comparison chipseeker.xml @ 5:3ff6333973aa draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit d83142dbe2432fcb0f56dcd6311a05c061628ecc

4:4fbd735886dd

<tool id="chipseeker" name="ChIPseeker" version="1.16.2">
    <description>for ChIP peak annotation and visualization</description>
    <requirements>
        <requirement type="package" version="1.16.1">bioconductor-chipseeker</requirement>
        <requirement type="package" version="1.4.4">r-optparse</requirement>
    </requirements>
    <version_command><![CDATA[
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: ")
    ]]></version_command>
    <command detect_errors="exit_code"><![CDATA[

        -i '$peaks'
        -G '$gtf'
        -u $adv.upstream
        -d $adv.downstream
        #if $adv.flankgeneinfo:
            -F $adv.flankgeneinfo
            -D $adv.flankgenedist
        #end if
        -f $format
        #if $pdf:
            -p $pdf
        #end if
        -r $rdata
    ]]>
    </command>
    <inputs>
        <param name="peaks" type="data" format="bed,interval,tabular" label="Peaks file" help="A peaks file in BED format." />

        <section name="adv" expanded="false" title="Advanced Options">
            <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." />
            <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."/>
            <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."/>
            <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."/>
        </section>
    </inputs>

        <outputs>
            <data name="out_tab" format="interval" from_work_dir="out.tab" label="${tool.name} on ${on_string}: Annotated Peaks" >

5:3ff6333973aa

<tool id="chipseeker" name="ChIPseeker" version="1.18.0">
    <description>for ChIP peak annotation and visualization</description>
    <requirements>
        <requirement type="package" version="1.18.0">bioconductor-chipseeker</requirement>
        <requirement type="package" version="1.6.1">r-optparse</requirement>
    </requirements>
    <version_command><![CDATA[
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: ")
    ]]></version_command>
    <command detect_errors="exit_code"><![CDATA[

        -i '$peaks'
        -G '$gtf'
        -u $adv.upstream
        -d $adv.downstream

        #if $adv.flankgeneinfo:
            -F $adv.flankgeneinfo
        #end if

        -D $adv.flankgenedist

        #if $adv.ignoreUpstream:
            -j $adv.ignoreUpstream
        #end if

        #if $adv.ignoreDownstream:
            -k $adv.ignoreDownstream
        #end if

        -f $format

        #if $pdf:
            -p $pdf
        #end if

        -r $rdata
    ]]>
    </command>
    <inputs>
        <param name="peaks" type="data" format="bed,interval,tabular" label="Peaks file" help="A peaks file in BED format." />

        <section name="adv" expanded="false" title="Advanced Options">
            <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." />
            <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."/>
            <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."/>
            <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."/>
            <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."/>
            <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."/>
        </section>
    </inputs>

        <outputs>
            <data name="out_tab" format="interval" from_work_dir="out.tab" label="${tool.name} on ${on_string}: Annotated Peaks" >