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1 <tool id="crac-index" name="CRAC index">
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2
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3 <description>Create genome indexes available to be used with CRAC mapping/annotation tool </description>
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4
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5 <command>
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6 crac-index-wrapper.sh "$output_name" "$output" "$output.files_path" "$bucket" "$input_file"
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7 </command>
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8
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9 <inputs>
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10 <param name="input_file" type="data" label="Source file" format="fasta" help="You must choose a fasta file containing the genome"/>
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11 <param name="output_name" type="text" value ="IndexOutput" label="Output name" help="Name must be different from 'index' word, otherwise CRAC-index will fail." />
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12 <param name="bucket" type="integer" value="100000000" label="Bucket size" help="The size of the bucket for the index construction (default 100000000)."/>
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13 </inputs>
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14
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15 <outputs>
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16 <data name="output" format="crac_index" label="${output_name}.crac-index" />
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17 </outputs>
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18
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19 <help>
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20
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21 **What it does**
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22
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23 Crac-index generates an indexed genome from a fasta file. This is especially useful for the Crac mapping/annotation tool.
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24
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25 ----------------------
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26
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27 **Input Formats**
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28
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29 Crac-index takes as input files any fasta or multi-fasta files.
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30
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31 ----------------------
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32
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33 **Outputs**
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34
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35 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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36
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37 ----------------------
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38
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39 **Crac-index settings**
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40
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41
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42 Usage : ./crac-index [options] command output_file input_file
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43
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44 command must be :
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45 index: create an index on the specified input file(s).
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46
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47 options can be :
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48
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49 -b bucket_size the size of the bucket for the index construction
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50 (default 100000000)
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51 -d diff-cover parameter for the index construction (default 1024)
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52 -v verbose mode
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53
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54 Examples:
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55 ./crac-index index myIndex sequence1.fa sequence2.fa sequence3.fa
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56 You can specify FASTA or MultiFASTA file(s).
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57 In this example, two files will be created:
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58 - myIndex.ssa (index storing the compressed sequences)
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59 - myIndex.conf (information on sequence names and length)
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60
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61 </help>
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62
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63
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64 </tool>
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