# 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 @@
-
- from matched fasta files
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- annotation_collector.py
- $out_file
- $input1 $label1
- #for $q in $queries
- ${q.input2} ${q.label2}
- #end for
- $title
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-.. class:: warningmark
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-**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.
-
------
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-**What it does**
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-Generates Annotation Table from fasta files
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\ 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
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-#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):
-#
-#
-#
-#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
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