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1 <tool id="bed_to_bigwig" name="bed_to_bigwig">
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2 <description>make bigwig from BED or BAM</description>
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3 <command interpreter="sh"> bed_to_bigwig.sh $input $outfile
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4 #if $inputa_format.bedorbam == "bed":
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5 bed
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6 #else:
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7 bam
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8 #end if
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9 $sorted $genome none $split >$log 2> $log </command>
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10 <inputs>
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11 <conditional name="inputa_format">
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12 <param name="bedorbam" type="select" label="Select input format" >
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13 <option value="bed" selected="true">BED</option>
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14 <option value="bam"> BAM</option>
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15 </param>
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16 <when value="bed">
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17 <param name="input" type="data" format="bed" label="Input file"/>
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18 </when>
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19 <when value="bam">
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20 <param name="input" type="data" format="bam" label="Input file"/>
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21 </when>
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22 </conditional>
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23 <param name="genome" type="select" label="Select chromsome size file" >
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24 <options from_file="chrsize.loc">
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25 <column name="name" index="0"/>
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26 <column name="value" index="1"/>
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27 </options>
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28 </param>
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29
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30 <param name="sorted" label="Check if the input is sorted" type="boolean" truevalue="sorted" falsevalue="none" checked="False"/>
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31 <param name="split" label="Split junctions" help="Treat 'split' BAM or BED12 entries as distinct BED intervals." type="boolean" truevalue="-split" falsevalue="" checked="False"/>
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32 </inputs>
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33 <outputs>
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34 <data format="txt" name="log" label="makebigwig LOG" />
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35 <data format="bigwig" name="outfile" />
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36
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37 </outputs>
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38 </tool>
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