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comparison chipseeker.xml @ 5:4c2dbe4dbb4e draft

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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
comparison
equal deleted inserted replaced
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