comparison chipseeker.xml @ 8:8bd92f2404dd draft default tip

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker commit d30c91c3b4f71ec45b72976f7c2f08ea7df1e376-dirty"

7:1b9a9409831d

<tool id="chipseeker" name="ChIPseeker" version="1.18.0+galaxy1">
    <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[

            <param name="gtf_hist" value="in.gtf"/>
            <param name="rscript" value="True"/>
            <param name="rdata" value="True"/>
            <output name="out_tab" ftype="interval" file="out.int" />
            <output name="out_plots" file="out.pdf" compare="sim_size"/>
            <output name="out_rscript" >
                <assert_contents>
                    <has_text_matching expression="peakAnno.*annotatePeak" />
                </assert_contents>
            </output>
            <output name="out_rdata" file="out.rdata" compare="sim_size" />
        </test>
        <!-- Ensure built-in GTF works -->
        <test expect_num_outputs="2">
            <param name="peaks" value="in.interval" ftype="interval"/>
            <param name="gtf_source_select" value="cached"/>

8:8bd92f2404dd

<tool id="chipseeker" name="ChIPseeker" version="1.28.3+galaxy0">
    <description>for ChIP peak annotation and visualization</description>
    <requirements>
        <requirement type="package" version="1.28.3">bioconductor-chipseeker</requirement>
        <requirement type="package" version="1.6.6">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[

            <param name="gtf_hist" value="in.gtf"/>
            <param name="rscript" value="True"/>
            <param name="rdata" value="True"/>
            <output name="out_tab" ftype="interval" file="out.int" />
            <output name="out_plots" file="out.pdf" compare="sim_size"/>
            <output name="out_rscript">
                <assert_contents>
                    <has_text_matching expression="peak_anno.*annotatePeak" />
                </assert_contents>
            </output>
            <output name="out_rdata">
                <assert_contents>
                        <has_size value="160346" delta="300"/>
                </assert_contents>
            </output>
        </test>
        <!-- Ensure built-in GTF works -->
        <test expect_num_outputs="2">
            <param name="peaks" value="in.interval" ftype="interval"/>
            <param name="gtf_source_select" value="cached"/>