Mercurial > repos > peterjc > seq_select_by_id
annotate tools/filters/seq_select_by_id.xml @ 2:28d52478ace9 draft
Uploaded v0.0.4 which adds a unit test.
author | peterjc |
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date | Mon, 15 Apr 2013 12:28:51 -0400 |
parents | 50a8a6917a9c |
children | 19e26966ed3e |
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2 | 1 <tool id="seq_select_by_id" name="Select sequences by ID" version="0.0.4"> |
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2 <description>from a tabular file</description> |
2 | 3 <version_command interpreter="python">seq_select_by_id.py --version</version_command> |
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4 <command interpreter="python"> |
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5 seq_select_by_id.py $input_tabular $column $input_file $input_file.ext $output_file |
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6 </command> |
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7 <inputs> |
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8 <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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9 <param name="input_tabular" type="data" format="tabular" label="Tabular file containing sequence identifiers"/> |
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10 <param name="column" type="data_column" data_ref="input_tabular" multiple="False" numerical="False" label="Column containing sequence identifiers"/> |
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11 </inputs> |
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12 <outputs> |
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13 <data name="output_file" format="fasta" label="Selected sequences"> |
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14 <!-- TODO - Replace this with format="input:input_fastq" if/when that works --> |
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15 <change_format> |
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16 <when input_dataset="input_file" attribute="extension" value="sff" format="sff" /> |
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17 <when input_dataset="input_file" attribute="extension" value="fastq" format="fastq" /> |
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18 <when input_dataset="input_file" attribute="extension" value="fastqsanger" format="fastqsanger" /> |
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19 <when input_dataset="input_file" attribute="extension" value="fastqsolexa" format="fastqsolexa" /> |
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20 <when input_dataset="input_file" attribute="extension" value="fastqillumina" format="fastqillumina" /> |
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21 <when input_dataset="input_file" attribute="extension" value="fastqcssanger" format="fastqcssanger" /> |
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22 </change_format> |
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23 </data> |
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24 </outputs> |
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25 <tests> |
2 | 26 <test> |
27 <param name="input_file" value="k12_ten_proteins.fasta" ftype="fasta" /> | |
28 <param name="input_tabular" value="k12_hypothetical.tabular" ftype="tabular" /> | |
29 <param name="column" value="1" /> | |
30 <output name="output_file" file="k12_hypothetical.fasta" ftype="fasta" /> | |
31 </test> | |
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32 </tests> |
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33 <requirements> |
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34 <requirement type="python-module">Bio</requirement> |
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35 </requirements> |
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36 <help> |
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37 |
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38 **What it does** |
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39 |
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40 Takes a FASTA, QUAL, FASTQ or Standard Flowgram Format (SFF) file and produces a |
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41 new sequence file (of the same format) containing only the records with identifiers |
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42 in the tabular file (in the order from the tabular file). |
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43 |
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44 WARNING: If you have any duplicates in the tabular file identifiers, you will get |
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45 duplicate sequences in the output. |
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46 |
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47 **Citation** |
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48 |
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49 This tool uses Biopython to read, write and index sequence files. If you use |
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50 this tool in scientific work leading to a publication, please cite the |
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51 Biopython application note (and Galaxy too of course): |
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52 |
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53 Cock et al 2009. Biopython: freely available Python tools for computational |
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54 molecular biology and bioinformatics. Bioinformatics 25(11) 1422-3. |
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55 http://dx.doi.org/10.1093/bioinformatics/btp163 pmid:19304878. |
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56 |
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57 </help> |
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58 </tool> |