Mercurial > repos > galaxyp > filter_by_fasta_ids
annotate filter_by_fasta_ids.xml @ 1:8d15aebf55fd draft
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author | galaxyp |
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date | Tue, 24 May 2016 13:05:22 -0400 |
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children | 1bd985f14938 |
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1 <tool id="filter_by_fasta_ids" version="1.0" name="Filter by FASTA IDs"> |
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2 <description>Extract sequences from a FASTA file based on a list of IDs</description> |
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3 <command> |
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4 <![CDATA[ |
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5 python $__tool_directory__/filter_by_fasta_ids.py |
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6 $dedup |
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7 '$identifiers' |
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8 '$input' |
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9 '$output' |
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10 ]]> |
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11 </command> |
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12 <inputs> |
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13 <param format="fasta" name="input" type="data" label="FASTA sequences"/> |
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14 <param format="txt" name="identifiers" type="data" label="List of IDs to extract sequences for"/> |
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15 <param name="dedup" type="boolean" truevalue="--dedup" falsevalue="" checked="true" label="Remove duplicate sequences" /> |
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16 </inputs> |
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17 <outputs> |
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18 <data format="fasta" name="output" label="FASTA sequences for ${identifiers.name}"/> |
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19 </outputs> |
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20 <tests> |
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21 <test> |
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22 <param name="input" ftype="fasta" value="input.fasta" /> |
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23 <param name="identifiers" ftype="txt" value="ids.txt" /> |
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24 <output name="output" file="output_dedup.fasta" /> |
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25 </test> |
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26 <test> |
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27 <param name="input" ftype="fasta" value="input.fasta" /> |
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28 <param name="identifiers" ftype="txt" value="ids.txt" /> |
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29 <param name="dedup" value="False" /> |
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30 <output name="output" file="output_not_dedup.fasta" /> |
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31 </test> |
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32 </tests> |
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33 <help> |
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34 <![CDATA[ |
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35 **What it does** |
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36 |
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37 Extract sequences from a FASTA file based on a list of IDs. |
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38 ]]> |
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39 </help> |
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40 </tool> |