Mercurial > repos > rnateam > chipseeker
annotate chipseeker.xml @ 5:4c2dbe4dbb4e draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 853e74181667ce9ac6a0c91d4a2b204c0b3fda06
author | rnateam |
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date | Tue, 04 Dec 2018 10:01:20 -0500 |
parents | 90fe78a19b55 |
children | b418a1d3585d |
rev | line source |
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5
4c2dbe4dbb4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 853e74181667ce9ac6a0c91d4a2b204c0b3fda06
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1 <tool id="chipseeker" name="ChIPseeker" version="1.16.2"> |
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58ef4507ce5a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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2 <description>for ChIP peak annotation and visualization</description> |
58ef4507ce5a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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3 <requirements> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 6f594126ac7369cc80c30a02a6df57e785dfb45a
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4 <requirement type="package" version="1.16.1">bioconductor-chipseeker</requirement> |
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95f779f4adb7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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5 <requirement type="package" version="1.4.4">r-optparse</requirement> |
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58ef4507ce5a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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parents:
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6 </requirements> |
58ef4507ce5a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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7 <version_command><![CDATA[ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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8 echo $(R --version | grep version | grep -v GNU)", ChIPseeker version" $(R --vanilla --slave -e "library(ChIPseeker); cat(sessionInfo()\$otherPkgs\$ChIPseeker\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", optparse version" $(R --vanilla --slave -e "library(optparse); cat(sessionInfo()\$otherPkgs\$optparse\$Version)" 2> /dev/null | grep -v -i "WARNING: ") |
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58ef4507ce5a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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9 ]]></version_command> |
58ef4507ce5a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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10 <command detect_errors="exit_code"><![CDATA[ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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11 #set gtf = "refgtf" |
95f779f4adb7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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12 #if $gtf_source.gtf_source_select == "history": |
95f779f4adb7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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13 ln -s '${gtf_source.gtf_hist}' $gtf && |
95f779f4adb7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
rnateam
parents:
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14 #else if $gtf_source.gtf_source_select == "cached": |
95f779f4adb7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
rnateam
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15 ln -s '${gtf_source.gtf_builtin.fields.path}' $gtf && |
95f779f4adb7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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16 #end if |
95f779f4adb7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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17 |
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58ef4507ce5a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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18 #if $rscript: |
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95f779f4adb7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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19 cp '$__tool_directory__/chipseeker.R' '$out_rscript' && |
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58ef4507ce5a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
rnateam
parents:
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20 #end if |
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95f779f4adb7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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21 |
95f779f4adb7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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22 Rscript '$__tool_directory__/chipseeker.R' |
95f779f4adb7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
rnateam
parents:
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23 |
95f779f4adb7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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24 -i '$peaks' |
95f779f4adb7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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25 -G '$gtf' |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit bae8cc7d7a88154b815acc3cd126010e7e965d5c
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26 -u $adv.upstream |
cb133602cd9b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit bae8cc7d7a88154b815acc3cd126010e7e965d5c
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27 -d $adv.downstream |
cb133602cd9b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit bae8cc7d7a88154b815acc3cd126010e7e965d5c
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28 #if $adv.flankgeneinfo: |
cb133602cd9b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit bae8cc7d7a88154b815acc3cd126010e7e965d5c
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29 -F $adv.flankgeneinfo |
cb133602cd9b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit bae8cc7d7a88154b815acc3cd126010e7e965d5c
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30 -D $adv.flankgenedist |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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31 #end if |
95f779f4adb7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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32 -f $format |
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4c2dbe4dbb4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 853e74181667ce9ac6a0c91d4a2b204c0b3fda06
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33 #if $pdf: |
4c2dbe4dbb4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 853e74181667ce9ac6a0c91d4a2b204c0b3fda06
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34 -p $pdf |
4c2dbe4dbb4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 853e74181667ce9ac6a0c91d4a2b204c0b3fda06
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35 #end if |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 861db0d1f76bb320f49c2501f4e656cf88d389ce
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36 -r $rdata |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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37 ]]> |
58ef4507ce5a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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38 </command> |
58ef4507ce5a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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39 <inputs> |
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cb133602cd9b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit bae8cc7d7a88154b815acc3cd126010e7e965d5c
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40 <param name="peaks" type="data" format="bed,interval,tabular" label="Peaks file" help="A peaks file in BED format." /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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41 <conditional name="gtf_source"> |
95f779f4adb7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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parents:
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42 <param name="gtf_source_select" type="select" label="Annotation source" help="Select a GTF to use for annotation source."> |
95f779f4adb7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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43 <option value="cached" selected="true">Use a built-in GTF</option> |
95f779f4adb7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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44 <option value="history">Use a GTF from history</option> |
95f779f4adb7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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45 </param> |
95f779f4adb7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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46 <when value="cached"> |
95f779f4adb7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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47 <param name="gtf_builtin" type="select" label="Select a built-in GTF" help="If the GTF file for your transcriptome of interest is not listed, contact your Galaxy administrator"> |
95f779f4adb7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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48 <options from_data_table="gene_sets"> |
95f779f4adb7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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49 <filter type="sort_by" column="2" /> |
95f779f4adb7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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50 <validator type="no_options" message="No GTF file is available." /> |
95f779f4adb7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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51 </options> |
95f779f4adb7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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52 </param> |
95f779f4adb7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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53 </when> |
95f779f4adb7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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54 <when value="history"> |
95f779f4adb7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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55 <param name="gtf_hist" type="data" format="gtf" label="Select a history GTF" /> |
95f779f4adb7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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56 </when> |
95f779f4adb7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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57 </conditional> |
95f779f4adb7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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58 <param name="format" type="select" label="Output Format"> |
95f779f4adb7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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59 <option value="interval" selected="True">Interval</option> |
95f779f4adb7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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60 <option value="tabular">Tabular (tab-separated)</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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61 </param> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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62 <param name="pdf" type="boolean" truevalue="True" falsevalue="" checked="True" label="Output PDF of plots?" help="Default: Yes" /> |
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58ef4507ce5a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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63 <param name="rscript" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="False" label="Output Rscript?" help="If this option is set to Yes, the Rscript used to annotate the IDs will be provided as a text file in the output. Default: No" /> |
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535321abf9a4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 861db0d1f76bb320f49c2501f4e656cf88d389ce
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64 <param name="rdata" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Output RData file?" |
535321abf9a4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 861db0d1f76bb320f49c2501f4e656cf88d389ce
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65 help="Output all the data used by R to construct the tables and plots, can be loaded into R. Default: No"> |
535321abf9a4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 861db0d1f76bb320f49c2501f4e656cf88d389ce
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66 </param> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit bae8cc7d7a88154b815acc3cd126010e7e965d5c
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67 |
cb133602cd9b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit bae8cc7d7a88154b815acc3cd126010e7e965d5c
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68 <section name="adv" expanded="false" title="Advanced Options"> |
cb133602cd9b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit bae8cc7d7a88154b815acc3cd126010e7e965d5c
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69 <param name="upstream" type="integer" min="0" value="3000" label="TSS upstream region" help="User can define TSS (transcription start site) region, by default TSS is defined from -3kb to +3kb." /> |
cb133602cd9b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit bae8cc7d7a88154b815acc3cd126010e7e965d5c
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70 <param name="downstream" type="integer" min="0" value="3000" label="TSS downstream region" help="User can define TSS (transcription start site) region, by default TSS is defined from -3kb to +3kb."/> |
cb133602cd9b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit bae8cc7d7a88154b815acc3cd126010e7e965d5c
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71 <param name="flankgeneinfo" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Add flanking gene information?" help="If specified all genes within the flanking gene distance are reported for each peak. Default: No."/> |
cb133602cd9b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit bae8cc7d7a88154b815acc3cd126010e7e965d5c
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72 <param name="flankgenedist" type="integer" min="0" value="5000" label="Flanking gene distance" help="If flanking gene info is turned on the flanking distance can be specified. Default: 5000."/> |
cb133602cd9b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit bae8cc7d7a88154b815acc3cd126010e7e965d5c
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73 </section> |
0
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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74 </inputs> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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75 |
58ef4507ce5a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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76 <outputs> |
1
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77 <data name="out_tab" format="interval" from_work_dir="out.tab" label="${tool.name} on ${on_string}: Annotated Peaks" > |
95f779f4adb7
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78 <change_format> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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79 <when input="format" value="tabular" format="tabular" /> |
95f779f4adb7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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80 </change_format> |
95f779f4adb7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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81 </data> |
0
58ef4507ce5a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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82 <data name="out_plots" format="pdf" from_work_dir="out.pdf" label="${tool.name} on ${on_string}: Plots"> |
58ef4507ce5a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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83 <filter>pdf</filter> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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84 </data> |
58ef4507ce5a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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85 <data name="out_rscript" format="txt" from_work_dir="out_rscript.txt" label="${tool.name} on ${on_string}: Rscript"> |
58ef4507ce5a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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86 <filter>rscript</filter> |
58ef4507ce5a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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87 </data> |
3
535321abf9a4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 861db0d1f76bb320f49c2501f4e656cf88d389ce
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88 <data name="out_rdata" format="rdata" from_work_dir="ChIPseeker_analysis.RData" label="${tool.name} on ${on_string}: RData file"> |
535321abf9a4
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89 <filter>rdata</filter> |
535321abf9a4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 861db0d1f76bb320f49c2501f4e656cf88d389ce
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90 </data> |
0
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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91 </outputs> |
58ef4507ce5a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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92 |
58ef4507ce5a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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93 <tests> |
1
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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94 <!-- Ensure bed and GTF inputs and all outputs work --> |
3
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 861db0d1f76bb320f49c2501f4e656cf88d389ce
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95 <test expect_num_outputs="4"> |
1
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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96 <param name="peaks" value="in.bed" ftype="bed"/> |
95f779f4adb7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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97 <param name="gtf_source_select" value="history"/> |
95f779f4adb7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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98 <param name="gtf_hist" value="in.gtf"/> |
0
58ef4507ce5a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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99 <param name="rscript" value="True"/> |
3
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 861db0d1f76bb320f49c2501f4e656cf88d389ce
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100 <param name="rdata" value="True"/> |
1
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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101 <output name="out_tab" ftype="interval" file="out.int" /> |
0
58ef4507ce5a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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102 <output name="out_plots" file="out.pdf" compare="sim_size"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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103 <output name="out_rscript" > |
58ef4507ce5a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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104 <assert_contents> |
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105 <has_text_matching expression="peakAnno.*annotatePeak" /> |
58ef4507ce5a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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106 </assert_contents> |
58ef4507ce5a
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107 </output> |
3
535321abf9a4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 861db0d1f76bb320f49c2501f4e656cf88d389ce
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108 <output name="out_rdata" file="out.rdata" compare="sim_size" /> |
0
58ef4507ce5a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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109 </test> |
1
95f779f4adb7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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110 <!-- Ensure built-in GTF works --> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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111 <test expect_num_outputs="2"> |
95f779f4adb7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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112 <param name="peaks" value="in.interval" ftype="interval"/> |
95f779f4adb7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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113 <param name="gtf_source_select" value="cached"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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114 <output name="out_tab" ftype="interval" file="outint.int" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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115 <output name="out_plots" file="out.pdf" compare="sim_size"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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116 </test> |
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117 <!-- Ensure tabular output works --> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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118 <test expect_num_outputs="2"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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119 <param name="peaks" value="in.interval" ftype="interval"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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120 <param name="gtf_source_select" value="history"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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121 <param name="gtf_hist" value="in.gtf"/> |
95f779f4adb7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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122 <param name="format" value="tabular"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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123 <output name="out_tab" ftype="tabular" file="outint.tab" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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124 <output name="out_plots" file="out.pdf" compare="sim_size"/> |
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125 </test> |
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126 <!-- Ensure TSS region specification works --> |
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127 <test expect_num_outputs="2"> |
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128 <param name="peaks" value="in.interval" ftype="interval"/> |
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129 <param name="gtf_source_select" value="history"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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130 <param name="gtf_hist" value="in.gtf"/> |
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131 <param name="upstream" value="1000" /> |
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132 <param name="downstream" value="1000" /> |
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133 <param name="format" value="tabular"/> |
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134 <output name="out_tab" ftype="tabular" file="outtss.tab" /> |
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135 <output name="out_plots" file="out.pdf" compare="sim_size"/> |
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136 </test> |
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137 <!-- Ensure flanking genes works --> |
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138 <test expect_num_outputs="2"> |
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139 <param name="peaks" value="in.interval" ftype="interval"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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140 <param name="gtf_source_select" value="history"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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141 <param name="gtf_hist" value="in.gtf"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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142 <param name="flankgeneinfo" value="True" /> |
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143 <param name="format" value="tabular"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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144 <output name="out_tab" ftype="tabular" file="outflank.tab" /> |
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145 <output name="out_plots" file="out.pdf" compare="sim_size"/> |
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146 </test> |
5
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147 <!-- Ensure the tool works when no plots are outputed --> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 853e74181667ce9ac6a0c91d4a2b204c0b3fda06
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148 <test expect_num_outputs="1"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 853e74181667ce9ac6a0c91d4a2b204c0b3fda06
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149 <param name="peaks" value="in.interval" ftype="interval"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 853e74181667ce9ac6a0c91d4a2b204c0b3fda06
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150 <param name="gtf_source_select" value="cached"/> |
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151 <param name="pdf" value=""/> |
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152 <output name="out_tab" ftype="interval" file="outint.int" /> |
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153 </test> |
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154 </tests> |
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155 <help><![CDATA[ |
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156 |
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157 .. class:: infomark |
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158 |
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159 **What it does** |
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160 |
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161 ChIPseeker_ is a Bioconductor package for annotating ChIP-seq data analysis. Peak Annotation is performed by the annotatePeak function. The position and strand information of nearest genes are reported, in addition to the distance from the peak to the TSS of its nearest gene. Users can define the TSS (transcription start site) region under **Advanced Options**, by default the TSS region is defined from -3kb to +3kb. The genomic region of the peak is reported in the annotation column. Since some annotations may overlap for a peak, ChIPseeker adopts the following priority in genomic annotation: |
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162 |
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163 * Promoter |
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164 * 5’ UTR |
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165 * 3’ UTR |
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166 * Exon |
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167 * Intron |
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168 * Downstream |
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169 * Intergenic |
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170 |
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171 ChIPseeker also produces plots to help users visualise the overlaps in annotation for peaks, for example, the vennpie and upsetplot. See the `ChIPseeker vignette`_ for more information. |
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172 |
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173 ----- |
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174 |
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175 **Inputs** |
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176 |
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177 A peaks file in BED, Interval or Tabular format e.g from MACS2 or DiffBind. |
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178 |
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179 Example: |
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180 |
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181 ===== ====== ====== ======== ===== ====== |
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182 Chrom Start End Name Score Strand |
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183 ===== ====== ====== ======== ===== ====== |
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184 18 394599 396513 DiffBind 0 . |
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185 18 111566 112005 DiffBind 0 . |
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186 18 346463 347342 DiffBind 0 . |
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187 18 399013 400382 DiffBind 0 . |
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188 18 371109 372102 DiffBind 0 . |
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189 ===== ====== ====== ======== ===== ====== |
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190 |
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191 A GTF file for annotation. The GTF file must have fields called "gene_id" and gene_name". |
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192 |
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193 ----- |
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194 |
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195 **Outputs** |
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196 |
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197 This tool outputs |
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198 |
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199 * a file of annotated peaks in Interval or Tabular format |
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200 * a PDF of plots (plotAnnoPie, vennpie, upsetplot) |
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201 |
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202 Optionally, you can choose to output |
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203 |
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204 * the R script used by this tool |
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205 * an RData file |
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206 |
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207 **Annotated peaks** |
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208 |
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209 Annotation similar to below will be added to the input file. |
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210 |
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211 Example - **Interval format**: |
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212 |
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213 ===== ====== ====== ===================================================================================================================================================== |
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214 Chrom Start End Comment |
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215 ===== ====== ====== ===================================================================================================================================================== |
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216 18 394599 396513 DiffBind|0|.|Intron (ENST00000400256/ENSG00000158270, intron 1 of 1)|1|346465|400382|53918|2|ENST00000400256| 3869|COLEC12|ENSG00000158270 |
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217 18 346463 347342 DiffBind|0|.|Exon (ENST00000400256/ENSG00000158270, exon 1 of 1)|1|346465|400382|53918|2|ENST00000400256|53040|COLEC12|ENSG00000158270 |
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218 18 399013 400382 DiffBind|0|.|Promoter (<=1kb)|1|346465|400382|53918|2|ENST00000400256| 0|COLEC12|ENSG00000158270 |
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219 18 371109 372102 DiffBind|0|.|Intron (ENST00000400256/ENSG00000158270, intron 1 of 1)|1|346465|400382|53918|2|ENST00000400256|28280|COLEC12|ENSG00000158270 |
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220 18 111566 112005 DiffBind|0|.|Promoter (<=1kb)|1|111568|112005| 438|1|ENST00000608049| 0|ROCK1P1|ENSG00000263006 |
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221 ===== ====== ====== ===================================================================================================================================================== |
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222 |
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223 Columns contain the following data: |
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224 |
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225 * **Chrom**: Chromosome name |
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226 * **Start**: Start position of site |
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227 * **End**: End position of site |
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228 * **Comment**: The pipe ("|") separated values in this column correspond to: |
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229 |
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230 * *<Any additional input columns>* |
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231 * *annotation* (Promoter, 5’ UTR, 3’ UTR, Exon, Intron, Downstream, Intergenic) |
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232 * *geneChr* |
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233 * *geneStart* |
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234 * *geneEnd* |
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235 * *geneLength* |
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236 * *geneStrand* |
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237 * *transcriptId* |
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238 * *distanceToTSS* |
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239 * *geneName* |
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240 * *geneId* |
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241 |
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242 Example - **Tabular format**: |
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243 |
3
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244 ===== ====== ====== ======== ====== ====== =========================================== ======================================================= ======= ========= ======= ========== ========== =============== ============= ======== =============== |
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245 Chrom Start End Name Score Strand Comment annotation geneChr geneStart geneEnd geneLength geneStrand transcriptId distanceToTSS geneName geneId |
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246 ===== ====== ====== ======== ====== ====== =========================================== ======================================================= ======= ========= ======= ========== ========== =============== ============= ======== =============== |
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247 18 394599 396513 DiffBind 0 . 1914|7.15|5.55|7.89|-2.35|7.06e-24|9.84e-21 Intron (ENST00000400256/ENSG00000158270, intron 1 of 1) 1 346465 400382 53918 2 ENST00000400256 3869 COLEC12 ENSG00000158270 |
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248 18 346463 347342 DiffBind 0 . 879|5|5.77|3.24|2.52|6.51e-06|0.00303 Exon (ENST00000400256/ENSG00000158270, exon 1 of 1) 1 346465 400382 53918 2 ENST00000400256 53040 COLEC12 ENSG00000158270 |
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249 18 399013 400382 DiffBind 0 . 1369|7.62|7|8.05|-1.04|1.04e-05|0.00364 Promoter (<=1kb) 1 346465 400382 53918 2 ENST00000400256 0 COLEC12 ENSG00000158270 |
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250 18 371109 372102 DiffBind 0 . 993|4.63|3.07|5.36|-2.3|8.1e-05|0.0226 Intron (ENST00000400256/ENSG00000158270, intron 1 of 1) 1 346465 400382 53918 2 ENST00000400256 28280 COLEC12 ENSG00000158270 |
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251 18 111566 112005 DiffBind 0 . 439|5.71|6.53|3.63|2.89|1.27e-08|8.88e-06 Promoter (<=1kb) 1 111568 112005 438 1 ENST00000608049 0 ROCK1P1 ENSG00000263006 |
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252 ===== ====== ====== ======== ====== ====== =========================================== ======================================================= ======= ========= ======= ========== ========== =============== ============= ======== =============== |
1
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253 |
0
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254 .. _ChIPseeker: https://bioconductor.org/packages/release/bioc/html/ChIPseeker.html |
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255 .. _`ChIPseeker vignette`: http://bioconductor.org/packages/release/bioc/vignettes/ChIPseeker/inst/doc/ChIPseeker.html |
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256 |
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257 ]]></help> |
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258 <citations> |
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259 <citation type="doi">10.1093/bioinformatics/btv145</citation> |
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260 </citations> |
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261 </tool> |