Mercurial > repos > peterjc > seq_rename
annotate tools/filters/seq_rename.xml @ 0:a4b9836f8f47
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
author | peterjc |
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date | Tue, 07 Jun 2011 17:43:26 -0400 |
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children | 9c8c5079c8af |
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Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
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1 <tool id="seq_rename" name="Rename sequences" version="0.0.1"> |
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2 <description>with ID mapping from a tabular file</description> |
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3 <command interpreter="python"> |
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4 seq_rename.py $input_tabular $old_column $new_column $input_file $input_file.ext $output_file |
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5 </command> |
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6 <inputs> |
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7 <param name="input_file" type="data" format="fasta,qual,fastq,sff" label="Sequence file" help="FASTA, QUAL, FASTQ, or SFF format." /> |
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8 <param name="input_tabular" type="data" format="tabular" label="Tabular file containing sequence identifiers"/> |
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9 <param name="old_column" type="data_column" data_ref="input_tabular" multiple="False" numerical="False" label="Column containing current (old) sequence identifiers"/> |
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10 <param name="new_column" type="data_column" data_ref="input_tabular" multiple="False" numerical="False" label="Column contai |
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11 ning new sequence identifiers"/> |
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12 </inputs> |
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13 <outputs> |
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14 <data name="output_file" format="fasta" label="Renamed ${on_string}"> |
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15 <!-- TODO - Replace this with format="input:input_fastq" if/when that works --> |
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16 <change_format> |
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17 <when input_dataset="input_file" attribute="extension" value="sff" format="sff" /> |
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18 <when input_dataset="input_file" attribute="extension" value="fastq" format="fastq" /> |
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19 <when input_dataset="input_file" attribute="extension" value="fastqsanger" format="fastqsanger" /> |
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20 <when input_dataset="input_file" attribute="extension" value="fastqsolexa" format="fastqsolexa" /> |
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21 <when input_dataset="input_file" attribute="extension" value="fastqillumina" format="fastqillumina" /> |
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22 <when input_dataset="input_file" attribute="extension" value="fastqcssanger" format="fastqcssanger" /> |
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23 </change_format> |
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24 </data> |
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25 </outputs> |
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26 <tests> |
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27 </tests> |
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28 <requirements> |
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29 <requirement type="python-module">Bio</requirement> |
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30 </requirements> |
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31 <help> |
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32 |
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33 **What it does** |
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34 |
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35 Takes a FASTA, QUAL, FASTQ or Standard Flowgram Format (SFF) file and produces a |
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36 new sequence file (of the same format) where the sequence identifiers have been |
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37 renamed according two the specified columns a the tabular file. |
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38 |
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39 WARNING: If you have any duplicates in the intput sequence file, you will still |
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40 have duplicate sequences in the output. |
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41 |
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42 WARNING: If the tabular file has more than one new name for any old ID, the |
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43 last one is used. |
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44 |
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45 **Citation** |
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46 |
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47 This tool uses Biopython to read and write SFF files. If you use this tool in |
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48 scientific work leading to a publication, please cite the Biopython application |
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49 note (and Galaxy too of course): |
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50 |
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51 Cock et al 2009. Biopython: freely available Python tools for computational |
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52 molecular biology and bioinformatics. Bioinformatics 25(11) 1422-3. |
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53 http://dx.doi.org/10.1093/bioinformatics/btp163 pmid:19304878. |
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54 |
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55 </help> |
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56 </tool> |