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comparison chipseeker.xml @ 6:b418a1d3585d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit d83142dbe2432fcb0f56dcd6311a05c061628ecc
author rnateam
date Wed, 13 Mar 2019 03:05:16 -0400
parents 4c2dbe4dbb4e
children 1b9a9409831d
comparison
equal deleted inserted replaced
5:4c2dbe4dbb4e 6:b418a1d3585d
1 <tool id="chipseeker" name="ChIPseeker" version="1.16.2"> 1 <tool id="chipseeker" name="ChIPseeker" version="1.18.0">
2 <description>for ChIP peak annotation and visualization</description> 2 <description>for ChIP peak annotation and visualization</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.16.1">bioconductor-chipseeker</requirement> 4 <requirement type="package" version="1.18.0">bioconductor-chipseeker</requirement>
5 <requirement type="package" version="1.4.4">r-optparse</requirement> 5 <requirement type="package" version="1.6.1">r-optparse</requirement>
6 </requirements> 6 </requirements>
7 <version_command><![CDATA[ 7 <version_command><![CDATA[
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: ") 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" $(R --vanilla --slave -e "library(optparse); cat(sessionInfo()\$otherPkgs\$optparse\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
9 ]]></version_command> 9 ]]></version_command>
10 <command detect_errors="exit_code"><![CDATA[ 10 <command detect_errors="exit_code"><![CDATA[
23 23
24 -i '$peaks' 24 -i '$peaks'
25 -G '$gtf' 25 -G '$gtf'
26 -u $adv.upstream 26 -u $adv.upstream
27 -d $adv.downstream 27 -d $adv.downstream
28
28 #if $adv.flankgeneinfo: 29 #if $adv.flankgeneinfo:
29 -F $adv.flankgeneinfo 30 -F $adv.flankgeneinfo
30 -D $adv.flankgenedist 31 #end if
31 #end if 32
33 -D $adv.flankgenedist
34
35 #if $adv.ignoreUpstream:
36 -j $adv.ignoreUpstream
37 #end if
38
39 #if $adv.ignoreDownstream:
40 -k $adv.ignoreDownstream
41 #end if
42
32 -f $format 43 -f $format
44
33 #if $pdf: 45 #if $pdf:
34 -p $pdf 46 -p $pdf
35 #end if 47 #end if
48
36 -r $rdata 49 -r $rdata
37 ]]> 50 ]]>
38 </command> 51 </command>
39 <inputs> 52 <inputs>
40 <param name="peaks" type="data" format="bed,interval,tabular" label="Peaks file" help="A peaks file in BED format." /> 53 <param name="peaks" type="data" format="bed,interval,tabular" label="Peaks file" help="A peaks file in BED format." />
68 <section name="adv" expanded="false" title="Advanced Options"> 81 <section name="adv" expanded="false" title="Advanced Options">
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." /> 82 <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." />
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."/> 83 <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."/>
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."/> 84 <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."/>
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."/> 85 <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."/>
86 <param name="ignoreUpstream" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Ignore upstream?" help="If Yes only annotate gene at the 3’ of the peak. Default: No."/>
87 <param name="ignoreDownstream" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Ignore downstream?" help="If Yes only annotate gene at the 5’ of the peak. Default: No."/>
73 </section> 88 </section>
74 </inputs> 89 </inputs>
75 90
76 <outputs> 91 <outputs>
77 <data name="out_tab" format="interval" from_work_dir="out.tab" label="${tool.name} on ${on_string}: Annotated Peaks" > 92 <data name="out_tab" format="interval" from_work_dir="out.tab" label="${tool.name} on ${on_string}: Annotated Peaks" >