Mercurial > repos > mingchen0919 > rmarkdown_mirdeep2
annotate mirdeep2.xml @ 4:543ee6fdadeb draft default tip
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit a23e23222252167ef7c3338a4872e84706df8f83-dirty
author | mingchen0919 |
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date | Tue, 08 Aug 2017 15:06:46 -0400 |
parents | 228117ad62bb |
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rev | line source |
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963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff
changeset
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1 <tool id="mirdeep2" name="mirdeep2" version="1.0.0"> |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
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2 <requirements> |
4
543ee6fdadeb
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit a23e23222252167ef7c3338a4872e84706df8f83-dirty
mingchen0919
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3 <requirement type="package" version="1.15.0.6-0">pandoc</requirement> |
0
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
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4 <requirement type="package" version="2.0.0.8">mirdeep2</requirement> |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
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5 <requirement type="package" version="1.20.0">r-getopt</requirement> |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
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6 <requirement type="package" version="1.2">r-rmarkdown</requirement> |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
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7 <requirement type="package" version="1.8.4">r-plyr</requirement> |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
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8 <requirement type="package" version="0.5.0">r-dplyr</requirement> |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
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9 <requirement type="package" version="0.3.5">r-htmltools</requirement> |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
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10 </requirements> |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
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11 <description> |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
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12 miRNA identification |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
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13 </description> |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
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14 <stdio> |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
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15 <regex match="Execution halted" |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
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16 source="both" |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
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17 level="fatal" |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
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18 description="Execution halted." /> |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
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19 <regex match="Error in" |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
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20 source="both" |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
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21 level="fatal" |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
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22 description="An undefined error occured, please check your intput carefully and contact your administrator." /> |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
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23 <regex match="Fatal error" |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
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24 source="both" |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
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25 level="fatal" |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
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26 description="An undefined error occured, please check your intput carefully and contact your administrator." /> |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
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27 </stdio> |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
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28 <command> |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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29 <![CDATA[ |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
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30 |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
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31 Rscript '${__tool_directory__}/mirdeep2_render.R' |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
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32 |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
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33 ## 1. input data |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
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34 -e $echo |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
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35 -a $collapsed_reads |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
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36 -b $reference_genome |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
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37 -c $reads_mapping |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
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38 |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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39 ## 2. output report and report site directory |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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40 -o $mirdeep2_site |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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41 -d $mirdeep2_site.files_path |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
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42 -r $csv_result |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
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43 -t $html_result |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
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44 -u $report_log |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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45 |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
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46 ## other paramters |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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47 |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
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48 -f $species_mature_mirna |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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49 -g $related_species_mature_mirna |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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50 -h $precursor_sequences |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
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51 -j $min_read_stack_height |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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52 -k $min_score_cutoff |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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53 -l $randfold_analysis |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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54 -m $max_precursor_number |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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55 -n $species |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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56 -q $switch |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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57 |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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58 ## 3. Rmd templates sitting in the tool directory |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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59 |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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60 ## other Rmd body template files |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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61 -p '${__tool_directory__}/mirdeep2.Rmd' |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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62 |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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63 |
963905bcb754
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64 ]]> |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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65 </command> |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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66 <inputs> |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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67 <param name="collapsed_reads" type="data" format="fasta" multiple="False" optional="False" |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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68 label="Read input file" help="Reads in fastq or fasta format"/> |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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69 <param name="reference_genome" type="data" format="fasta" multiple="False" optional="False" |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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70 label="Reference genome from history" |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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71 help="Reference genome in fasta format"/> |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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72 <param name="reads_mapping" type="data" format="tabular" multiple="False" optional="False" |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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73 label="reads mappings" help="reads mappings in arf format"/> |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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74 <param name="species_mature_mirna" type="data" format="fasta" multiple="False" optional="True" |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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75 label="miRBase mature miRNA for this species" |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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76 help="mature miRNA in fasta format"/> |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
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77 <param name="related_species_mature_mirna" type="data" format="fasta" multiple="False" optional="TRUE" |
963905bcb754
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78 label="miRBase mature miRNA from related species" |
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79 help="mature miRNA in fasta format"/> |
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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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80 <param name="precursor_sequences" type="data" format="fasta" multiple="False" optional="TRUE" |
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81 label="precursor sequences" help="miRBase miRNA precursor sequences in fasta format"/> |
963905bcb754
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82 <param name="min_read_stack_height" type="integer" argument="-a" optional="True" |
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83 label="minimum read stack height" |
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84 help="minimum read stack height that triggers analysis. Using this option disables |
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85 automatic estimation of the optimal value."/> |
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86 <param name="min_score_cutoff" type="integer" value="0" argument="-b" label="minimum score cut-off" |
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87 help="minimum score cut-off for predicted novel miRNAs to be displayed in the overview |
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88 table. This score cut-off is by default 0."/> |
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89 <param name="randfold_analysis" type="boolean" truevalue="TRUE" falsevalue="FALSE" argument="-c" checked="False" |
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90 label="randfold analysis" help="disable randfold analysis"/> |
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91 <param name="max_precursor_number" type="integer" value="50000" argument="-g" label="maximum number of precursors" |
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92 help="maximum number of precursors to analyze when automatic excision gearing is used. |
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93 default=50000, if set to -1 all precursors will be analyzed"/> |
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94 <param name="species" type="select" label="Search in species"> |
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95 <option value="all">All species</option> |
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96 <option value="tni">tetraodon</option> |
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97 <option value="dps">d.pseudoobscura</option> |
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98 <option value="dya">d.yakuba</option> |
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99 <option value="ame">a.mellifera</option> |
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100 <option value="dmo">d.mojavensis</option> |
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101 <option value="cel">worm</option> |
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102 <option value="aga">a.gambiae</option> |
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103 <option value="cbr">c.briggsae</option> |
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104 <option value="cin">c.intestinalis</option> |
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105 <option value="mmu">mouse</option> |
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106 <option value="xtr">x.tropicalis</option> |
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107 <option value="eca">horse</option> |
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108 <option value="cfa">dog</option> |
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109 <option value="fru">fugu</option> |
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110 <option value="bta">cow</option> |
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111 <option value="der">d.erecta</option> |
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112 <option value="dgr">d.grimshawi</option> |
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113 <option value="gga">chicken</option> |
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114 <option value="spu">s.purpuratus</option> |
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115 <option value="bfl">lancelet</option> |
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116 <option value="ptr">chimp</option> |
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117 <option value="dse">d.sechellia</option> |
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118 <option value="dpe">d.persimilis</option> |
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119 <option value="dvi">d.virilis</option> |
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120 <option value="rno">rat</option> |
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121 <option value="dme">d.melanogaster</option> |
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122 <option value="lca">cat</option> |
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123 <option value="sja">c.japonica</option> |
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124 <option value="dan">d.ananassae</option> |
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125 <option value="hsa">human</option> |
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126 <option value="dsi">d.simulans</option> |
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127 </param> |
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128 <param name="switch" type="boolean" truevalue="TRUE" falsevalue="FALSE" |
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129 label="mature_ref_miRNAs contain miRBase v18 identifiers?" |
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130 help="use this switch if mature_ref_miRNAs contain miRBase v18 identifiers (5p and 3p) instead of previous ids from v17"/> |
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131 |
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132 |
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133 <param name="echo" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Display analysis code in report?" /> |
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134 </inputs> |
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135 <outputs> |
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136 <data format="html" name="mirdeep2_site" label="mirdeep2 miRNA identification" /> |
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137 <data name="csv_result" format="csv" label="miRNA in csv format" /> |
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138 <data name="html_result" format="html" label="miRNA in html format" from_work_dir="result.html"/> |
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139 <data name="report_log" format="txt" label="report log" from_work_dir="result.csv"/> |
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140 </outputs> |
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141 <citations> |
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142 @article{friedlander2011mirdeep2, |
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143 title={miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades}, |
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144 author={Friedl{\"a}nder, Marc R and Mackowiak, Sebastian D and Li, Na and Chen, Wei and Rajewsky, Nikolaus}, |
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145 journal={Nucleic acids research}, |
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146 volume={40}, |
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147 number={1}, |
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148 pages={37--52}, |
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149 year={2011}, |
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150 publisher={Oxford University Press} |
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151 } |
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152 <citation type="bibtex"> |
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153 @article{allaire2016rmarkdown, |
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154 title={rmarkdown: Dynamic Documents for R, 2016}, |
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155 author={Allaire, J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan and Chang, Winston and Allen, Jeff and Wickham, Hadley and Atkins, Aron and Hyndman, Rob}, |
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156 journal={R package version 0.9}, |
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157 volume={6}, |
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158 year={2016} |
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159 } |
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160 </citation> |
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161 <citation type="bibtex"> |
2
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162 @article{allaire2016rmarkdown, |
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163 title={rmarkdown: Dynamic Documents for R, 2016}, |
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164 author={Allaire, J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan and Chang, Winston and Allen, Jeff and Wickham, Hadley and Atkins, Aron and Hyndman, Rob}, |
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165 journal={R package version 0.9}, |
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166 volume={6}, |
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167 year={2016} |
0
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168 } |
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169 </citation> |
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170 <citation type="bibtex"> |
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171 @book{xie2015dynamic, |
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172 title={Dynamic Documents with R and knitr}, |
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173 author={Xie, Yihui}, |
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174 volume={29}, |
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175 year={2015}, |
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176 publisher={CRC Press} |
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177 } |
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178 </citation> |
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179 </citations> |
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180 </tool> |