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1 <tool id="react_cal_pipeline" name="Reactivity calculation" version="1.0">
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2 <description></description>
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3 <command interpreter="python">react_cal.py $dist_file1 $dist_file2 $seq_file $nt_spec $flag_in $threshold $output </command>
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4 <requirements>
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5 <requirement type="package" version="1.61">biopython</requirement>
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6 <requirement type="package" version="1.7">numpy</requirement>
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7 </requirements>
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8 <inputs>
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9 <param name="dist_file1" type="data" format="txt" label="RTSC file for (+) library"/>
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10 <param name="dist_file2" type="data" format="txt" label="RTSC file for (-) library"/>
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11 <param name="seq_file" type="data" format="fasta" label="Reference library"/>
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12 <param name="nt_spec" type="select" label="Nucleotide specificity">
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13 <option value="AC">AC</option>
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14 <option value="ATCG">AUCG</option>
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15 </param>
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16 <param name="flag_in" type="boolean" checked="true" truevalue = "1" falsevalue = "0" label="Normalization is performed if checked"/>
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17 <param name="threshold" type="float" value = "7" optional = "true" label="Value to cap the reactivities"/>
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18 </inputs>
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19 <outputs>
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20 <data name="output" format="txt"/>
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21 </outputs>
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22
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23 <help>
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24
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25
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26 **TIPS**:
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27
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28 -----
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29
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30 **Input**:
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31
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32 * 1. RTSC files (Output of II) for (+) and (-) library
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33 * 2. Reference file (fasta) used to map the reads
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34 * 3. Nucleotide Specificity (Type of nucleotide to have reactivity, e.g. AC for DMS and ACTG for SHAPE)
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35 * [Optional]:
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36 * 1. A threshold to cap the structural reactivities. {Default: 7}
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37 * 2. Flag that determines whether to perform 2%-8% normalization {Default: yes}
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38
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39 -----
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40
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41 **Output**:
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42
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43 A text file with structural reactivity for each nucleotide (Reactivity file)
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44
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45
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46
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47 </help>
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48 </tool>
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