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1 <tool id="Sibelia" name="sibelia">
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2 <command interpreter="python">
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3 #if $p_s.p_s_select == "-s" #Sibelia_wrapper.py -s $p_s.simplification $ram -m $b_size $single_ou $postprocess -i $iter $fasta
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4 #else #Sibelia_wrapper.py -k $p_s.cpfile $ram -m $b_size $single_ou $postprocess -i $iter $fasta
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5 #end if#
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6 </command>
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7 <inputs>
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8 <conditional name="p_s">
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9 <param name="p_s_select" type="select" label="Parameters set">
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10 <option value="-s">Select parameters set</option>
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11 <option value="-k">Custom parameteres set</option>
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12 </param>
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13 <when value="-k">
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14 <param name="cpfile" size="50" type="text" label="File of custom parameters set" />
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15 </when>
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16 <when value="-s">
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17 <param name="simplification" type="select" label="Simplification">
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18 <option value="loose">Loose</option>
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19 <option value="fine">Fine</option>
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20 </param>
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21 </when>
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22 </conditional>
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23 <param name="ram" type="boolean" truevalue="-r" falsevalue="" label="Store temporary files in RAM?" />
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24 <param name="single_ou" type="boolean" truevalue="-a" falsevalue="" label="Find blocks that occur exactly once in each input sequence" />
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25 <param name="postprocess" type="boolean" truevalue="--nopostprocess" falsevalue="" label="Turn off postprocessing?" />
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26 <param name="iter" type="integer" value="4" label="Number of iterations" />
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27 <param name="b_size" type="integer" value="2000" label="Minimum block size" />
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28 <param name="fasta" size="50" type="text" label="Path to input fasta file" />
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29 </inputs>
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30 <outputs>
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31 <data format="txt" name="outperm" label="Genomes permutations" from_work_dir="genomes_permutations.txt" />
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32 <data format="txt" name="outblc" label="Blocks coords" from_work_dir="blocks_coords.txt" />
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33 <data format="txt" name="outcov" label="Coverage report" from_work_dir="coverage_report.txt" />
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34 <data format="html" name="outbld" label="Blocks diagram" from_work_dir="d3_blocks_diagram.html" />
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35 </outputs>
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36 <!-- <tests>
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37 <test>
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38 <param name="p_s_select" value="-s" />
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39 <param name="simplification" value="loose" />
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40 <param name="ram" value="0" />
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41 <param name="single_ou" value="0" />
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42 <param name="postprocess" value="0" />
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43 <param name="fasta" value="Helicobacter_pylori.fasta" />
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44 </test>
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45 <test>
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46 <param name="p_s_select" value="-k" />
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47 <param name="cpfile" value="CPFile.txt" />
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48 <param name="ram" value="0" />
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49 <param name="single_ou" value="0" />
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50 <param name="postprocess" value="0" />
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51 <param name="fasta" value="Helicobacter_pylori.fasta" />
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52 </test>
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53 </tests> -->
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54 <help>
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55 .. class:: infomark
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56 Sibelia -- "Sibelia" is a tool for finding synteny blocks in closely related genomes, like different strains of the same bacterial species. It takes a set of FASTA files with genomes and locates coordinates of the synteny blocks in these sequences. It also represents genomes as permutations of the blocks.
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57 </help>
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58 </tool> |