Mercurial > repos > rnateam > graphclust_preprocessing

annotate preprocessing.xml @ 1:cf2673f7eb44 draft

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author rnateam
date Sat, 21 Jan 2017 17:41:56 -0500
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1 <tool id="preproc" name="Preprocessing" version="0.1">
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2 <requirements>
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3 <requirement type="package" version="0.1.7">graphclust-wrappers</requirement>
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4 </requirements>
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5 <stdio>
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6 <exit_code range="1:" />
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7 </stdio>
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8 <command>
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9 <![CDATA[
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11 'preprocessing.pl'
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12 '$fastaFile' $max_length $in_winShift $min_seq_length
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14 ]]>
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15 </command>
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16 <inputs>
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17 <param type="data" name="fastaFile" format="fasta" />
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18 <param name="max_length" type="integer" value="10000" size="5" label="window size"/>
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19 <param name="in_winShift" type="integer" value="100" size="5" label="window shift in percent"/>
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20 <param name="min_seq_length" type="integer" value="5" size="5" label="minimum sequence length"/>
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21 </inputs>
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23 <outputs>
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24 <data name="data.fasta" format="fasta" from_work_dir="FASTA/data.fasta" label="data.fasta"/>
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25 <data name="data.map" format="txt" from_work_dir="FASTA/data.map" label="data.map"/>
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26 <data name="data.names" format="txt" from_work_dir="FASTA/data.names" label="data.names"/>
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27 <data name="data.fasta.scan" format="fasta" from_work_dir="FASTA/data.fasta.scan" label="data.fasta.scan"/>
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28 <data name="FASTA" format="zip" from_work_dir="FASTA.zip" label="FASTA.ZIP"/>
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29 </outputs>
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32 <tests>
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33 <test>
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34 <param name="fastaFile" value="input.fa"/>
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35 <param name="max_length" value="10000"/>
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36 <param name="in_winShift" value="100"/>
3eb088816194 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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37 <param name="min_seq_length" value="5"/>
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38 <output name="data.fasta" file="FASTA/data.fasta"/>
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39 <output name="data.map" file="FASTA/data.map" />
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40 <output name="data.names" file="FASTA/data.names"/>
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41 <output name="data.fasta.scan" file="FASTA/data.fasta.scan" />
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42 </test>
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43 </tests>
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45 <help>
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46 <![CDATA[
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48 **What it does**
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49
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50 The tool takes as an input file of sequences in Fasta format and creates the final input for GraphCLust based on given parameters.
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52 **Parameters**
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53
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54 + **window size** : All input sequences are splitted into fragments of this length.
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55 The shift of the sliding window can be defined via option *window shift in percent*.
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56 This paramter reflects the expected length of signals to be found.
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57 Slightly larger windows are usually ok. Too small windows can disturb existing signals.
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58
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62 + **window shift in percent** : Relative window size in % for window shift during input preprocessing.
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63 Please note that a small shift results in much more fragments for clustering. The benefit is that RNA
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64 motifs/structures are not destroyed by arbitrary split points. Smaller
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65 shifts usually increase the cluster quality. Too small shifts (<20) are not
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66 recommended as a dense center is "polluted" by overlapping fragments and
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67 no other occurences in the dataset can be found.
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73 + **minimum sequence length** : Minimal length of input sequences.
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74 Every input sequence below that length is ignored completely during clustering.
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75
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77 ]]></help>
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80 <citations>
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81 <citation type="doi">10.1093/bioinformatics/bts224</citation>
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82 </citations>
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84
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85 </tool>