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planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/fasta_add_barcode commit e857f7126443e115f11954085423f8999bc870aa-dirty
author bebatut
date Fri, 15 Apr 2016 06:01:42 -0400
parents 0ea7700e08ba
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1 <tool id="fasta_add_barcode" name="Add barcodes" version="1.0">
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3 <description>to FASTA sequences</description>
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5 <requirements>
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6 </requirements>
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8 <stdio>
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9 </stdio>
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11 <version_command>python -version</version_command>
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13 <!--<command>-->
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14 <command><![CDATA[
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15 python $__tool_directory__/fasta_add_barcode.py
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16 --input_sequence_file $sequence_file
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17 --input_mapping_file $mapping_file
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18 --output_sequence_file $output_sequence_file
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19 ]]>
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20 </command>
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22 <inputs>
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23 <param name="sequence_file" type="data" format="fasta" label="Sequence
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24 zfile" help=""/>
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25 <param name="mapping_file" type="data" format="tabular"
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26 label="Mapping file between sequence identifier and barcode to add"
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27 help="The mapping file must be a tabular delimited file with
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28 two columns. The first column contains sequence identifier and
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29 the second column corresponding barcode to add at the beginning
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30 of each sequence."/>
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31 </inputs>
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33 <outputs>
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34 <data format="fasta" name="output_sequence_file" metadata_source="sequence_file"
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35 label="Sequences with added barcodes from ${on_string}" />
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36 </outputs>
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38 <tests>
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39 <test>
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40 <param name="sequence_file" value="input_sequences.fasta"/>
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41 <param name="mapping_file" value="mapping_file.txt"/>
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42 <output name="output_sequence_file" file="output_test.fasta" />
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43 </test>
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44 </tests>
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46 <help><![CDATA[
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48 **What it does**
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50 This tool takes a FASTA file and add at the beginning of each sequence a barcode.
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52 The barcode of each sequence is determined given its sequence identifier. The mapping between sequence identifier and corresponding barcode is defined inside the mapping file. This file must be a tabular delimited file with two columns: the first with sequence identifiers and the second the corresponding barcode.
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54 ]]>
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55 </help>
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57 <citations>
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58 </citations>
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59 </tool>
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