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1 <tool id="find_motif" name="findMotif" version="1.0.0">
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2 <description>Find specified motif in sequence</description>
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3 <command>findMotif -motif="$motif" "$input1"
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4 #if str( $options_type.options_type_selector ) == "advanced":
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5 -chr="${options_type.chr}"
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6 -strand="${options_type.strand}
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7 "${options_type.wigOutput}"
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8 #end if
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9 > "$output"
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10 </command>
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11 <inputs>
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12 <param format="fasta" name="input1" type="data" label="Sequences"/>
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13 <param name="motif" type="text" value="acgt" size="17" />
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14
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15 <conditional name="options_type">
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16 <param name="options_type_selector" type="select" label="Options Configuration">
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17 <option value="basic" selected="true">Basic</option>
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18 <option value="advanced">Advanced</option>
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19 </param>
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20 <when value="basic">
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21 <!-- do nothing here -->
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22 </when>
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23 <when value="advanced">
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24
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25 <param name="chr" size="6" type="integer" value="1" label="Process only this chr from the sequence"/>
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26 <param name="strand" type="select" label="Limit to only one strand">
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27 <option value="+">+</option>
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28 <option value="-">-</option>
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29 </param>
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30 <param name="wigOutput" label="Output wiggle data format instead of bed file" type="boolean" truevalue="-wigOutput" falsevalue="" checked="False"/>
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31 </when>
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32 </conditional>
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33 </inputs>
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34 <outputs>
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35 <data format="bed" name="output" label="${tool.name} on ${on_string} (bed)"/>
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36 </outputs>
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37
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38 <tests>
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39 <test>
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40 <param name="input1" value="find_motif_input.fa"/>
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41 <output name="output" file="find_motif__output.bed"/>
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42 </test>
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43 </tests>
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44
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45 <help>
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46 Find specified motif in a sequence from a FASTA file.
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47 </help>
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48
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49 </tool>
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50
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