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comparison chipseeker.xml @ 7:e23396bf7bdb draft default tip

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker commit d30c91c3b4f71ec45b72976f7c2f08ea7df1e376-dirty"
author rnateam
date Fri, 27 Aug 2021 10:50:18 +0000
parents 7da70e9119b2
children
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6:7da70e9119b2 7:e23396bf7bdb
1 <tool id="chipseeker" name="ChIPseeker" version="1.18.0+galaxy1"> 1 <tool id="chipseeker" name="ChIPseeker" version="1.28.3+galaxy0">
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="1.18.0">bioconductor-chipseeker</requirement> 4 <requirement type="package" version="1.28.3">bioconductor-chipseeker</requirement>
5 <requirement type="package" version="1.6.1">r-optparse</requirement> 5 <requirement type="package" version="1.6.6">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[
115 <param name="gtf_hist" value="in.gtf"/> 115 <param name="gtf_hist" value="in.gtf"/>
116 <param name="rscript" value="True"/> 116 <param name="rscript" value="True"/>
117 <param name="rdata" value="True"/> 117 <param name="rdata" value="True"/>
118 <output name="out_tab" ftype="interval" file="out.int" /> 118 <output name="out_tab" ftype="interval" file="out.int" />
119 <output name="out_plots" file="out.pdf" compare="sim_size"/> 119 <output name="out_plots" file="out.pdf" compare="sim_size"/>
120 <output name="out_rscript" > 120 <output name="out_rscript">
121 <assert_contents> 121 <assert_contents>
122 <has_text_matching expression="peakAnno.*annotatePeak" /> 122 <has_text_matching expression="peak_anno.*annotatePeak" />
123 </assert_contents> 123 </assert_contents>
124 </output> 124 </output>
125 <output name="out_rdata" file="out.rdata" compare="sim_size" /> 125 <output name="out_rdata">
126 <assert_contents>
127 <has_size value="160346" delta="300"/>
128 </assert_contents>
129 </output>
126 </test> 130 </test>
127 <!-- Ensure built-in GTF works --> 131 <!-- Ensure built-in GTF works -->
128 <test expect_num_outputs="2"> 132 <test expect_num_outputs="2">
129 <param name="peaks" value="in.interval" ftype="interval"/> 133 <param name="peaks" value="in.interval" ftype="interval"/>
130 <param name="gtf_source_select" value="cached"/> 134 <param name="gtf_source_select" value="cached"/>