf207ee6 -r 2120acb92e0b mississippi_gcc/bowtie_indices.loc.sample
--- a/mississippi_gcc/bowtie_indices.loc.sample	Tue Jun 24 11:40:49 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,37 +0,0 @@
-#This is a sample file distributed with Galaxy that enables tools
-#to use a directory of Bowtie indexed sequences data files. You will
-#need to create these data files and then create a bowtie_indices.loc
-#file similar to this one (store it in this directory) that points to
-#the directories in which those files are stored. The bowtie_indices.loc
-#file has this format (longer white space characters are TAB characters):
-#
-#<unique_build_id>   <dbkey>   <display_name>   <file_base_path>
-#
-#So, for example, if you had hg18 indexed stored in
-#/depot/data2/galaxy/bowtie/hg18/,
-#then the bowtie_indices.loc entry would look like this:
-#
-#hg18	hg18	hg18	/depot/data2/galaxy/bowtie/hg18/hg18
-#
-#and your /depot/data2/galaxy/bowtie/hg18/ directory
-#would contain hg18.*.ebwt files:
-#
-#-rw-r--r--  1 james    universe 830134 2005-09-13 10:12 hg18.1.ebwt
-#-rw-r--r--  1 james    universe 527388 2005-09-13 10:12 hg18.2.ebwt
-#-rw-r--r--  1 james    universe 269808 2005-09-13 10:12 hg18.3.ebwt
-#...etc...
-#
-#Your bowtie_indices.loc file should include an entry per line for each
-#index set you have stored. The "file" in the path does not actually
-#exist, but it is the prefix for the actual index files. For example:
-#
-#hg18canon			hg18	hg18 Canonical	/depot/data2/galaxy/bowtie/hg18/hg18canon
-#hg18full			hg18	hg18 Full		/depot/data2/galaxy/bowtie/hg18/hg18full
-#/orig/path/hg19	hg19	hg19			/depot/data2/galaxy/bowtie/hg19/hg19
-#...etc...
-#
-#Note that for backwards compatibility with workflows, the unique ID of
-#an entry must be the path that was in the original loc file, because that
-#is the value stored in the workflow for that parameter. That is why the
-#hg19 entry above looks odd. New genomes can be better-looking.
-#
diff -r 5839bf207ee6 -r 2120acb92e0b mississippi_gcc/tool_data_table_conf.xml.sample
--- a/mississippi_gcc/tool_data_table_conf.xml.sample	Tue Jun 24 11:40:49 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,68 +0,0 @@
-<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc-->
-<tables>
-    <!-- Locations of all fasta files under genome directory -->
-    <table name="all_fasta" comment_char="#">
-        <columns>value, dbkey, name, path</columns>
-        <file path="tool-data/all_fasta.loc" />
-    </table>
-    <!-- Locations of indexes in the BFAST mapper format -->
-    <table name="bfast_indexes" comment_char="#">
-        <columns>value, dbkey, formats, name, path</columns>
-        <file path="tool-data/bfast_indexes.loc" />
-    </table>
-    <!-- Locations of nucleotide (mega)blast databases -->
-    <table name="blastdb" comment_char="#">
-        <columns>value, name, path</columns>
-        <file path="tool-data/blastdb.loc" />
-    </table>
-    <!-- Locations of protein (mega)blast databases -->
-    <table name="blastdb_p" comment_char="#">
-        <columns>value, name, path</columns>
-        <file path="tool-data/blastdb_p.loc" />
-    </table>
-    <!-- Locations of indexes in the BWA mapper format -->
-    <table name="bwa_indexes" comment_char="#">
-        <columns>value, dbkey, name, path</columns>
-        <file path="tool-data/bwa_index.loc" />
-    </table>
-    <!-- Locations of indexes in the BWA color-space mapper format -->
-    <table name="bwa_indexes_color" comment_char="#">
-        <columns>value, dbkey, name, path</columns>
-        <file path="tool-data/bwa_index_color.loc" />
-    </table>
-    <!-- Locations of MAF files that have been indexed with bx-python -->
-    <table name="indexed_maf_files">
-        <columns>name, value, dbkey, species</columns>
-        <file path="tool-data/maf_index.loc" />
-    </table>
-    <!-- Locations of fasta files appropriate for NGS simulation -->
-    <table name="ngs_sim_fasta" comment_char="#">
-        <columns>value, dbkey, name, path</columns>
-        <file path="tool-data/ngs_sim_fasta.loc" />
-    </table>
-    <!-- Locations of PerM base index files -->
-    <table name="perm_base_indexes" comment_char="#">
-        <columns>value, name, path</columns>
-        <file path="tool-data/perm_base_index.loc" />
-    </table>
-    <!-- Locations of PerM color-space index files -->
-    <table name="perm_color_indexes" comment_char="#">
-        <columns>value, name, path</columns>
-        <file path="tool-data/perm_color_index.loc" />
-    </table>
-    <!-- Location of Picard dict file and other files -->
-    <table name="picard_indexes" comment_char="#">
-        <columns>value, dbkey, name, path</columns>
-        <file path="tool-data/picard_index.loc" />
-    </table>
-    <!-- Location of SRMA dict file and other files -->
-    <table name="srma_indexes" comment_char="#">
-        <columns>value, dbkey, name, path</columns>
-        <file path="tool-data/picard_index.loc" />
-    </table>
-    <!-- Location of Mosaik files -->
-    <table name="mosaik_indexes" comment_char="#">
-        <columns>value, dbkey, name, path</columns>
-        <file path="tool-data/mosaik_index.loc" />
-    </table>
-</tables>