Mercurial > repos > drosofff > cherry_pick_fasta
annotate cherry_pick_fasta.xml @ 0:c7a0ec8263b4 draft
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author | drosofff |
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date | Sun, 21 Jun 2015 14:30:50 -0400 |
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children | f7684171dab3 |
rev | line source |
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0
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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 $output |
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7 </command> |
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8 |
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9 <inputs> |
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10 <param name="query" type="text" size="30" value="" label="Select sequences with this string in their header" help="exemple: gi|40557596"> |
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11 <sanitizer> |
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12 <valid initial="string.printable"> |
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13 <remove value="""/> |
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14 <remove value="\"/> |
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15 </valid> |
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16 <mapping initial="none"> |
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17 <add source=""" target="\""/> |
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18 <add source="\" target="\\"/> |
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19 </mapping> |
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20 </sanitizer> |
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21 </param> |
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22 <param format="fasta" label="Source file" name="input" type="data" /> |
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23 </inputs> |
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24 <outputs> |
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25 <data name="output" format="fasta" label="${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="gi|81971654" /> |
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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> |