Mercurial > repos > chaimae_eljaouhari > basicplot
annotate basicplot.xml @ 0:da8c70a64f0c draft default tip
planemo upload for repository https://github.com/chamaelj/tools-artbio/tree/master/tools/basicplot commit 09c37709000f22d9fb378ec1a4ec0e8f46e6bf73-dirty
author | chaimae_eljaouhari |
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date | Fri, 31 Mar 2017 07:23:53 -0400 |
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da8c70a64f0c
planemo upload for repository https://github.com/chamaelj/tools-artbio/tree/master/tools/basicplot commit 09c37709000f22d9fb378ec1a4ec0e8f46e6bf73-dirty
chaimae_eljaouhari
parents:
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1 <tool id="Basicplot" name="basicplot" version="0.9.0"> |
da8c70a64f0c
planemo upload for repository https://github.com/chamaelj/tools-artbio/tree/master/tools/basicplot commit 09c37709000f22d9fb378ec1a4ec0e8f46e6bf73-dirty
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2 <description>Basic plot</description> |
da8c70a64f0c
planemo upload for repository https://github.com/chamaelj/tools-artbio/tree/master/tools/basicplot commit 09c37709000f22d9fb378ec1a4ec0e8f46e6bf73-dirty
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3 <requirements> |
da8c70a64f0c
planemo upload for repository https://github.com/chamaelj/tools-artbio/tree/master/tools/basicplot commit 09c37709000f22d9fb378ec1a4ec0e8f46e6bf73-dirty
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4 <requirement type="package" version="3.1.2">R</requirement> |
da8c70a64f0c
planemo upload for repository https://github.com/chamaelj/tools-artbio/tree/master/tools/basicplot commit 09c37709000f22d9fb378ec1a4ec0e8f46e6bf73-dirty
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5 </requirements> |
da8c70a64f0c
planemo upload for repository https://github.com/chamaelj/tools-artbio/tree/master/tools/basicplot commit 09c37709000f22d9fb378ec1a4ec0e8f46e6bf73-dirty
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6 <command><![CDATA[ |
da8c70a64f0c
planemo upload for repository https://github.com/chamaelj/tools-artbio/tree/master/tools/basicplot commit 09c37709000f22d9fb378ec1a4ec0e8f46e6bf73-dirty
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7 Rscript '$basicplot' "\${GALAXY_SLOTS:-1}" |
da8c70a64f0c
planemo upload for repository https://github.com/chamaelj/tools-artbio/tree/master/tools/basicplot commit 09c37709000f22d9fb378ec1a4ec0e8f46e6bf73-dirty
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8 ]]></command> |
da8c70a64f0c
planemo upload for repository https://github.com/chamaelj/tools-artbio/tree/master/tools/basicplot commit 09c37709000f22d9fb378ec1a4ec0e8f46e6bf73-dirty
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parents:
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9 <configfiles> |
da8c70a64f0c
planemo upload for repository https://github.com/chamaelj/tools-artbio/tree/master/tools/basicplot commit 09c37709000f22d9fb378ec1a4ec0e8f46e6bf73-dirty
chaimae_eljaouhari
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10 <configfile name="basicplot"> |
da8c70a64f0c
planemo upload for repository https://github.com/chamaelj/tools-artbio/tree/master/tools/basicplot commit 09c37709000f22d9fb378ec1a4ec0e8f46e6bf73-dirty
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parents:
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11 <![CDATA[ |
da8c70a64f0c
planemo upload for repository https://github.com/chamaelj/tools-artbio/tree/master/tools/basicplot commit 09c37709000f22d9fb378ec1a4ec0e8f46e6bf73-dirty
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parents:
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12 ## Setup R error handling to go to stderr |
da8c70a64f0c
planemo upload for repository https://github.com/chamaelj/tools-artbio/tree/master/tools/basicplot commit 09c37709000f22d9fb378ec1a4ec0e8f46e6bf73-dirty
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13 options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } ) |
da8c70a64f0c
planemo upload for repository https://github.com/chamaelj/tools-artbio/tree/master/tools/basicplot commit 09c37709000f22d9fb378ec1a4ec0e8f46e6bf73-dirty
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parents:
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14 options(warn=-1) |
da8c70a64f0c
planemo upload for repository https://github.com/chamaelj/tools-artbio/tree/master/tools/basicplot commit 09c37709000f22d9fb378ec1a4ec0e8f46e6bf73-dirty
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parents:
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15 Table = read.delim("${input}", header=TRUE) |
da8c70a64f0c
planemo upload for repository https://github.com/chamaelj/tools-artbio/tree/master/tools/basicplot commit 09c37709000f22d9fb378ec1a4ec0e8f46e6bf73-dirty
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parents:
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16 pdf("${output}") |
da8c70a64f0c
planemo upload for repository https://github.com/chamaelj/tools-artbio/tree/master/tools/basicplot commit 09c37709000f22d9fb378ec1a4ec0e8f46e6bf73-dirty
chaimae_eljaouhari
parents:
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17 pairs(Table[ ,-1], main="${title}", log="xy", pch = 20) |
da8c70a64f0c
planemo upload for repository https://github.com/chamaelj/tools-artbio/tree/master/tools/basicplot commit 09c37709000f22d9fb378ec1a4ec0e8f46e6bf73-dirty
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parents:
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18 dev.off() |
da8c70a64f0c
planemo upload for repository https://github.com/chamaelj/tools-artbio/tree/master/tools/basicplot commit 09c37709000f22d9fb378ec1a4ec0e8f46e6bf73-dirty
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parents:
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19 ]]> |
da8c70a64f0c
planemo upload for repository https://github.com/chamaelj/tools-artbio/tree/master/tools/basicplot commit 09c37709000f22d9fb378ec1a4ec0e8f46e6bf73-dirty
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parents:
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20 </configfile> |
da8c70a64f0c
planemo upload for repository https://github.com/chamaelj/tools-artbio/tree/master/tools/basicplot commit 09c37709000f22d9fb378ec1a4ec0e8f46e6bf73-dirty
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parents:
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21 </configfiles> |
da8c70a64f0c
planemo upload for repository https://github.com/chamaelj/tools-artbio/tree/master/tools/basicplot commit 09c37709000f22d9fb378ec1a4ec0e8f46e6bf73-dirty
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parents:
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22 <inputs> |
da8c70a64f0c
planemo upload for repository https://github.com/chamaelj/tools-artbio/tree/master/tools/basicplot commit 09c37709000f22d9fb378ec1a4ec0e8f46e6bf73-dirty
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parents:
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23 <param name="input" type="data" format="tabular" label="tabular file"/> |
da8c70a64f0c
planemo upload for repository https://github.com/chamaelj/tools-artbio/tree/master/tools/basicplot commit 09c37709000f22d9fb378ec1a4ec0e8f46e6bf73-dirty
chaimae_eljaouhari
parents:
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24 <param name="title" type="text" size="25" value="Title" label="Main Title"/> |
da8c70a64f0c
planemo upload for repository https://github.com/chamaelj/tools-artbio/tree/master/tools/basicplot commit 09c37709000f22d9fb378ec1a4ec0e8f46e6bf73-dirty
chaimae_eljaouhari
parents:
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25 </inputs> |
da8c70a64f0c
planemo upload for repository https://github.com/chamaelj/tools-artbio/tree/master/tools/basicplot commit 09c37709000f22d9fb378ec1a4ec0e8f46e6bf73-dirty
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parents:
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26 <outputs> |
da8c70a64f0c
planemo upload for repository https://github.com/chamaelj/tools-artbio/tree/master/tools/basicplot commit 09c37709000f22d9fb378ec1a4ec0e8f46e6bf73-dirty
chaimae_eljaouhari
parents:
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27 <data name="output" format="pdf" label="plot" /> |
da8c70a64f0c
planemo upload for repository https://github.com/chamaelj/tools-artbio/tree/master/tools/basicplot commit 09c37709000f22d9fb378ec1a4ec0e8f46e6bf73-dirty
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parents:
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28 </outputs> |
da8c70a64f0c
planemo upload for repository https://github.com/chamaelj/tools-artbio/tree/master/tools/basicplot commit 09c37709000f22d9fb378ec1a4ec0e8f46e6bf73-dirty
chaimae_eljaouhari
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29 <tests> |
da8c70a64f0c
planemo upload for repository https://github.com/chamaelj/tools-artbio/tree/master/tools/basicplot commit 09c37709000f22d9fb378ec1a4ec0e8f46e6bf73-dirty
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30 <test> |
da8c70a64f0c
planemo upload for repository https://github.com/chamaelj/tools-artbio/tree/master/tools/basicplot commit 09c37709000f22d9fb378ec1a4ec0e8f46e6bf73-dirty
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parents:
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31 <param name="input" value="data.tab" ftype="tabular"/> |
da8c70a64f0c
planemo upload for repository https://github.com/chamaelj/tools-artbio/tree/master/tools/basicplot commit 09c37709000f22d9fb378ec1a4ec0e8f46e6bf73-dirty
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parents:
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32 <param name="title" value="Title"/> |
da8c70a64f0c
planemo upload for repository https://github.com/chamaelj/tools-artbio/tree/master/tools/basicplot commit 09c37709000f22d9fb378ec1a4ec0e8f46e6bf73-dirty
chaimae_eljaouhari
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33 <output name="output" file="basicplot.pdf" ftype="pdf"/> |
da8c70a64f0c
planemo upload for repository https://github.com/chamaelj/tools-artbio/tree/master/tools/basicplot commit 09c37709000f22d9fb378ec1a4ec0e8f46e6bf73-dirty
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34 </test> |
da8c70a64f0c
planemo upload for repository https://github.com/chamaelj/tools-artbio/tree/master/tools/basicplot commit 09c37709000f22d9fb378ec1a4ec0e8f46e6bf73-dirty
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35 </tests> |
da8c70a64f0c
planemo upload for repository https://github.com/chamaelj/tools-artbio/tree/master/tools/basicplot commit 09c37709000f22d9fb378ec1a4ec0e8f46e6bf73-dirty
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36 <help> |
da8c70a64f0c
planemo upload for repository https://github.com/chamaelj/tools-artbio/tree/master/tools/basicplot commit 09c37709000f22d9fb378ec1a4ec0e8f46e6bf73-dirty
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37 |
da8c70a64f0c
planemo upload for repository https://github.com/chamaelj/tools-artbio/tree/master/tools/basicplot commit 09c37709000f22d9fb378ec1a4ec0e8f46e6bf73-dirty
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38 **What it does** |
da8c70a64f0c
planemo upload for repository https://github.com/chamaelj/tools-artbio/tree/master/tools/basicplot commit 09c37709000f22d9fb378ec1a4ec0e8f46e6bf73-dirty
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39 |
da8c70a64f0c
planemo upload for repository https://github.com/chamaelj/tools-artbio/tree/master/tools/basicplot commit 09c37709000f22d9fb378ec1a4ec0e8f46e6bf73-dirty
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40 Take on tabular file of numerical data as input and produces pairwise plots of numerical data, in log-log scale. |
da8c70a64f0c
planemo upload for repository https://github.com/chamaelj/tools-artbio/tree/master/tools/basicplot commit 09c37709000f22d9fb378ec1a4ec0e8f46e6bf73-dirty
chaimae_eljaouhari
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41 The first column of the data frame is ignored. |
da8c70a64f0c
planemo upload for repository https://github.com/chamaelj/tools-artbio/tree/master/tools/basicplot commit 09c37709000f22d9fb378ec1a4ec0e8f46e6bf73-dirty
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42 |
da8c70a64f0c
planemo upload for repository https://github.com/chamaelj/tools-artbio/tree/master/tools/basicplot commit 09c37709000f22d9fb378ec1a4ec0e8f46e6bf73-dirty
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43 Example of input data: |
da8c70a64f0c
planemo upload for repository https://github.com/chamaelj/tools-artbio/tree/master/tools/basicplot commit 09c37709000f22d9fb378ec1a4ec0e8f46e6bf73-dirty
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44 |
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planemo upload for repository https://github.com/chamaelj/tools-artbio/tree/master/tools/basicplot commit 09c37709000f22d9fb378ec1a4ec0e8f46e6bf73-dirty
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45 <![CDATA[ |
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planemo upload for repository https://github.com/chamaelj/tools-artbio/tree/master/tools/basicplot commit 09c37709000f22d9fb378ec1a4ec0e8f46e6bf73-dirty
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46 |
da8c70a64f0c
planemo upload for repository https://github.com/chamaelj/tools-artbio/tree/master/tools/basicplot commit 09c37709000f22d9fb378ec1a4ec0e8f46e6bf73-dirty
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47 gene sample1 sample2 sample3 sample4 sample5 sample6 |
da8c70a64f0c
planemo upload for repository https://github.com/chamaelj/tools-artbio/tree/master/tools/basicplot commit 09c37709000f22d9fb378ec1a4ec0e8f46e6bf73-dirty
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48 |
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planemo upload for repository https://github.com/chamaelj/tools-artbio/tree/master/tools/basicplot commit 09c37709000f22d9fb378ec1a4ec0e8f46e6bf73-dirty
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49 tRNA:Ala-AGC-2-3 4407 4506 2267 2423 2736 1153 |
da8c70a64f0c
planemo upload for repository https://github.com/chamaelj/tools-artbio/tree/master/tools/basicplot commit 09c37709000f22d9fb378ec1a4ec0e8f46e6bf73-dirty
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50 |
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planemo upload for repository https://github.com/chamaelj/tools-artbio/tree/master/tools/basicplot commit 09c37709000f22d9fb378ec1a4ec0e8f46e6bf73-dirty
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51 tRNA:Asp-GTC-1-10 2111 2931 3302 3499 3809 1682 |
da8c70a64f0c
planemo upload for repository https://github.com/chamaelj/tools-artbio/tree/master/tools/basicplot commit 09c37709000f22d9fb378ec1a4ec0e8f46e6bf73-dirty
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52 |
da8c70a64f0c
planemo upload for repository https://github.com/chamaelj/tools-artbio/tree/master/tools/basicplot commit 09c37709000f22d9fb378ec1a4ec0e8f46e6bf73-dirty
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53 tRNA:Asp-GTC-1-11 2099 2936 3349 3556 4124 1629 |
da8c70a64f0c
planemo upload for repository https://github.com/chamaelj/tools-artbio/tree/master/tools/basicplot commit 09c37709000f22d9fb378ec1a4ec0e8f46e6bf73-dirty
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54 |
da8c70a64f0c
planemo upload for repository https://github.com/chamaelj/tools-artbio/tree/master/tools/basicplot commit 09c37709000f22d9fb378ec1a4ec0e8f46e6bf73-dirty
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55 tRNA:Glu-TTC-1-6 1095 1376 1189 1162 1120 561 |
da8c70a64f0c
planemo upload for repository https://github.com/chamaelj/tools-artbio/tree/master/tools/basicplot commit 09c37709000f22d9fb378ec1a4ec0e8f46e6bf73-dirty
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56 |
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planemo upload for repository https://github.com/chamaelj/tools-artbio/tree/master/tools/basicplot commit 09c37709000f22d9fb378ec1a4ec0e8f46e6bf73-dirty
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57 tRNA:Glu-TTC-1-5 1022 1415 1156 1081 1120 578 |
da8c70a64f0c
planemo upload for repository https://github.com/chamaelj/tools-artbio/tree/master/tools/basicplot commit 09c37709000f22d9fb378ec1a4ec0e8f46e6bf73-dirty
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58 |
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planemo upload for repository https://github.com/chamaelj/tools-artbio/tree/master/tools/basicplot commit 09c37709000f22d9fb378ec1a4ec0e8f46e6bf73-dirty
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59 tRNA:Glu-TTC-1-4 1047 1336 1156 1182 1127 602 |
da8c70a64f0c
planemo upload for repository https://github.com/chamaelj/tools-artbio/tree/master/tools/basicplot commit 09c37709000f22d9fb378ec1a4ec0e8f46e6bf73-dirty
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60 |
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planemo upload for repository https://github.com/chamaelj/tools-artbio/tree/master/tools/basicplot commit 09c37709000f22d9fb378ec1a4ec0e8f46e6bf73-dirty
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61 tRNA:Glu-CTC-3-4 3613 3414 8161 9021 9776 5248 |
da8c70a64f0c
planemo upload for repository https://github.com/chamaelj/tools-artbio/tree/master/tools/basicplot commit 09c37709000f22d9fb378ec1a4ec0e8f46e6bf73-dirty
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62 |
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planemo upload for repository https://github.com/chamaelj/tools-artbio/tree/master/tools/basicplot commit 09c37709000f22d9fb378ec1a4ec0e8f46e6bf73-dirty
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63 tRNA:Glu-CTC-3-5 3741 3292 7893 8845 9833 5074 |
da8c70a64f0c
planemo upload for repository https://github.com/chamaelj/tools-artbio/tree/master/tools/basicplot commit 09c37709000f22d9fb378ec1a4ec0e8f46e6bf73-dirty
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64 |
da8c70a64f0c
planemo upload for repository https://github.com/chamaelj/tools-artbio/tree/master/tools/basicplot commit 09c37709000f22d9fb378ec1a4ec0e8f46e6bf73-dirty
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65 tRNA:Glu-CTC-3-6 3619 3379 7663 8737 9513 5021 |
da8c70a64f0c
planemo upload for repository https://github.com/chamaelj/tools-artbio/tree/master/tools/basicplot commit 09c37709000f22d9fb378ec1a4ec0e8f46e6bf73-dirty
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66 |
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planemo upload for repository https://github.com/chamaelj/tools-artbio/tree/master/tools/basicplot commit 09c37709000f22d9fb378ec1a4ec0e8f46e6bf73-dirty
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67 tRNA:Glu-CTC-3-8 7249 5809 80760 39479 62652 27404 |
da8c70a64f0c
planemo upload for repository https://github.com/chamaelj/tools-artbio/tree/master/tools/basicplot commit 09c37709000f22d9fb378ec1a4ec0e8f46e6bf73-dirty
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68 |
da8c70a64f0c
planemo upload for repository https://github.com/chamaelj/tools-artbio/tree/master/tools/basicplot commit 09c37709000f22d9fb378ec1a4ec0e8f46e6bf73-dirty
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69 tRNA:Glu-CTC-3-9 3770 3367 8007 8969 9976 5100 |
da8c70a64f0c
planemo upload for repository https://github.com/chamaelj/tools-artbio/tree/master/tools/basicplot commit 09c37709000f22d9fb378ec1a4ec0e8f46e6bf73-dirty
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70 |
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71 ]]> |
da8c70a64f0c
planemo upload for repository https://github.com/chamaelj/tools-artbio/tree/master/tools/basicplot commit 09c37709000f22d9fb378ec1a4ec0e8f46e6bf73-dirty
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72 |
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planemo upload for repository https://github.com/chamaelj/tools-artbio/tree/master/tools/basicplot commit 09c37709000f22d9fb378ec1a4ec0e8f46e6bf73-dirty
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73 |
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planemo upload for repository https://github.com/chamaelj/tools-artbio/tree/master/tools/basicplot commit 09c37709000f22d9fb378ec1a4ec0e8f46e6bf73-dirty
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74 </help> |
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planemo upload for repository https://github.com/chamaelj/tools-artbio/tree/master/tools/basicplot commit 09c37709000f22d9fb378ec1a4ec0e8f46e6bf73-dirty
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75 <citations> |
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planemo upload for repository https://github.com/chamaelj/tools-artbio/tree/master/tools/basicplot commit 09c37709000f22d9fb378ec1a4ec0e8f46e6bf73-dirty
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76 <citation type="bibtex"> |
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planemo upload for repository https://github.com/chamaelj/tools-artbio/tree/master/tools/basicplot commit 09c37709000f22d9fb378ec1a4ec0e8f46e6bf73-dirty
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77 @Manual{, |
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planemo upload for repository https://github.com/chamaelj/tools-artbio/tree/master/tools/basicplot commit 09c37709000f22d9fb378ec1a4ec0e8f46e6bf73-dirty
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78 title = {R: A Language and Environment for Statistical Computing}, |
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planemo upload for repository https://github.com/chamaelj/tools-artbio/tree/master/tools/basicplot commit 09c37709000f22d9fb378ec1a4ec0e8f46e6bf73-dirty
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79 author = {{R Core Team}}, |
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planemo upload for repository https://github.com/chamaelj/tools-artbio/tree/master/tools/basicplot commit 09c37709000f22d9fb378ec1a4ec0e8f46e6bf73-dirty
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80 organization = {R Foundation for Statistical Computing}, |
da8c70a64f0c
planemo upload for repository https://github.com/chamaelj/tools-artbio/tree/master/tools/basicplot commit 09c37709000f22d9fb378ec1a4ec0e8f46e6bf73-dirty
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81 address = {Vienna, Austria}, |
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planemo upload for repository https://github.com/chamaelj/tools-artbio/tree/master/tools/basicplot commit 09c37709000f22d9fb378ec1a4ec0e8f46e6bf73-dirty
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82 year = {2014}, |
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planemo upload for repository https://github.com/chamaelj/tools-artbio/tree/master/tools/basicplot commit 09c37709000f22d9fb378ec1a4ec0e8f46e6bf73-dirty
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83 url = {http://www.R-project.org/}, |
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planemo upload for repository https://github.com/chamaelj/tools-artbio/tree/master/tools/basicplot commit 09c37709000f22d9fb378ec1a4ec0e8f46e6bf73-dirty
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84 } |
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planemo upload for repository https://github.com/chamaelj/tools-artbio/tree/master/tools/basicplot commit 09c37709000f22d9fb378ec1a4ec0e8f46e6bf73-dirty
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85 </citation> |
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planemo upload for repository https://github.com/chamaelj/tools-artbio/tree/master/tools/basicplot commit 09c37709000f22d9fb378ec1a4ec0e8f46e6bf73-dirty
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86 </citations> |
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87 |
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planemo upload for repository https://github.com/chamaelj/tools-artbio/tree/master/tools/basicplot commit 09c37709000f22d9fb378ec1a4ec0e8f46e6bf73-dirty
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88 </tool> |
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planemo upload for repository https://github.com/chamaelj/tools-artbio/tree/master/tools/basicplot commit 09c37709000f22d9fb378ec1a4ec0e8f46e6bf73-dirty
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89 |