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1 <tool id="fasta_filter_by_length" name="Filter sequences by length" version="1.1">
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2 <description></description>
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3 <command interpreter="python">fasta_filter_by_length.py $input $min_length $max_length $output </command>
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4 <inputs>
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5 <param name="input" type="data" format="fasta" label="Fasta file"/>
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6 <param name="min_length" type="integer" size="15" value="0" label="Minimal length" />
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7 <param name="max_length" type="integer" size="15" value="0" label="Maximum length" help="Setting to '0' will return all sequences longer than the 'Minimal length'"/>
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8 </inputs>
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9 <outputs>
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10 <data name="output" format="fasta"/>
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11 </outputs>
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12 <tests>
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13 <test>
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14 <param name="input" value="454.fasta" />
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15 <param name="min_length" value="10" />
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16 <param name="max_length" value="0" />
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17 <output name="output" file="fasta_tool_filter_length_1.out" />
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18 </test>
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19 </tests>
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20 <help>
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21
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22 .. class:: infomark
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23
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24 **TIP**. To return sequences longer than a certain length, set *Minimal length* to desired value and leave *Maximum length* set to '0'.
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25
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26 -----
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27
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28 **What it does**
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29
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30 Outputs sequences between *Minimal length* and *Maximum length*.
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31
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32 -----
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33
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34 **Example**
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35
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36 Suppose you have the following FASTA formatted sequences::
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37
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38 >seq1
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39 TCATTTAATGAC
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40 >seq2
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41 ATGGC
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42 >seq3
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43 TCACATGATGCCG
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44 >seq4
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45 ATGGAAGC
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46
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47 Setting the **Minimal length** to **10**, and the **Maximum length** to **0** will return all sequences longer than 10 bp::
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48
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49 >seq1
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50 TCATTTAATGAC
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51 >seq3
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52 TCACATGATGCCG
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53
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54
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55 </help>
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56 </tool> |
