Mercurial > repos > rnateam > chipseeker
comparison chipseeker.xml @ 5:4c2dbe4dbb4e draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 853e74181667ce9ac6a0c91d4a2b204c0b3fda06
| author | rnateam |
|---|---|
| date | Tue, 04 Dec 2018 10:01:20 -0500 |
| parents | 90fe78a19b55 |
| children | b418a1d3585d |
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| 4:90fe78a19b55 | 5:4c2dbe4dbb4e |
|---|---|
| 1 <tool id="chipseeker" name="ChIPseeker" version="1.16.1"> | 1 <tool id="chipseeker" name="ChIPseeker" version="1.16.2"> |
| 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="1.16.1">bioconductor-chipseeker</requirement> |
| 5 <requirement type="package" version="1.4.4">r-optparse</requirement> | 5 <requirement type="package" version="1.4.4">r-optparse</requirement> |
| 6 </requirements> | 6 </requirements> |
| 28 #if $adv.flankgeneinfo: | 28 #if $adv.flankgeneinfo: |
| 29 -F $adv.flankgeneinfo | 29 -F $adv.flankgeneinfo |
| 30 -D $adv.flankgenedist | 30 -D $adv.flankgenedist |
| 31 #end if | 31 #end if |
| 32 -f $format | 32 -f $format |
| 33 -p $pdf | 33 #if $pdf: |
| 34 -p $pdf | |
| 35 #end if | |
| 34 -r $rdata | 36 -r $rdata |
| 35 ]]> | 37 ]]> |
| 36 </command> | 38 </command> |
| 37 <inputs> | 39 <inputs> |
| 38 <param name="peaks" type="data" format="bed,interval,tabular" label="Peaks file" help="A peaks file in BED format." /> | 40 <param name="peaks" type="data" format="bed,interval,tabular" label="Peaks file" help="A peaks file in BED format." /> |
| 140 <param name="flankgeneinfo" value="True" /> | 142 <param name="flankgeneinfo" value="True" /> |
| 141 <param name="format" value="tabular"/> | 143 <param name="format" value="tabular"/> |
| 142 <output name="out_tab" ftype="tabular" file="outflank.tab" /> | 144 <output name="out_tab" ftype="tabular" file="outflank.tab" /> |
| 143 <output name="out_plots" file="out.pdf" compare="sim_size"/> | 145 <output name="out_plots" file="out.pdf" compare="sim_size"/> |
| 144 </test> | 146 </test> |
| 147 <!-- Ensure the tool works when no plots are outputed --> | |
| 148 <test expect_num_outputs="1"> | |
| 149 <param name="peaks" value="in.interval" ftype="interval"/> | |
| 150 <param name="gtf_source_select" value="cached"/> | |
| 151 <param name="pdf" value=""/> | |
| 152 <output name="out_tab" ftype="interval" file="outint.int" /> | |
| 153 </test> | |
| 145 </tests> | 154 </tests> |
| 146 <help><![CDATA[ | 155 <help><![CDATA[ |
| 147 | 156 |
| 148 .. class:: infomark | 157 .. class:: infomark |
| 149 | 158 |