Mercurial > repos > mvdbeek > zerone_damid
diff zerone_damid.xml @ 0:7fbff19b4485 draft default tip
planemo upload for repository https://github.com/galaxyproject/mvdbeek/tree/master/tools/zerone commit 35b6256bc4fe6138f03228795e88da46068ac14e
| author | mvdbeek |
|---|---|
| date | Fri, 14 Sep 2018 04:52:55 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/zerone_damid.xml Fri Sep 14 04:52:55 2018 -0400 @@ -0,0 +1,41 @@ +<tool id="zerone_damid" name="Discretize DamID experiments with Zerone" version="1.0"> + <requirements> + <requirement type="package" version="1.0">r-zerone</requirement> + <requirement type="package" version="2.9.3">rpy2</requirement> + <requirement type="package" version="0.23">pandas</requirement> + <requirement type="package" version="6.7">click</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ +python '$__tool_directory__/r-zerone.py' +#for c in $control_files: +--control_files '$c' +#end for +#for d in $fusion_files: +--fusion_files '$d' +#end for +--output '$output' + ]]></command> + <inputs> + <param argument="--control_files" type="data" format="bed" multiple="true" label="BED file(s) containing GATC counts for DamID control" help="You can produce these files uing bedtools coverageBed"/> + <param argument="--fusion_files" type="data" format="bed" multiple="true" label="BED file(s) containing GATC counts for DamID fusion" help="You can produce these files uing bedtools coverageBed"/> + </inputs> + <outputs> + <data name="output" label="Discretized DamID profile for ${on_string}" format="bed"/> + </outputs> + <tests> + <test> + <param name="control_files" value="c1.bed,c2.bed" ftype="bed"/> + <param name="damid_files" value="d1.bed,d2.bed" ftype="bed"/> + <output name="output" value="discrete.bed" ftype="bed"/> + </test> + </tests> + <help><![CDATA[ + +Zerone discretizes several ChIP-seq replicates simultaneously and resolves conflicts between them. After the job is done, Zerone checks the results and tells you whether it passes the quality control. + +This wrapper uses the zerone R package to discretize quantified GATC counts. + ]]></help> + <citations> + <citation type="doi">10.1093/bioinformatics/btw336</citation> + </citations> +</tool>