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1 <tool id="get_read_pipeline" name="Get RT Stop Counts" version="1.0">
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2 <description></description>
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3 <command interpreter="python">get_read.py $lib_file $map_file $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="1.7.1">numpy</requirement>
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7 <requirement type="package" version="0.1.18">samtools</requirement>
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8 </requirements>
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9 <inputs>
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10 <param name="lib_file" type="data" format="fasta" label="Reference genome/transcriptome"/>
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11 <param name="map_file" type="data" format="bam" label="Mapped file"/>
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12 </inputs>
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13 <outputs>
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14 <data name="output" format="txt"/>
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15 </outputs>
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16 <tests>
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17 <test>
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18 <param name="lib_file" value="test.bam" />
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19 <param name="map_file" value="com_rna.txt" />
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20 <output name="output" file="get_RT_stop_test.out" />
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21 </test>
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22 </tests>
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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. A mapped (bam) file from Bowtie (or any other mapping program)
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33 * 2. Reference library sequences (fasta) used to map the reads to
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34
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35 -----
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36
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37 **Output**:
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38
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39 A text file with reverse transcription stop counts mapped to each nucleotide (RTSC file)
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40
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41
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42
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43 </help>
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44 </tool>
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