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annotate rename_scaffold.xml @ 0:1a0e39acb62f draft

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author yating-l
date Mon, 19 Dec 2016 17:14:55 -0500
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1 <tool id="rename_scaffold" name="rename the scaffolds" version="0.1.0">
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2 <description>Rename the scaffolds so that they won't exceed 31 characters</description>
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3 <stdio>
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4 <exit_code range="1:" />
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5 </stdio>
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6 <command><![CDATA[
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7 python $__tool_directory__/rename.py $input $output $index
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8 ]]></command>
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9 <inputs>
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10 <param name="input" type="data" format="fasta"/>
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11 </inputs>
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12 <outputs>
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13 <data name="output" format="fasta" label="${tool.name} on ${on_string}: renamed_reference" />
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14 <data name="index" format="fasta" label="${tool.name} on ${on_string}: name mapping"/>
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15 </outputs>
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16 <tests>
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17 <test>
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18 <!-- Test with Dbia3.fa -->
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19 <param name="input" value="Dbia3.fa" />
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20 <output name="output" file="Dbia3_renamed.fa"/>
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21 <output name="index" file="Dbia3_index.fa"/>
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22 </test>
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23 </tests>
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24 <help><![CDATA[
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25 This tool is to rename scaffolds in reference genome so that the sequence names are less than 31 characters. Rename all scaffolds to scaffold_1, scaffold_2, ..., scaffold_N and provide a name mapping file
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26
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27 ]]></help>
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28 <citations>
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29 </citations>
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30 </tool>