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1 <tool id="pyCalculateChromosomeLengths" name="pyCalculateChromosomeLengths">
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2 <requirements>
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3 <requirement type="package">pyCRAC</requirement>
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4 </requirements>
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5 <command interpreter="python">
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6 /usr/local/bin/pyCalculateChromosomeLengths.py
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7 -f $ftype.input
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8 --file_type $ftype.filetype
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9 -o $output </command>
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10 <version_command>/usr/local/bin/pyCalculateChromosomeLengths.py --version</version_command>
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11 <inputs>
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12 <conditional name="ftype">
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13 <param name="filetype" type="select" label="File type">
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14 <option value="fasta" selected="true">Fasta</option>
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15 <option value="tab">Tab</option>
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16 </param>
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17 <when value="fasta">
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18 <param name="input" type="data" format="fasta" label="Input file" help="Fasta or Tab file"/>
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19 </when>
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20 <when value="tab">
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21 <param name="input" type="data" format="tabular" label="Input file" help="Fasta or Tab file"/>
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22 </when>
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23 </conditional>
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24 </inputs>
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25 <param name="label" type="text" format="txt" size="30" value="pyCalculateChromosomeLengths" label="Enter output file label -o" />
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26 <outputs>
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27 <data name="output" format="txt" label="${label.value}.len"/>
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28 </outputs>
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29 <help>
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30
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31 .. class:: infomark
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32
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33 **pyCalculateChromosomeLengths**
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34
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35 pyCalculateChromosomeLengths is part of the pyCRAC_ package. Takes a genome sequence in fasta or tab format and generates a tab-delimited file showing chromosome name and chromosome length.
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36
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37 .. _pyCRAC: http://sandergranneman.bio.ed.ac.uk/Granneman_Lab/pyCRAC_software.html
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38
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39 -------
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40
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41 **Parameter list**
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42
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43 Options::
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44
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45 -f chromosomes.fasta, --input_file=chromosomes.fasta
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46 provide the name and path of your fasta or tab genomic
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47 sequence file. Default is standard input.
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48 --file_type=fasta
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49 provide the file type (fasta or tab). Default is fasta
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50
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51 </help>
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52 </tool>
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53
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