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1 <tool id="pfamScam" name="PFAM Annotator">
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2 <description>Annotate PFAM domains. </description>
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3 <command> /home/inmare/galaxy/tools/pfamScan/pfam_scan.pl -fasta $input -cpu 2 -dir /home/inmare/galaxy/tools/pfamScan/hmm > $output</command>
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4
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5 <inputs>
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6 <param format="fasta" name="input" type="data" label="Source file"/>
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7 </inputs>
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8
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9 <outputs>
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10 <data format="tabular" name="output" />
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11 </outputs>
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12
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13 <tests>
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14 <test>
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15 <param name="input" value="htt.fas"/>
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16 <output name="out_file1" file="htt.dom.txt"/>
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17 </test>
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18 </tests>
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19 <citations>
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20 Predicting active site residue annotations in the Pfam database.
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21 (2007) BMC bioinformatics 8 :298
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22 PMID: 17688688
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23
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24 The EMBL-EBI bioinformatics web and programmatic tools framework.
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25 (2015 July 01) Nucleic acids research 43 (W1) :W580-4
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26 PMID: 25845596
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27
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28 </citations>
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29 <help>
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30 The pfam_scan.pl script is used to annotate PFAM domains on the input file sequences. Only PFAM A class domains are predicted. See http://www.ebi.ac.uk/Tools/pfa/pfamscan/help/ for instructions on how to obtain pfamSCAN and for a brief description of the output format.
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31 </help>
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32 </tool>
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