Mercurial > repos > drosofff > cherry_pick_fasta

annotate cherry_pick_fasta.xml @ 6:81acc77ee539 draft

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author drosofff
date Tue, 09 Jun 2015 03:43:54 -0400
parents e364eb867438
children 98ce1c31ea30
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1 <tool id="cherry_pick_fasta" name="Pick Fasta sequences" version="0.9.0">
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2 <description>with header satisfying a query string</description>
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3 <command interpreter="python">cherry_pick_fasta.py
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4 --input $input
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5 --query-string "$query"
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6 --output $output
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7 </command>
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9 <inputs>
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10 <param name="query" type="text" size="30" value="" label="Select sequences with this string in their header" help="exemple: gi|40557596">
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11 <sanitizer>
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12 <valid initial="string.printable">
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13 <remove value="&quot;"/>
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14 <remove value="\"/>
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15 </valid>
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16 <mapping initial="none">
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17 <add source="&quot;" target="\&quot;"/>
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18 <add source="\" target="\\"/>
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19 </mapping>
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20 </sanitizer>
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21 </param>
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22 <param format="fasta" label="Source file" name="input" type="data" />
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23 </inputs>
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24 <outputs>
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25 <data name="output" format="fasta" label="${tool.name} on ${on_string} including '${query.value}' in header" />
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26 </outputs>
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27 <tests>
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28 <test>
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29 <param ftype="fasta" name="input" value="input.fa" />
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30 <param name="query" value="AAR88092.1" />
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31 <output name="output" ftype="fasta" file="output.fa" />
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32 </test>
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33 </tests>
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34 <help>
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35 **What it does**
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36
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37 This tool retrieves nucleotide/peptide sequences from a fasta file whose headers match a given query string
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38
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39 It is Copyright © 2015 `CNRS and University Pierre et Marie Curie`_ and is released under the `MIT license`_.
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40
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41 .. _CNRS and University Pierre et Marie Curie: http://www.upmc.fr/en/index.html
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42 .. _MIT license: http://opensource.org/licenses/MIT
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43
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44 </help>
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45 <citations>
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46 <citation></citation>
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47 </citations>
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48 </tool>