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1 <tool id="pyFasta2Tab" name="pyFasta2Tab">
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2 <description>converter</description>
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3 <requirements>
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4 <requirement type="package">pyCRAC</requirement>
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5 </requirements>
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6 <command interpreter="python">/usr/local/bin/pyFasta2tab.py -f $input -o $output
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7 </command>
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8 <version_command>/usr/local/bin/pyFasta2tab.py --version</version_command>
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9 <inputs>
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10 <param name="input" type="data" format="fasta" label="Fasta file -f"/>
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11 </inputs>
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12 <param name="label" type="text" format="txt" size="30" value="pyFasta2Tab" label="Enter output file label -o" />
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13 <outputs>
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14 <data name="output" format="tabular" label="${label.value}.tab"/>
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15 </outputs>
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16 <help>
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17
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18 .. class:: infomark
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19
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20 **pyFasta2Tab**
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21
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22 pyFasta2Tab is part of the pyCRAC_ package. Converts fasta to tabular format. Is used to convert your reference sequences in fasta format to the tabular format that pyCRAC uses for almost all tools.
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23
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24 Example::
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25
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26 >sequence1
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27 ATAGGATACATAACCATATTATGAGACC
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28
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29 Is converted into::
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30
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31 sequence1 ATAGGATACATAACCATATTATGAGACC
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32
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33 The pyCRAC package lo
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34
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35 .. _pyCRAC: http://sandergranneman.bio.ed.ac.uk/Granneman_Lab/pyCRAC_software.html
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36
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37 -------
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38
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39 **Parameter list**
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40
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41 Options::
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42
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43 -f fasta_file, --input_file=fasta_file
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44 provide the name and path of your fasta input file.
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45 Default is standard input.
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46
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47
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48
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49 </help>
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50 </tool>
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51
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