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> |
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