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1 <tool id="region_motif_intersect" name="Region Motif Intersect">
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2 <description>for computing the motifs that lie inside a region set</description>
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3 <command interpreter="Rscript">
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4 region_motif_intersect.r --args $bgz_file.fields.path $tbi_file.fields.path $in_bed $out_tab
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5 </command>
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6 <inputs>
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7 <param name="in_bed" type="data" format="bed" label="Input BED File" />
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8
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9 <param name="bgz_file" type="select" label="Using motif database BGZ file">
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10 <options from_data_table="motif_databases"/>
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11 </param>
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12 <param name="tbi_file" type="select" label="Using motif database TBI file">
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13 <options from_data_table="motif_databases"/>
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14 </param>
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15
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16 <!--<param name="db_type" type="select" label="Select Motif Database" >
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17 <option value="t">Test Encode Motifs (hg19)</option>
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18 <option value="e">Encode Motifs (hg19)</option>
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19 <option value="j">Jaspar and Jolma Motifs (hg19)</option>
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20 <option value="m">Mouse Motifs (mm9)</option>
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21 </param>-->
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22 </inputs>
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23 <outputs>
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24 <data name="out_tab" format="tabular" />
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25 </outputs>
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26
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27 <tests>
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28 <test>
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29 <param name="in_bed" value="XXX.bed" />
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30 <param name="bgz_file" value="XXX" />
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31 <param name="tbi_file" value="XXX" />
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32 <output name="output" file="XXX.tab" />
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33 </test>
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34 <test>
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35 <param name="in_bed" value="XXX.bed" />
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36 <param name="bgz_file" value="XXX" />
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37 <param name="tbi_file" value="XXX" />
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38 <output name="out_tab" file="XXX.tab" />
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39 </test>
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40 </tests>
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41
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42 <help>
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43 This tool computes the motifs and the number of motifs that intersect
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44 any region in a input set of regions.
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45 </help>
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46
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47 </tool> |
