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1 <tool id="exparna" name="ExpaRNA" version="0.1.0">
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2 <description></description>
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3 <requirements>
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4 <requirement type="package" version="1.0">exparna</requirement>
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5 <requirement type="package" version="1.8.5">vienna_rna</requirement>
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6 <requirement type="set_environment">EXPARNA_SCRIPT_PATH</requirement>
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7 </requirements>
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8 <command>
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9 ExpaRNA
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10 -t$emp_scoring
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11 #if $check == "no":
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12 -n$max_used_sub
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13 #end if
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14 -s$min_incl_sub
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15 $locarna_input
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16 $alignment_to_file
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17 $list_in_file
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18 $all_in_file
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19 $fastafile;
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20 mkdir $outfile.files_path;
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21 cp ./ExpaRNA-results/* $outfile.files_path;
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22 python \$EXPARNA_SCRIPT_PATH/create_html.py $outfile $outfile.files_path;
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23 #if $locarna_input:
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24 cp ./ExpaRNA-results/LCSEPM_LocARNA_* $locarna_inputfile
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25 #end if
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26 </command>
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27 <stdio>
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28 <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error" />
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29 <exit_code range=":-1" level="fatal" description="Error occurred. Please check Tool Standard Error" />
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30 </stdio>
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31 <inputs>
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32 <param format="fasta" name="fastafile" type="data" label="Fasta Input File" />
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33 <param name="min_incl_sub" label="Minimal size of included substructures" type="integer" value="7" help="-s" />
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34 <conditional name="check">
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35 <param name="check_all" type="boolean" truevalue="yes" falsevalue="no" label="Use all substructures" help="" checked="true" />
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36 <when value="no">
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37 <param name="max_used_sub" label="Maximum number of used substructures" type="integer" value="0" help="-n" />
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38 </when>
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39 </conditional>
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40
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41 <param name="emp_scoring" type="select" value="no" label="EPM Scoring" help="-t">
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42 <option value="1" selected="true">Default</option>
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43 <option value="2">Prefer Larger Patterns</option>
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44 </param>
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45 <!-- output parameter alles booleans
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46 /!-->
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47 <param name="locarna_input" type="boolean" checked="true" truevalue="-i" falsevalue="" label="Write ExpaRNA result as input for LocARNA with anchor constraints" help="-i" />
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48 <param name="alignment_to_file" type="boolean" checked="false" truevalue="-o" falsevalue="" label="Write ExpaRNA result as alignment into text file" help="-o" />
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49 <param name="list_in_file" type="boolean" checked="false" truevalue="-e" falsevalue="" label="Write ExpaRNA result as list in file" help="-e" />
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50 <param name="all_in_file" type="boolean" checked="false" truevalue="-a" falsevalue="" label="Write all EPMs into file" help="-a" />
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51 </inputs>
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52 <outputs>
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53 <data format="fasta" name="locarna_inputfile" label="Output generated for Locarna">
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54 <filter>locarna_input is True</filter>
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55 </data>
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56 <data name="outfile" format="zip" />
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57 </outputs>
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58 <tests>
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59 <test>
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60 <param name="fastafile" value="input.fasta" />
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61 <output name="output" file="output.zip" compare="sim_size" />
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62 <param name="locarna_input" value="" />
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63 <param name="check_all" value="yes" />
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64 </test>
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65
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66 </tests>
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67 <help>**What it does**
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68 http://rna.informatik.uni-freiburg.de/ExpaRNA/Input.jsp
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69
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70 ExpaRNA is a fast, motif-based comparison and alignment tool for RNA molecules. Instead of computing a full sequence-structure alignment, it computes the best arrangement of sequence-structure motifs common to two RNAs. A motif is a local (or isolated) substructure which is identical to both RNAs. ExpaRNA requires a given nested secondary structure for both RNAs. If no structure is available, RNAfold from Vienna RNA Package is used for a structure prediction. The accuracy of the algorithm is mainly controlled by the minimal size of the included sequence-structure motifs. ExpaRNA is especially useful for comparative structural RNA analysis and to speed-up complex sequence-structure alignment methods. For this purpose, the predicted common substructures by ExpaRNA are used as anchor constraints for a full structural alignment.
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71
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72 **Output**
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73
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74 You will receive a zip file containing all output files and optionally the outputfile made for postprocessing with locarna.
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75 </help>
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76 </tool>
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