Mercurial > repos > iuc > pe_histogram
annotate pe_histogram.xml @ 3:bd1416eea1f0 draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 4731e16b619f4ea176b6f68e34b8f9f9ac1a776c"
author | iuc |
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date | Wed, 04 Dec 2019 08:18:34 -0500 |
parents | 9be99db0304a |
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rev | line source |
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1
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"> |
0
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> |
3
bd1416eea1f0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 4731e16b619f4ea176b6f68e34b8f9f9ac1a776c"
iuc
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4 <requirement type="package" version="11.0.1">openjdk</requirement> |
bd1416eea1f0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 4731e16b619f4ea176b6f68e34b8f9f9ac1a776c"
iuc
parents:
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5 <requirement type="package" version="1">fonts-conda-ecosystem</requirement> |
0
2f6c7f82ad4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 05bab1b3b5838d62307a2d0d1172445b765b7f55
iuc
parents:
diff
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6 </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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7 <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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8 ln -s '${input_bam}' localbam.bam && |
9be99db0304a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 3954cb556516f7154287656f492e2e20e5776fb3
iuc
parents:
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9 ln -f -s '${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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10 java -jar '$__tool_directory__/PEHistogram.jar' |
9be99db0304a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 3954cb556516f7154287656f492e2e20e5776fb3
iuc
parents:
1
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11 -B localbam.bam |
9be99db0304a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 3954cb556516f7154287656f492e2e20e5776fb3
iuc
parents:
1
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12 -I localbam.bam.bai |
9be99db0304a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 3954cb556516f7154287656f492e2e20e5776fb3
iuc
parents:
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13 #if str($lower_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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14 -l $lower_limit |
9be99db0304a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 3954cb556516f7154287656f492e2e20e5776fb3
iuc
parents:
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15 #end if |
9be99db0304a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 3954cb556516f7154287656f492e2e20e5776fb3
iuc
parents:
1
diff
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16 #if str($upper_limit): |
9be99db0304a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 3954cb556516f7154287656f492e2e20e5776fb3
iuc
parents:
1
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17 -u $upper_limit |
9be99db0304a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 3954cb556516f7154287656f492e2e20e5776fb3
iuc
parents:
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18 #end if |
9be99db0304a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 3954cb556516f7154287656f492e2e20e5776fb3
iuc
parents:
1
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19 -p '$output1' |
9be99db0304a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 3954cb556516f7154287656f492e2e20e5776fb3
iuc
parents:
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20 -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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21 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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22 ]]></command> |
0
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 <inputs> |
2f6c7f82ad4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 05bab1b3b5838d62307a2d0d1172445b765b7f55
iuc
parents:
diff
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24 <param name="input_bam" type="data" format="bam" label="BAM file" /> |
3
bd1416eea1f0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 4731e16b619f4ea176b6f68e34b8f9f9ac1a776c"
iuc
parents:
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25 <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."/> |
bd1416eea1f0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 4731e16b619f4ea176b6f68e34b8f9f9ac1a776c"
iuc
parents:
2
diff
changeset
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26 <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." /> |
0
2f6c7f82ad4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 05bab1b3b5838d62307a2d0d1172445b765b7f55
iuc
parents:
diff
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27 </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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28 <outputs> |
2f6c7f82ad4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 05bab1b3b5838d62307a2d0d1172445b765b7f55
iuc
parents:
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29 <data name="output1" format="png" /> |
2f6c7f82ad4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 05bab1b3b5838d62307a2d0d1172445b765b7f55
iuc
parents:
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30 <data name="output2" format="tabular" /> |
2f6c7f82ad4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 05bab1b3b5838d62307a2d0d1172445b765b7f55
iuc
parents:
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31 </outputs> |
2f6c7f82ad4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 05bab1b3b5838d62307a2d0d1172445b765b7f55
iuc
parents:
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32 <tests> |
2f6c7f82ad4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 05bab1b3b5838d62307a2d0d1172445b765b7f55
iuc
parents:
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33 <test> |
2f6c7f82ad4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 05bab1b3b5838d62307a2d0d1172445b765b7f55
iuc
parents:
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34 <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
parents:
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35 <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
parents:
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36 <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
parents:
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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
parents:
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38 <test> |
2f6c7f82ad4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 05bab1b3b5838d62307a2d0d1172445b765b7f55
iuc
parents:
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39 <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
parents:
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40 <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
parents:
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41 <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
parents:
diff
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42 <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
parents:
diff
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43 <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
iuc
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44 </test> |
2f6c7f82ad4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 05bab1b3b5838d62307a2d0d1172445b765b7f55
iuc
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45 </tests> |
2f6c7f82ad4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 05bab1b3b5838d62307a2d0d1172445b765b7f55
iuc
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46 <help> |
2f6c7f82ad4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 05bab1b3b5838d62307a2d0d1172445b765b7f55
iuc
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47 |
2f6c7f82ad4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 05bab1b3b5838d62307a2d0d1172445b765b7f55
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48 **What it does** |
2f6c7f82ad4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 05bab1b3b5838d62307a2d0d1172445b765b7f55
iuc
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49 |
2f6c7f82ad4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 05bab1b3b5838d62307a2d0d1172445b765b7f55
iuc
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50 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
iuc
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51 |
2f6c7f82ad4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 05bab1b3b5838d62307a2d0d1172445b765b7f55
iuc
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52 - 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
iuc
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53 - 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
iuc
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54 |
2f6c7f82ad4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 05bab1b3b5838d62307a2d0d1172445b765b7f55
iuc
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55 ----- |
2f6c7f82ad4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 05bab1b3b5838d62307a2d0d1172445b765b7f55
iuc
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56 |
2f6c7f82ad4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 05bab1b3b5838d62307a2d0d1172445b765b7f55
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57 **Options** |
2f6c7f82ad4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 05bab1b3b5838d62307a2d0d1172445b765b7f55
iuc
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58 |
2f6c7f82ad4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 05bab1b3b5838d62307a2d0d1172445b765b7f55
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59 * **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
iuc
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60 * **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
iuc
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61 |
2f6c7f82ad4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 05bab1b3b5838d62307a2d0d1172445b765b7f55
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62 </help> |
2f6c7f82ad4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 05bab1b3b5838d62307a2d0d1172445b765b7f55
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63 <citations> |
2f6c7f82ad4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 05bab1b3b5838d62307a2d0d1172445b765b7f55
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64 <citation type="bibtex"> |
2f6c7f82ad4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 05bab1b3b5838d62307a2d0d1172445b765b7f55
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65 @unpublished{None, |
2f6c7f82ad4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 05bab1b3b5838d62307a2d0d1172445b765b7f55
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66 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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67 title = {None}, |
2f6c7f82ad4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 05bab1b3b5838d62307a2d0d1172445b765b7f55
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68 year = {None}, |
2f6c7f82ad4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 05bab1b3b5838d62307a2d0d1172445b765b7f55
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69 eprint = {None}, |
2f6c7f82ad4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 05bab1b3b5838d62307a2d0d1172445b765b7f55
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70 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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71 }</citation> |
2f6c7f82ad4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 05bab1b3b5838d62307a2d0d1172445b765b7f55
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72 </citations> |
2f6c7f82ad4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 05bab1b3b5838d62307a2d0d1172445b765b7f55
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73 </tool> |