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1 <!--
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2 # =====================================================
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3 # $Id: ExtractSeqsFromFasta.xml 90 2011-01-19 13:20:31Z pieter.neerincx@gmail.com $
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4 # $URL: https://trac.nbic.nl/svn/galaxytools/trunk/tools/general/FastaTools/ExtractSeqsFromFasta.xml $
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5 # $LastChangedDate: 2011-01-19 07:20:31 -0600 (Wed, 19 Jan 2011) $
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6 # $LastChangedRevision: 90 $
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7 # $LastChangedBy: pieter.neerincx@gmail.com $
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8 # =====================================================
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9 -->
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10 <tool id="ExtractSeqsFromFasta1" version="1.1" name="ExtractSeqsFromFasta">
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11 <description>Extract sequences from a FASTA file based on a list of IDs</description>
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12 <command interpreter="perl">ExtractSeqsFromFasta.pl $ignore_accession_number_versions -f $identifiers -i $input -o $output -l WARN</command>
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13 <inputs>
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14 <param format="fasta" name="input" type="data" label="FASTA sequences"/>
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15 <param format="txt" name="identifiers" type="data" label="List of IDs to extract sequences for"/>
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16 <param name="ignore_accession_number_versions" type="boolean" truevalue="-u" falsevalue="" optional="true" label="Ignore accession number versions"/>
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17 </inputs>
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18 <outputs>
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19 <data format="fasta" name="output" label="FASTA sequences for ${identifiers.name}"/>
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20 </outputs>
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21 <!--
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22 <tests>
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23 <test>
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24 <param name="input" value="*.fasta"/>
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25 <param name="identifiers" value="*.txt"/>
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26 <output name="output" file="*.fasta"/>
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27 </test>
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28 </tests>
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29 -->
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30 <help>
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31
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32 .. class:: infomark
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33
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34 **What it does**
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35
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36 This tool filters a set of FASTA sequences for certain identifiers (IDs) or accession numbers. \
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37 Only sequences whose ID or accession number is present in the supplied list will remain in the filtered FASTA output. \
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38 The list of IDs or accession numbers to filter for must be a flat text file with one ID or accession per line.
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39
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40 This tool can match IDs with and without colon prefixed database namespaces in FASTA sequence header line. \
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41 Hence your FASTA header can contain both >UniProtKB:Q86Y46 ... or just plain >Q86Y46 ... . \
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42 Database namespace prefixes should not be present in the list of IDs that you want to extract sequences for.
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43
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44 FASTA headers may contain multiple IDs separated with pipe symbols (|) or semi colons (;). \
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45 If multiple IDs are supplied these should not contain any white space as everything after the \
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46 first white space is considered to be the (optional) description, which will not be matched against the list \
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47 of IDs to extract.
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48
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49 If your FASTA file contains versioned IDs / accessions, your list of IDs / accessions to extract must also contain \
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50 versioned IDs / accessions and the version numbers must match.
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51
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52 -----
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53
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54 **Example**
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55
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56 If the FASTA header is this::
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57
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58 >IPI:CON_IPI00174775.2|TREMBL:Q32MB2;Q86Y46 Tax_Id=9606 Gene_Symbol=KRT73 Keratin-73
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59
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60 The following IDs / accession numbers will match this sequence header::
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61
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62 CON_IPI00174775.2
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63 Q32MB2
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64 Q86Y46
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65
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66 These will not match::
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67
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68 IPI:CON_IPI00174775.2 (prefix should be removed)
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69 KRT73 (ID part of description and not part of list of IDs,
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70 which is everything up until the first white space.)
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71
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72 And finally these will not match unless *ignore accession number versions* is enabled::
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73
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74 CON_IPI00174775 (no version number, while FASTA file does contain versioned accession numbers)
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75 CON_IPI00174775.1 (wrong version number)
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76
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77 </help>
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78 </tool>
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