Mercurial > repos > devteam > fasta_compute_length

annotate fasta_compute_length.xml @ 4:79cd53e23207 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
author devteam
date Sun, 01 Mar 2020 12:22:12 +0000
parents 19caae8fd9d4
children a51da10f8caf
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79cd53e23207 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
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1 <tool id="fasta_compute_length" name="Compute sequence length" version="1.0.2" profile="16.04">
2
d75972d4bd2a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6e148b31fed1b322ce720804d8525088ec6d43f9
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2 <description></description>
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79cd53e23207 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
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3 <requirements>
79cd53e23207 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
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4 <requirement type="package" version="3.7">python</requirement>
79cd53e23207 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
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5 </requirements>
3
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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6 <command>
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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7 #if $ref.ref_source == 'dbkey':
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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8 cp '${ref.index.fields.len_path}' '$output'
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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9 #else:
4
79cd53e23207 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
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10 python '$__tool_directory__/fasta_compute_length.py'
3
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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11 #if $ref.ref_source == 'history':
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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12 '$input'
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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13 #else:
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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14 '${ref.index.fields.path}'
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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15 #end if
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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16 '$output'
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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17 $ref.keep_first
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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18 $ref.keep_first_word
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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19 #end if
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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20 </command>
2
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21 <inputs>
3
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22 <conditional name="ref">
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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23 <param name="ref_source" type="select" label="Sequences">
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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24 <option value="history" selected="True">From History</option>
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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25 <option value="dbkey">Locally Cached (pre-built length files)</option>
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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26 <option value="fasta">Locally Cached (full genomes)</option>
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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27 </param>
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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28 <when value="history">
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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29 <param name="input" type="data" format="fasta" label="Compute length for these sequences"/>
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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30 <param name="keep_first" type="integer" value="0" label="How many title characters to keep?" help="'0' = keep the whole thing"/>
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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31 <param name="keep_first_word" type="boolean" truevalue="id_only" falsevalue="id_and_desc"
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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32 label="Strip fasta description from header?"
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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33 help="Stripping the description will truncate the fasta header to just the sequence ID. Otherwise the header description will be kept. This step is done before the 'How many characters to keep' option."/>
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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34 </when>
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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35 <when value="dbkey">
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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36 <param name="index" type="select" label="Source Genome Build">
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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37 <options from_data_table="__dbkeys__"/>
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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38 </param>
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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39 </when>
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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40 <when value="fasta">
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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41 <param name="index" type="select" label="Source Genome Build">
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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42 <options from_data_table="all_fasta"/>
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43 </param>
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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44 <param name="keep_first" type="integer" value="0" label="How many title characters to keep?" help="'0' = keep the whole thing"/>
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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45 <param name="keep_first_word" type="boolean" truevalue="id_only" falsevalue="id_and_desc"
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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46 label="Strip fasta description from header?"
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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47 help="Stripping the description will truncate the fasta header to just the sequence ID. Otherwise the header description will be kept. This step is done before the 'How many characters to keep' option."/>
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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48 </when>
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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49 </conditional>
2
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50
d75972d4bd2a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6e148b31fed1b322ce720804d8525088ec6d43f9
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51 </inputs>
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52 <outputs>
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53 <data name="output" format="tabular"/>
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54 </outputs>
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55 <tests>
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56 <test>
3
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57 <param name="ref|input" value="454.fasta" />
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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58 <param name="ref|keep_first" value="0"/>
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59 <param name="ref|keep_first_word" value="id_and_desc" />
2
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60 <output name="output" file="fasta_tool_compute_length_1.out" />
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61 </test>
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62
d75972d4bd2a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6e148b31fed1b322ce720804d8525088ec6d43f9
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63 <test>
3
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64 <param name="ref|input" value="extract_genomic_dna_out1.fasta" />
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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65 <param name="ref|keep_first" value="0"/>
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66 <param name="ref|keep_first_word" value="id_and_desc" />
2
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67 <output name="output" file="fasta_tool_compute_length_2.out" />
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68 </test>
d75972d4bd2a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6e148b31fed1b322ce720804d8525088ec6d43f9
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d75972d4bd2a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6e148b31fed1b322ce720804d8525088ec6d43f9
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70 <test>
3
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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71 <param name="ref|input" value="454.fasta" />
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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72 <param name="ref|keep_first" value="14"/>
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73 <param name="ref|keep_first_word" value="id_and_desc" />
2
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74 <output name="output" file="fasta_tool_compute_length_3.out" />
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75 </test>
3
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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76
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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77 <test>
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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78 <param name="ref|ref_source" value="fasta" />
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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79 <param name="ref|index" value="test_id"/>
19caae8fd9d4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
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80 <param name="ref|keep_first_word" value="id_only" />
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81 <output name="output" file="merged.tab" />
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82 </test>
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83
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84 <test>
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85 <param name="ref|ref_source" value="dbkey" />
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86 <param name="ref|index" value="test_id"/>
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87 <output name="output" file="merged.tab" />
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88 </test>
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89 </tests>
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90 <help><![CDATA[
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91
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92 **What it does**
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93
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94 This tool counts the length of each fasta sequence in the file. The output file has two columns per line (separated by tab): fasta titles and lengths of the sequences. The option *How many characters to keep?* allows to select a specified number of letters from the beginning of each FASTA entry.
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95
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96 -----
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97
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98 **Example**
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99
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100 Suppose you have the following FASTA formatted sequences from a Roche (454) FLX sequencing run::
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101
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102 >EYKX4VC02EQLO5 length=108 xy=1826_0455 region=2 run=R_2007_11_07_16_15_57_
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103 TCCGCGCCGAGCATGCCCATCTTGGATTCCGGCGCGATGACCATCGCCCGCTCCACCACG
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104 TTCGGCCGGCCCTTCTCGTCGAGGAATGACACCAGCGCTTCGCCCACG
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105 &gt;EYKX4VC02D4GS2 length=60 xy=1573_3972 region=2 run=R_2007_11_07_16_15_57_
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106 AATAAAACTAAATCAGCAAAGACTGGCAAATACTCACAGGCTTATACAATACAAATGTAAfa
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107
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108 Running this tool while setting **How many characters to keep?** to **14** will produce this::
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109
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110 EYKX4VC02EQLO5 108
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111 EYKX4VC02D4GS2 60
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112
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113 However, if your IDs are not all the same length, you may wish to just keep the fasta ID, and not the description::
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114
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115 >EYKX4VC02EQLO5 length=108 xy=1826_0455 region=2 run=R_2007_11_07_16_15_57_
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116 TCCGCGCCGAGCATGCCCATCTTGGATTCCGGCGCGATGACCATCGCCCGCTCCACCACG
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117 TTCGGCCGGCCCTTCTCGTCGAGGAATGACACCAGCGCTTCGCCCACG
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118 >EYKX4VC length=60 xy=1573_3972 region=2 run=R_2007_11_07_16_15_57_
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119 AATAAAACTAAATCAGCAAAGACTGGCAAATACTCACAGGCTTATACAATACAAATGTAAfa
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120
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121 Running this tool with **Strip fasta description from header** set to **True** and **How many characters to keep?** set to **0** will produce::
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122
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123 EYKX4VC02EQLO5 108
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124 EYKX4VC 60
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125
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126
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127 ]]></help>
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128 <citations>
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129 <citation type="doi">10.1093/bioinformatics/btq281</citation>
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130 </citations>
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131 </tool>