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3
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1 <tool id="create_ribosome_profiles" name="Create Ribosome Profiles" version="1.a">
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0
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2 <description>Produce a sorted bed file from a sorted BAM file with the option of introducing an offset to the A-Site of a ribosome protected fragment.</description>
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3 <requirements>
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3
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4 <requirement type="package" version="1.73">biopython</requirement>
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0
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5 <requirement type="package" version="0.19.0">pysam</requirement>
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6 </requirements>
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1
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7 <command>python $__tool_directory__/bam_to_ribosome_profile.py ${input1} ${input2} ${input3} ${input4} ${output1}</command>
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0
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8 <inputs>
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9 <param name="input1" type="data" format="bam" label="BAM file to process"/>
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10 <param name="input2" type="integer" value="15" label="Offset to use" help="Use 15 for elongating ribosomes, 12 for initiating and 0 form RNA-seq reads"/>
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11 <param name="input3" type="data" format="fasta" label="FASTA file to which the reads were aligned"/>
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12 <param name="input4" type="select" label="Approach" help ="Use Offset for RNase and Weight for MNase">
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13 <option value="offset" selected="true">Use offset approach</option>
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14 <option value="weight">Use weight centered approach</option>
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15 </param>
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16 </inputs>
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17 <outputs>
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2
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18 <data name="output1" format="bed"/>
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0
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19 </outputs>
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20 <tests>
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21 <test>
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22 <param name="input1" value="test.bam.sorted"/>
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23 <param name="input2" value="15"/>
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24 <param name="input3" value="sacCer3_transcripts.fasta"/>
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25 <param name="input4" value="offset"/>
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2
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26 <output name="output1" file="test.bam.sorted.bed.sorted " ftype="bed" lines_diff="4" />
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0
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27 </test>
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28 </tests>
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29 <help>
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30 **What it does**
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31
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32 Produce a sorted bed file from a sorted BAM file with the option of introducing an offset to the A-Site of a ribosome protected fragment.
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33
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34 </help>
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35 <citations/>
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36 </tool>
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