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1 <tool id="pe_histogram" name="Paired-end histogram" version="1.0.0">
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2 <description>of insert size frequency</description>
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3 <requirements>
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4 <requirement type="package" version="8.0.45">java-jdk</requirement>
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5 </requirements>
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6 <stdio>
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7 <!-- Anything other than zero is an error -->
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8 <exit_code range=":-1" />
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9 <exit_code range="1:" />
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10 <!-- Check stderr in case the return code has not been set -->
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11 <regex match="Error:" />
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12 <regex match="Exception:" />
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13 </stdio>
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14 <command>
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15 <![CDATA[
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16 ln -s "${input_bam}" "localbam.bam" &&
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17 ln -f -s "${input_bam.metadata.bam_index}" "localbam.bam.bai" &&
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18 java -jar $__tool_directory__/PEHistogram.jar
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19 -B "localbam.bam"
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20 -I "localbam.bam.bai"
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21 #if str($lower_limit) != '':
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22 -l $lower_limit
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23 #end if
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24 #if str($upper_limit) != '':
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25 -u $upper_limit
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26 #end if
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27 -p "$output1"
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28 -t "$output2" 1>/dev/null
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29 ]]>
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30 </command>
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31 <inputs>
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32 <param name="input_bam" type="data" format="bam" label="BAM file" />
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33 <param name="lower_limit" type="integer" value="" optional="True" min="0" label="Lower bp limit (optional)" help="The lower bp limit on insert size for calculating the histogram."/>
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34 <param name="upper_limit" type="integer" value="" optional="True" min="0" label="Upper bp limit (optional)" help="The upper bp limit on insert size for calculating the histogram." />
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35 </inputs>
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36 <outputs>
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37 <data name="output1" format="png" />
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38 <data name="output2" format="tabular" />
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39 </outputs>
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40 <tests>
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41 <test>
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42 <param name="input_bam" value="input.bam" ftype="bam" />
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43 <output name="output1" file="output1.png" ftype="png" compare="sim_size" />
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44 <output name="output2" file="output1.tabular" ftype="tabular" compare="contains" />
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45 </test>
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46 <test>
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47 <param name="input_bam" value="input.bam" ftype="bam" />
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48 <param name="lower_limit" value="200" />
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49 <param name="upper_limit" value="300" />
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50 <output name="output1" file="output2.png" ftype="png" compare="sim_size" />
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51 <output name="output2" file="output2.tabular" ftype="tabular" compare="contains" />
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52 </test>
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53 </tests>
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54 <help>
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55
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56 **What it does**
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57
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58 Produces an insert size histogram and basic statistics for a paired-end BAM file. Two outputs are produced:
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59
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60 - a png image consisting of the histogram of the insert size frequency
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61 - a tabular file containing the alignment statistics
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62
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63 -----
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64
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65 **Options**
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66
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67 * **Lower bp limit** - the lower bp limit on insert size for calculating the histogram.
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68 * **Upper bp limit** - the upper bp limit on insert size for calculating the histogram.
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69
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70 </help>
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71 <citations>
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72 <citation type="bibtex">
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73 @unpublished{None,
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74 author = {Lai, William},
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75 title = {None},
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76 year = {None},
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77 eprint = {None},
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78 url = {http://www.huck.psu.edu/content/research/independent-centers-excellence/center-for-eukaryotic-gene-regulation}
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79 }</citation>
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80 </citations>
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81 </tool>
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