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4
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1 <tool id="create_ribosome_profiles" name="Create Ribosome Profiles" version="1.1">
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8
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2 <description>Produce a Sorted BED File of A-Site profiles of RPFs.</description>
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0
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3 <requirements>
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4
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4 <requirement type="package" version="1.79">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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4
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7 <command>python $__tool_directory__/bam_to_ribosome_profile.py ${input1} ${input2} $refGenomeSource.genomeSource
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8 #if $refGenomeSource.genomeSource == "builtin":
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9 none ${refGenomeSource.input1_builtin.fields.path} ${input4} ${output1}
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10 #else:
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11 ${refGenomeSource.input1_file} none ${input4} ${output1}
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12 #end if
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13 </command>
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0
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14 <inputs>
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6
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15 <param name="input1" type="data" format="bam" label="BAM file to process"/>
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16 <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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5
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17 <conditional name="refGenomeSource">
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18 <param name="genomeSource" type="select" label="Will you select a reference from your history or use a built-in FASTA?">
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19 <option value="builtin">Use a built-in FASTA</option>
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20 <option value="history">Use one from the history</option>
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4
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21 </param>
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5
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22 <when value="builtin">
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23 <param name="input1_builtin" type="select" format="fasta" label="Select a reference" help="if your reference of interest is not listed - contact RiboGalaxy team">
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24 <options from_data_table="builtin_fastas">
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25 <filter type="sort_by" column="2" />
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26 <validator type="no_options" message="No built-ins are available" />
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27 </options>
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28 </param>
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29 </when>
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30 <when value="history">
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31 <param name="input1_file" type="data" format="fasta" label="FASTA File" />
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32 </when>
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33 </conditional>
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0
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34 <param name="input4" type="select" label="Approach" help ="Use Offset for RNase and Weight for MNase">
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35 <option value="offset" selected="true">Use offset approach</option>
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36 <option value="weight">Use weight centered approach</option>
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37 </param>
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38 </inputs>
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39 <outputs>
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2
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40 <data name="output1" format="bed"/>
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0
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41 </outputs>
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42 <tests>
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43 <test>
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44 <param name="input1" value="test.bam.sorted"/>
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45 <param name="input2" value="15"/>
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46 <param name="input3" value="sacCer3_transcripts.fasta"/>
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47 <param name="input4" value="offset"/>
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2
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48 <output name="output1" file="test.bam.sorted.bed.sorted " ftype="bed" lines_diff="4" />
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0
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49 </test>
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50 </tests>
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51 <help>
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52 **What it does**
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53
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54 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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55
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56 </help>
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57 <citations/>
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58 </tool>
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