Mercurial > repos > iuc > pe_histogram

annotate pe_histogram.xml @ 3:99c86046c72a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 3954cb556516f7154287656f492e2e20e5776fb3
author iuc
date Tue, 11 Jul 2017 14:36:43 -0400
parents d23480305b5a
children 784273cfcebc
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d23480305b5a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 37b1832f15c9960e02c6cae831b1f9f717818af8
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1 <tool id="pe_histogram" name="Paired-end histogram" version="1.0.1">
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2 <description>of insert size frequency</description>
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3 <requirements>
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d23480305b5a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 37b1832f15c9960e02c6cae831b1f9f717818af8
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4 <requirement type="package" version="8.0.112">openjdk</requirement>
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5 </requirements>
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99c86046c72a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 3954cb556516f7154287656f492e2e20e5776fb3
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6 <command detect_errors="aggressive"><![CDATA[
99c86046c72a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 3954cb556516f7154287656f492e2e20e5776fb3
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7 ln -s '${input_bam}' localbam.bam &&
99c86046c72a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 3954cb556516f7154287656f492e2e20e5776fb3
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8 ln -f -s '${input_bam.metadata.bam_index}' localbam.bam.bai &&
99c86046c72a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 3954cb556516f7154287656f492e2e20e5776fb3
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9 java -jar '$__tool_directory__/PEHistogram.jar'
99c86046c72a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 3954cb556516f7154287656f492e2e20e5776fb3
iuc
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10 -B localbam.bam
99c86046c72a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 3954cb556516f7154287656f492e2e20e5776fb3
iuc
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11 -I localbam.bam.bai
99c86046c72a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 3954cb556516f7154287656f492e2e20e5776fb3
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12 #if str($lower_limit):
99c86046c72a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 3954cb556516f7154287656f492e2e20e5776fb3
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13 -l $lower_limit
99c86046c72a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 3954cb556516f7154287656f492e2e20e5776fb3
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14 #end if
99c86046c72a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 3954cb556516f7154287656f492e2e20e5776fb3
iuc
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15 #if str($upper_limit):
99c86046c72a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 3954cb556516f7154287656f492e2e20e5776fb3
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16 -u $upper_limit
99c86046c72a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 3954cb556516f7154287656f492e2e20e5776fb3
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17 #end if
99c86046c72a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 3954cb556516f7154287656f492e2e20e5776fb3
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18 -p '$output1'
99c86046c72a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 3954cb556516f7154287656f492e2e20e5776fb3
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19 -t '$output2'
99c86046c72a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 3954cb556516f7154287656f492e2e20e5776fb3
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20 1>/dev/null
99c86046c72a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 3954cb556516f7154287656f492e2e20e5776fb3
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21 ]]></command>
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22 <inputs>
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23 <param name="input_bam" type="data" format="bam" label="BAM file" />
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24 <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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25 <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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26 </inputs>
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27 <outputs>
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28 <data name="output1" format="png" />
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29 <data name="output2" format="tabular" />
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30 </outputs>
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31 <tests>
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32 <test>
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33 <param name="input_bam" value="input.bam" ftype="bam" />
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34 <output name="output1" file="output1.png" ftype="png" compare="sim_size" />
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35 <output name="output2" file="output1.tabular" ftype="tabular" compare="contains" />
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36 </test>
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37 <test>
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38 <param name="input_bam" value="input.bam" ftype="bam" />
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39 <param name="lower_limit" value="200" />
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40 <param name="upper_limit" value="300" />
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41 <output name="output1" file="output2.png" ftype="png" compare="sim_size" />
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42 <output name="output2" file="output2.tabular" ftype="tabular" compare="contains" />
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43 </test>
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44 </tests>
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45 <help>
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46
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47 **What it does**
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48
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49 Produces an insert size histogram and basic statistics for a paired-end BAM file. Two outputs are produced:
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50
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51 - a png image consisting of the histogram of the insert size frequency
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52 - a tabular file containing the alignment statistics
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53
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54 -----
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55
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56 **Options**
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57
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58 * **Lower bp limit** - the lower bp limit on insert size for calculating the histogram.
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59 * **Upper bp limit** - the upper bp limit on insert size for calculating the histogram.
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60
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61 </help>
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62 <citations>
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63 <citation type="bibtex">
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64 @unpublished{None,
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65 author = {Lai, William},
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66 title = {None},
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67 year = {None},
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68 eprint = {None},
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69 url = {http://www.huck.psu.edu/content/research/independent-centers-excellence/center-for-eukaryotic-gene-regulation}
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70 }</citation>
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71 </citations>
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72 </tool>