Mercurial > repos > peterjc > seq_select_by_id

annotate tools/seq_select_by_id/seq_select_by_id.xml @ 4:6842c0c7bc70 draft

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author peterjc
date Mon, 28 Oct 2013 05:21:45 -0400
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children 91f55ee8fea5
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1 <tool id="seq_select_by_id" name="Select sequences by ID" version="0.0.6">
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2 <description>from a tabular file</description>
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3 <requirements>
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4 <requirement type="package" version="1.62">biopython</requirement>
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5 <requirement type="python-module">Bio</requirement>
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6 </requirements>
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7 <version_command interpreter="python">seq_select_by_id.py --version</version_command>
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8 <command interpreter="python">
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9 seq_select_by_id.py $input_tabular $column $input_file $input_file.ext $output_file
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10 </command>
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11 <stdio>
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12 <!-- Anything other than zero is an error -->
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13 <exit_code range="1:" />
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14 <exit_code range=":-1" />
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15 </stdio>
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16 <inputs>
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17 <param name="input_file" type="data" format="fasta,qual,fastq,sff" label="Sequence file to select from" help="FASTA, QUAL, FASTQ, or SFF format." />
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18 <param name="input_tabular" type="data" format="tabular" label="Tabular file containing sequence identifiers"/>
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19 <param name="column" type="data_column" data_ref="input_tabular" multiple="False" numerical="False" label="Column containing sequence identifiers"/>
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20 </inputs>
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21 <outputs>
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22 <data name="output_file" format="fasta" label="Selected sequences">
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23 <!-- TODO - Replace this with format="input:input_fastq" if/when that works -->
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24 <change_format>
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25 <when input_dataset="input_file" attribute="extension" value="sff" format="sff" />
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26 <when input_dataset="input_file" attribute="extension" value="fastq" format="fastq" />
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27 <when input_dataset="input_file" attribute="extension" value="fastqsanger" format="fastqsanger" />
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28 <when input_dataset="input_file" attribute="extension" value="fastqsolexa" format="fastqsolexa" />
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29 <when input_dataset="input_file" attribute="extension" value="fastqillumina" format="fastqillumina" />
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30 <when input_dataset="input_file" attribute="extension" value="fastqcssanger" format="fastqcssanger" />
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31 </change_format>
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32 </data>
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33 </outputs>
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34 <tests>
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35 <test>
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36 <param name="input_file" value="k12_ten_proteins.fasta" ftype="fasta" />
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37 <param name="input_tabular" value="k12_hypothetical.tabular" ftype="tabular" />
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38 <param name="column" value="1" />
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39 <output name="output_file" file="k12_hypothetical.fasta" ftype="fasta" />
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40 </test>
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41 </tests>
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42 <help>
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43 **What it does**
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44
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45 Takes a FASTA, QUAL, FASTQ or Standard Flowgram Format (SFF) file and produces a
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46 new sequence file (of the same format) containing only the records with identifiers
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47 in the tabular file (in the order from the tabular file).
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48
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49 WARNING: If you have any duplicates in the tabular file identifiers, you will get
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50 duplicate sequences in the output.
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51
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52 **References**
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53
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54 If you use this Galaxy tool in work leading to a scientific publication please
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55 cite the following papers:
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56
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57 Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013).
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58 Galaxy tools and workflows for sequence analysis with applications
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59 in molecular plant pathology. PeerJ 1:e167
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60 http://dx.doi.org/10.7717/peerj.167
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61
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62 This tool uses Biopython to read, write and index sequence files, so you may
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63 also wish to cite the Biopython application note (and Galaxy too of course):
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64
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65 Cock et al (2009). Biopython: freely available Python tools for computational
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66 molecular biology and bioinformatics. Bioinformatics 25(11) 1422-3.
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67 http://dx.doi.org/10.1093/bioinformatics/btp163 pmid:19304878.
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68
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69 This tool is available to install into other Galaxy Instances via the Galaxy
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70 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/seq_select_by_id
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71 </help>
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72 </tool>