diff crac-index.xml @ 3:4cf2808854bc draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/crac-index.xml	Fri Sep 13 10:01:00 2013 -0400
@@ -0,0 +1,64 @@
+<tool id="crac-index" name="CRAC index">
+
+   <description>Create genome indexes available to be used with CRAC mapping/annotation tool </description>
+
+   <command>
+     crac-index-wrapper.sh "$output_name" "$output" "$output.files_path" "$bucket" "$input_file"
+   </command>
+
+   <inputs>
+      <param name="input_file" type="data" label="Source file" format="fasta" help="You must choose a fasta file containing the genome"/>
+      <param name="output_name" type="text" value ="IndexOutput" label="Output name" help="Name must be different from 'index' word, otherwise CRAC-index will fail." />
+      <param name="bucket" type="integer" value="100000000" label="Bucket size" help="The size of the bucket for the index construction (default 100000000)."/>
+   </inputs>
+  
+   <outputs>
+      <data name="output" format="crac_index" label="${output_name}.crac-index" />
+   </outputs>
+
+   <help>
+
+**What it does**
+
+Crac-index generates an indexed genome from a fasta file. This is especially useful for the Crac mapping/annotation tool.
+
+----------------------
+
+**Input Formats**
+
+Crac-index takes as input files any fasta or multi-fasta files.
+
+----------------------
+
+**Outputs**
+
+Crac-index on Galaxy produces a composite output named crac-index, which is made of a ssa file and a conf file. Both are required to the use of your index. 
+
+----------------------
+
+**Crac-index settings**
+
+
+Usage : ./crac-index [options] command output_file input_file
+
+  command must be :
+    index: create an index on the specified input file(s).
+
+  options can be :
+
+  -b bucket_size	 the size of the bucket for the index construction
+                  	 (default 100000000)
+  -d diff-cover 	 parameter for the index construction (default 1024)
+  -v              	 verbose mode
+
+  Examples: 
+		./crac-index index myIndex sequence1.fa sequence2.fa sequence3.fa
+			You can specify FASTA or MultiFASTA file(s).
+			In this example, two files will be created:
+			- myIndex.ssa (index storing the compressed sequences)
+			- myIndex.conf (information on sequence names and length)
+
+   </help>
+
+
+</tool>