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1 <tool id="crispr_recognition_tool" name="CRISPR Recognition Tool" version="1.2.0">
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2 <description>(CRT)</description>
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1
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3 <!-- split_size needs to be 1, because CRT does not support multi fasta file -->
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4 <parallelism method="multi" split_inputs="input" split_mode="to_size" split_size="1" merge_outputs="output,output_region" />
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5 <requirements>
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6 <requirement type="package" version="1.2">crisper_recognition_tool</requirement>
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7 <requirement type="set_environment">CRISPR_RECOGNITION_TOOL_SCRIPT_PATH</requirement>
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8 </requirements>
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9 <stdio>
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10 <exit_code range=":-1" level="fatal" />
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11 <exit_code range="1:" level="fatal" />
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12 </stdio>
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13 <command>
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14 temp_output=\$(mktemp);
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15 java -cp \$CRISPR_RECOGNITION_TOOL_JAR_PATH/CRT1.2-CLI.jar crt
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16 -minNR $minNR
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17 -minRL $minRL
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18 -maxRL $maxRL
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19 -minSL $minSL
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20 -maxSL $maxSL
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21 #if str($searchWL) != 'none':
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22 -searchWL $searchWL
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23 #end if
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24 $input
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25 \$temp_output
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26 ;
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27
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28 python \$CRISPR_RECOGNITION_TOOL_SCRIPT_PATH/reformat.py \$temp_output $output_region $output
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29 </command>
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30 <inputs>
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31 <param format="fasta" name="input" type="data" label="Input sequence as FASTA"/>
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32
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33 <param name="minNR" type="integer" value="3" label="Minimum number of repeats a CRISPER must have"/>
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34 <param name="minRL" type="integer" value="19" label="Minimum length of a CRISPER repeated region"/>
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35 <param name="maxRL" type="integer" value="38" label="Maximum length of a CRISPER repeated region"/>
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36 <param name="minSL" type="integer" value="19" label="Minimum length of CRISPER non repeated region" help="or spacer region"/>
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37 <param name="maxSL" type="integer" value="48" label="Maximum length of CRISPER non repeated region" help="or spacer region"/>
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38 <param name="searchWL" type="select" label="Length of search window to used to discover CRISPERs">
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39 <option value="none" selected="true">default</option>
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40 <option value="6">6</option>
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41 <option value="7">7</option>
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42 <option value="8">8</option>
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43 <option value="9">9</option>
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44 </param>
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45 </inputs>
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46 <outputs>
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47 <data format="tabular" name="output" label="${tool.name} on ${on_string}" />
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48 <data format="bed" name="output_region" label="${tool.name} on ${on_string} - BED file" />
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49 </outputs>
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50 <tests>
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51 <test>
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52 <param name="input" value="sequence.fasta" ftype="fasta" />
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53 <param name="minNR" value="3" />
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54 <param name="minRL" value="29" />
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55 <param name="maxRL" value="38" />
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56 <param name="minSL" value="19" />
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57 <param name="maxSL" value="48" />
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58 <param name="searchWL" value="none" />
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59 <output name="output" file="crt.tabular" ftype="tabular" />
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60 <output name="output_region" file="crt.bed" ftype="bed" />
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61 </test>
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62 </tests>
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63 <help>
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64 CRISPR Recognition Tool - a tool for automatic detection of clustered regularly interspaced palindromic repeats
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65
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66 http://www.room220.com/crt/
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67
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68 **Citation**
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69
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70 For the underlying tool, please cite `Bland C, Ramsey TL, Sabree F, Lowe M, Brown K, Kyrpides NC, Hugenholtz P:
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71 CRISPR Recognition Tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats. BMC Bioinformatics. 2007 Jun 18;8(1):209`
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72
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73 </help>
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74 </tool>
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75
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