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<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.

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**Input Formats**

Crac-index takes as input files any fasta or multi-fasta files.

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**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. 

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**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>