Mercurial > repos > peterjc > seq_select_by_id
annotate tools/filters/seq_select_by_id.xml @ 3:19e26966ed3e draft
Uploaded v0.0.6, handles Biopython dependency via the ToolShed, adopted MIT license, using reStructuredTest for the README file.
No functional changes.
author | peterjc |
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date | Mon, 29 Jul 2013 09:13:13 -0400 |
parents | 28d52478ace9 |
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rev | line source |
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Uploaded v0.0.6, handles Biopython dependency via the ToolShed, adopted MIT license, using reStructuredTest for the README file.
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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> |
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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Uploaded v0.0.6, handles Biopython dependency via the ToolShed, adopted MIT license, using reStructuredTest for the README file.
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7 <stdio> |
19e26966ed3e
Uploaded v0.0.6, handles Biopython dependency via the ToolShed, adopted MIT license, using reStructuredTest for the README file.
peterjc
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8 <!-- Anything other than zero is an error --> |
19e26966ed3e
Uploaded v0.0.6, handles Biopython dependency via the ToolShed, adopted MIT license, using reStructuredTest for the README file.
peterjc
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9 <exit_code range="1:" /> |
19e26966ed3e
Uploaded v0.0.6, handles Biopython dependency via the ToolShed, adopted MIT license, using reStructuredTest for the README file.
peterjc
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2
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10 <exit_code range=":-1" /> |
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Uploaded v0.0.6, handles Biopython dependency via the ToolShed, adopted MIT license, using reStructuredTest for the README file.
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11 </stdio> |
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12 <inputs> |
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13 <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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14 <param name="input_tabular" type="data" format="tabular" label="Tabular file containing sequence identifiers"/> |
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15 <param name="column" type="data_column" data_ref="input_tabular" multiple="False" numerical="False" label="Column containing sequence identifiers"/> |
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16 </inputs> |
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17 <outputs> |
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18 <data name="output_file" format="fasta" label="Selected sequences"> |
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19 <!-- TODO - Replace this with format="input:input_fastq" if/when that works --> |
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20 <change_format> |
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21 <when input_dataset="input_file" attribute="extension" value="sff" format="sff" /> |
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22 <when input_dataset="input_file" attribute="extension" value="fastq" format="fastq" /> |
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23 <when input_dataset="input_file" attribute="extension" value="fastqsanger" format="fastqsanger" /> |
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24 <when input_dataset="input_file" attribute="extension" value="fastqsolexa" format="fastqsolexa" /> |
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25 <when input_dataset="input_file" attribute="extension" value="fastqillumina" format="fastqillumina" /> |
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26 <when input_dataset="input_file" attribute="extension" value="fastqcssanger" format="fastqcssanger" /> |
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27 </change_format> |
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28 </data> |
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29 </outputs> |
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30 <tests> |
2 | 31 <test> |
32 <param name="input_file" value="k12_ten_proteins.fasta" ftype="fasta" /> | |
33 <param name="input_tabular" value="k12_hypothetical.tabular" ftype="tabular" /> | |
34 <param name="column" value="1" /> | |
35 <output name="output_file" file="k12_hypothetical.fasta" ftype="fasta" /> | |
36 </test> | |
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37 </tests> |
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38 <requirements> |
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39 <requirement type="python-module">Bio</requirement> |
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40 </requirements> |
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41 <help> |
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42 |
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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 **Citation** |
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53 |
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54 This tool uses Biopython to read, write and index sequence files. If you use |
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55 this tool in scientific work leading to a publication, please cite the |
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56 Biopython application note (and Galaxy too of course): |
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57 |
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58 Cock et al 2009. Biopython: freely available Python tools for computational |
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59 molecular biology and bioinformatics. Bioinformatics 25(11) 1422-3. |
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60 http://dx.doi.org/10.1093/bioinformatics/btp163 pmid:19304878. |
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61 |
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62 This tool is available to install into other Galaxy Instances via the Galaxy |
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Uploaded v0.0.6, handles Biopython dependency via the ToolShed, adopted MIT license, using reStructuredTest for the README file.
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63 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/seq_select_by_id |
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64 </help> |
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65 </tool> |