Mercurial > repos > devteam > fasta_filter_by_length
annotate fasta_filter_by_length.xml @ 4:8cacfcf96a52 draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
author | devteam |
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date | Sun, 01 Mar 2020 07:24:42 -0500 |
parents | e626b3ff9922 |
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8cacfcf96a52
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
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1 <tool id="fasta_filter_by_length" name="Filter sequences by length" version="1.2" profile="16.04"> |
8cacfcf96a52
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
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2 <description></description> |
8cacfcf96a52
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
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3 <requirements> |
8cacfcf96a52
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
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4 <requirement type="package" version="3.7">python</requirement> |
8cacfcf96a52
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
devteam
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5 </requirements> |
8cacfcf96a52
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
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6 <command> |
8cacfcf96a52
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
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7 python '$__tool_directory__/fasta_filter_by_length.py' '$input' $min_length $max_length '$output' |
8cacfcf96a52
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
devteam
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8 </command> |
8cacfcf96a52
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
devteam
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9 <inputs> |
8cacfcf96a52
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
devteam
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10 <param name="input" type="data" format="fasta" label="Fasta file"/> |
8cacfcf96a52
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
devteam
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11 <param name="min_length" type="integer" value="0" label="Minimal length" /> |
8cacfcf96a52
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
devteam
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12 <param name="max_length" type="integer" value="0" label="Maximum length" help="Setting to '0' will return all sequences longer than the 'Minimal length'"/> |
8cacfcf96a52
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
devteam
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13 </inputs> |
8cacfcf96a52
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
devteam
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14 <outputs> |
8cacfcf96a52
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
devteam
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15 <data name="output" format="fasta"/> |
8cacfcf96a52
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
devteam
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16 </outputs> |
8cacfcf96a52
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
devteam
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17 <tests> |
8cacfcf96a52
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
devteam
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18 <test> |
8cacfcf96a52
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
devteam
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19 <param name="input" value="454.fasta" /> |
8cacfcf96a52
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
devteam
parents:
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20 <param name="min_length" value="10" /> |
8cacfcf96a52
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
devteam
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21 <param name="max_length" value="0" /> |
8cacfcf96a52
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
devteam
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22 <output name="output" file="fasta_tool_filter_length_1.out" /> |
8cacfcf96a52
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
devteam
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23 </test> |
8cacfcf96a52
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
devteam
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24 <test> |
8cacfcf96a52
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
devteam
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25 <param name="input" value="4.fasta" /> |
8cacfcf96a52
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
devteam
parents:
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26 <param name="min_length" value="0" /> |
8cacfcf96a52
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
devteam
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27 <param name="max_length" value="60" /> |
8cacfcf96a52
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
devteam
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28 <output name="output" file="fasta_tool_filter_length_2.out" /> |
8cacfcf96a52
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
devteam
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29 </test> |
8cacfcf96a52
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
devteam
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30 </tests> |
8cacfcf96a52
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
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31 <help><![CDATA[ |
0 | 32 |
33 .. class:: infomark | |
34 | |
35 **TIP**. To return sequences longer than a certain length, set *Minimal length* to desired value and leave *Maximum length* set to '0'. | |
36 | |
37 ----- | |
38 | |
39 **What it does** | |
4
8cacfcf96a52
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
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40 |
2
2fd6033d0e9c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length commit ad697ba869f1a81bb78168d3b81e360996fd2d52
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41 Outputs sequences greater than or equal to *Minimal length* and less than or equal to *Maximum length*. |
0 | 42 |
43 ----- | |
44 | |
45 **Example** | |
46 | |
47 Suppose you have the following FASTA formatted sequences:: | |
48 | |
4
8cacfcf96a52
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
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49 >seq1 |
8cacfcf96a52
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
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50 TCATTTAATGAC |
8cacfcf96a52
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
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51 >seq2 |
8cacfcf96a52
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
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52 ATGGC |
8cacfcf96a52
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
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53 >seq3 |
8cacfcf96a52
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
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54 TCACATGATGCCG |
8cacfcf96a52
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
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55 >seq4 |
8cacfcf96a52
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
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56 ATGGAAGC |
0 | 57 |
58 Setting the **Minimal length** to **10**, and the **Maximum length** to **0** will return all sequences longer than 10 bp:: | |
59 | |
4
8cacfcf96a52
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
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60 >seq1 |
8cacfcf96a52
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
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61 TCATTTAATGAC |
8cacfcf96a52
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
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62 >seq3 |
8cacfcf96a52
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
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63 TCACATGATGCCG |
0 | 64 |
65 | |
4
8cacfcf96a52
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
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66 ]]></help> |
2
2fd6033d0e9c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length commit ad697ba869f1a81bb78168d3b81e360996fd2d52
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67 </tool> |