# HG changeset patch
# User rnateam
# Date 1393066876 18000
# Node ID e97db054a88d6f136355e4ac2a7583bf59d7e9c8
Uploaded
diff -r 000000000000 -r e97db054a88d segemehl.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/segemehl.xml Sat Feb 22 06:01:16 2014 -0500
@@ -0,0 +1,160 @@
+
+ based short read aligner
+
+ segemehl
+
+
+ ## prepare segemehl index if no reference genome is supplied
+ temp_index = `mktemp`;
+ #if $refGenomeSource.genomeSource == "history":
+ segemehl.x -x $temp_index -d $refGenomeSource.own_reference_genome;
+ #else:
+ $temp_index = ${refGenomeSource.index.fields.index_path}
+ #end if
+
+
+ ## execute segemehl
+ segemehl.x
+
+ ## number of threads
+ -t "\${GALAXY_SLOTS:-12}"
+
+ ## db file path
+ -d ${refGenomeSource.index.fields.db_path}
+
+ -i $temp_index
+
+ ## check for single/pair-end
+ #if str( $library.type ) == "single":
+ #set $query_list = list()
+ ## prepare inputs
+ #for $fastq in $library.reads:
+ $query_list.append('%s' %($fastq.input_query))
+ #end for
+ -q "#echo ' '.join( $query_list )#"
+ #else
+ ## prepare inputs
+
+ #set $mate1 = list()
+ #set $mate2 = list()
+ #for $mate_pair in $library.mate_list:
+ $mate1.append( str($mate_pair.first_strand_query) )
+ $mate2.append( str($mate_pair.second_strand_query) )
+ #end for
+
+ -q #echo ','.join($mate1)
+ -p #echo ','.join($mate2)
+
+ -I $library.maxinsertsize
+ #end if
+ -m $minsize
+ -A $accuracy
+ -H $hitstrategy
+ #if str( $prime5 ).strip():
+ -P $prime5
+ #end if
+ #if str( $prime3 ).strip():
+ -Q $prime3
+ #end if
+ $polyA
+ $autoclip
+ $hardclip
+ $order
+ -s
+ -o $segemehl_out
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+.. class:: infomark
+
+**What it does**
+
+Segemehl_ is a short read mapper with gaps.
+
+Segemehl_ is a software to map short sequencer reads to reference genomes.
+Unlike other methods, segemehl is able to detect not only mismatches but also insertions and deletions.
+Furthermore, segemehl is not limited to a specific read length and is able to mapprimer- or polyadenylation contaminated reads correctly.
+segemehl implements a matching strategy based on enhanced suffix arrays (ESA). Segemehl_ allows bisulfite sequencing mapping and split read mapping.
+
+.. _Segemehl: http://www.bioinf.uni-leipzig.de/Software/segemehl/
+
+**References**
+
+Hoffmann S, Otto C, Kurtz S, Sharma CM, Khaitovich P, Vogel J, Stadler PF, Hackermueller J: "Fast mapping of short sequences with mismatches, insertions and deletions using index structures", PLoS Comput Biol (2009) vol. 5 (9) pp. e1000502
+download latest version: 0.1.6 manual: download here new stuff: faster multiple split read mapping bug fixes: bugfixes: increased sensitivity for strand switches changes: - default accuracy now 90% older segemehl indices are still usable. issues: untraceable errors with gcc compiler gcc-4.5. zlib linker problems with some ubuntu versions complaint department: steve bioinf uni leipzig deshapeimage_1_link_0shapeimage_1_link_1
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diff -r 000000000000 -r e97db054a88d tool-data/segemehl_indices.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/segemehl_indices.loc.sample Sat Feb 22 06:01:16 2014 -0500
@@ -0,0 +1,29 @@
+#This is a sample file that enables the segemehl mapper to find genome indices
+#and database files. You will need to create these data files and then create
+#a segemehl_indices.loc file similar to this one (store it in this directory)
+#that points to the directories in which those files are stored.
+#The segemehl_indices.loc file has this format (longer white space characters are TAB characters):
+#
+#
+#
+#So, for example, if you had hg18 indexed stored in
+#/data/0/galaxy/segemehl/hg18/,
+#then the segemehl_indices.loc entry would look like this:
+#
+#hg18 hg18 hg18 /data/0/galaxy/segemehl/hg18/chromosomes.fa /data/0/galaxy/segemehl/hg18/chromosomes.idx
+#
+#and your /data/0/galaxy/segemehl/hg18/ directory
+#would contain hg18.*.ebwt files:
+#
+#-rw-r--r-- 1 bag bag 539833 2013-10-13 10:12 chromosomes.idx
+#-rw-r--r-- 1 bag bag 342562 2013-10-13 10:12 chromosomes.fa
+#...etc...
+#
+#Your segemehl_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 /data/0/galaxy/segemehl/hg18/chromosomes_can.fa /data/0/galaxy/segemehl/hg18/chromosomes_can.idx
+#hg18full hg18 hg18 Full /data/0/galaxy/segemehl/hg18/chromosomes_full.fa /data/0/galaxy/segemehl/hg18/chromosomes_full.idx
+#...etc...
+#
diff -r 000000000000 -r e97db054a88d tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Sat Feb 22 06:01:16 2014 -0500
@@ -0,0 +1,8 @@
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