Mercurial > repos > iuc > pe_histogram
annotate pe_histogram.xml @ 2:9be99db0304a draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 3954cb556516f7154287656f492e2e20e5776fb3
author | iuc |
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date | Tue, 11 Jul 2017 14:36:59 -0400 |
parents | b1a427b17e9c |
children | bd1416eea1f0 |
rev | line source |
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b1a427b17e9c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 37b1832f15c9960e02c6cae831b1f9f717818af8
iuc
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1 <tool id="pe_histogram" name="Paired-end histogram" version="1.0.1"> |
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2f6c7f82ad4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 05bab1b3b5838d62307a2d0d1172445b765b7f55
iuc
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2 <description>of insert size frequency</description> |
2f6c7f82ad4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 05bab1b3b5838d62307a2d0d1172445b765b7f55
iuc
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3 <requirements> |
1
b1a427b17e9c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 37b1832f15c9960e02c6cae831b1f9f717818af8
iuc
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4 <requirement type="package" version="8.0.112">openjdk</requirement> |
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2f6c7f82ad4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 05bab1b3b5838d62307a2d0d1172445b765b7f55
iuc
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5 </requirements> |
2
9be99db0304a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 3954cb556516f7154287656f492e2e20e5776fb3
iuc
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6 <command detect_errors="aggressive"><![CDATA[ |
9be99db0304a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 3954cb556516f7154287656f492e2e20e5776fb3
iuc
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7 ln -s '${input_bam}' localbam.bam && |
9be99db0304a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 3954cb556516f7154287656f492e2e20e5776fb3
iuc
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8 ln -f -s '${input_bam.metadata.bam_index}' localbam.bam.bai && |
9be99db0304a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 3954cb556516f7154287656f492e2e20e5776fb3
iuc
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9 java -jar '$__tool_directory__/PEHistogram.jar' |
9be99db0304a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 3954cb556516f7154287656f492e2e20e5776fb3
iuc
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10 -B localbam.bam |
9be99db0304a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 3954cb556516f7154287656f492e2e20e5776fb3
iuc
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11 -I localbam.bam.bai |
9be99db0304a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 3954cb556516f7154287656f492e2e20e5776fb3
iuc
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12 #if str($lower_limit): |
9be99db0304a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 3954cb556516f7154287656f492e2e20e5776fb3
iuc
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13 -l $lower_limit |
9be99db0304a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 3954cb556516f7154287656f492e2e20e5776fb3
iuc
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14 #end if |
9be99db0304a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 3954cb556516f7154287656f492e2e20e5776fb3
iuc
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15 #if str($upper_limit): |
9be99db0304a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 3954cb556516f7154287656f492e2e20e5776fb3
iuc
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16 -u $upper_limit |
9be99db0304a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 3954cb556516f7154287656f492e2e20e5776fb3
iuc
parents:
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17 #end if |
9be99db0304a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 3954cb556516f7154287656f492e2e20e5776fb3
iuc
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18 -p '$output1' |
9be99db0304a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 3954cb556516f7154287656f492e2e20e5776fb3
iuc
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19 -t '$output2' |
9be99db0304a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 3954cb556516f7154287656f492e2e20e5776fb3
iuc
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20 1>/dev/null |
9be99db0304a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 3954cb556516f7154287656f492e2e20e5776fb3
iuc
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21 ]]></command> |
0
2f6c7f82ad4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 05bab1b3b5838d62307a2d0d1172445b765b7f55
iuc
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22 <inputs> |
2f6c7f82ad4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 05bab1b3b5838d62307a2d0d1172445b765b7f55
iuc
parents:
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23 <param name="input_bam" type="data" format="bam" label="BAM file" /> |
2f6c7f82ad4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 05bab1b3b5838d62307a2d0d1172445b765b7f55
iuc
parents:
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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."/> |
2f6c7f82ad4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 05bab1b3b5838d62307a2d0d1172445b765b7f55
iuc
parents:
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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." /> |
2f6c7f82ad4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 05bab1b3b5838d62307a2d0d1172445b765b7f55
iuc
parents:
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26 </inputs> |
2f6c7f82ad4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 05bab1b3b5838d62307a2d0d1172445b765b7f55
iuc
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27 <outputs> |
2f6c7f82ad4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 05bab1b3b5838d62307a2d0d1172445b765b7f55
iuc
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28 <data name="output1" format="png" /> |
2f6c7f82ad4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 05bab1b3b5838d62307a2d0d1172445b765b7f55
iuc
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29 <data name="output2" format="tabular" /> |
2f6c7f82ad4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 05bab1b3b5838d62307a2d0d1172445b765b7f55
iuc
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30 </outputs> |
2f6c7f82ad4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 05bab1b3b5838d62307a2d0d1172445b765b7f55
iuc
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31 <tests> |
2f6c7f82ad4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 05bab1b3b5838d62307a2d0d1172445b765b7f55
iuc
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32 <test> |
2f6c7f82ad4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 05bab1b3b5838d62307a2d0d1172445b765b7f55
iuc
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33 <param name="input_bam" value="input.bam" ftype="bam" /> |
2f6c7f82ad4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 05bab1b3b5838d62307a2d0d1172445b765b7f55
iuc
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34 <output name="output1" file="output1.png" ftype="png" compare="sim_size" /> |
2f6c7f82ad4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 05bab1b3b5838d62307a2d0d1172445b765b7f55
iuc
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35 <output name="output2" file="output1.tabular" ftype="tabular" compare="contains" /> |
2f6c7f82ad4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 05bab1b3b5838d62307a2d0d1172445b765b7f55
iuc
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36 </test> |
2f6c7f82ad4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 05bab1b3b5838d62307a2d0d1172445b765b7f55
iuc
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37 <test> |
2f6c7f82ad4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 05bab1b3b5838d62307a2d0d1172445b765b7f55
iuc
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38 <param name="input_bam" value="input.bam" ftype="bam" /> |
2f6c7f82ad4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 05bab1b3b5838d62307a2d0d1172445b765b7f55
iuc
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39 <param name="lower_limit" value="200" /> |
2f6c7f82ad4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 05bab1b3b5838d62307a2d0d1172445b765b7f55
iuc
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40 <param name="upper_limit" value="300" /> |
2f6c7f82ad4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 05bab1b3b5838d62307a2d0d1172445b765b7f55
iuc
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41 <output name="output1" file="output2.png" ftype="png" compare="sim_size" /> |
2f6c7f82ad4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 05bab1b3b5838d62307a2d0d1172445b765b7f55
iuc
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42 <output name="output2" file="output2.tabular" ftype="tabular" compare="contains" /> |
2f6c7f82ad4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 05bab1b3b5838d62307a2d0d1172445b765b7f55
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43 </test> |
2f6c7f82ad4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 05bab1b3b5838d62307a2d0d1172445b765b7f55
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44 </tests> |
2f6c7f82ad4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 05bab1b3b5838d62307a2d0d1172445b765b7f55
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45 <help> |
2f6c7f82ad4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 05bab1b3b5838d62307a2d0d1172445b765b7f55
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46 |
2f6c7f82ad4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 05bab1b3b5838d62307a2d0d1172445b765b7f55
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47 **What it does** |
2f6c7f82ad4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 05bab1b3b5838d62307a2d0d1172445b765b7f55
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48 |
2f6c7f82ad4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 05bab1b3b5838d62307a2d0d1172445b765b7f55
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49 Produces an insert size histogram and basic statistics for a paired-end BAM file. Two outputs are produced: |
2f6c7f82ad4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 05bab1b3b5838d62307a2d0d1172445b765b7f55
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50 |
2f6c7f82ad4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 05bab1b3b5838d62307a2d0d1172445b765b7f55
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51 - a png image consisting of the histogram of the insert size frequency |
2f6c7f82ad4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 05bab1b3b5838d62307a2d0d1172445b765b7f55
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52 - a tabular file containing the alignment statistics |
2f6c7f82ad4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 05bab1b3b5838d62307a2d0d1172445b765b7f55
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53 |
2f6c7f82ad4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 05bab1b3b5838d62307a2d0d1172445b765b7f55
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54 ----- |
2f6c7f82ad4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 05bab1b3b5838d62307a2d0d1172445b765b7f55
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55 |
2f6c7f82ad4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 05bab1b3b5838d62307a2d0d1172445b765b7f55
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56 **Options** |
2f6c7f82ad4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 05bab1b3b5838d62307a2d0d1172445b765b7f55
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57 |
2f6c7f82ad4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 05bab1b3b5838d62307a2d0d1172445b765b7f55
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58 * **Lower bp limit** - the lower bp limit on insert size for calculating the histogram. |
2f6c7f82ad4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 05bab1b3b5838d62307a2d0d1172445b765b7f55
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59 * **Upper bp limit** - the upper bp limit on insert size for calculating the histogram. |
2f6c7f82ad4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 05bab1b3b5838d62307a2d0d1172445b765b7f55
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60 |
2f6c7f82ad4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 05bab1b3b5838d62307a2d0d1172445b765b7f55
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61 </help> |
2f6c7f82ad4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 05bab1b3b5838d62307a2d0d1172445b765b7f55
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62 <citations> |
2f6c7f82ad4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 05bab1b3b5838d62307a2d0d1172445b765b7f55
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63 <citation type="bibtex"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 05bab1b3b5838d62307a2d0d1172445b765b7f55
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64 @unpublished{None, |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 05bab1b3b5838d62307a2d0d1172445b765b7f55
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65 author = {Lai, William}, |
2f6c7f82ad4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 05bab1b3b5838d62307a2d0d1172445b765b7f55
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66 title = {None}, |
2f6c7f82ad4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 05bab1b3b5838d62307a2d0d1172445b765b7f55
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67 year = {None}, |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 05bab1b3b5838d62307a2d0d1172445b765b7f55
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68 eprint = {None}, |
2f6c7f82ad4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 05bab1b3b5838d62307a2d0d1172445b765b7f55
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69 url = {http://www.huck.psu.edu/content/research/independent-centers-excellence/center-for-eukaryotic-gene-regulation} |
2f6c7f82ad4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 05bab1b3b5838d62307a2d0d1172445b765b7f55
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70 }</citation> |
2f6c7f82ad4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 05bab1b3b5838d62307a2d0d1172445b765b7f55
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71 </citations> |
2f6c7f82ad4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 05bab1b3b5838d62307a2d0d1172445b765b7f55
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72 </tool> |