Mercurial > repos > mvdbeek > zerone_damid
comparison 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 |
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| date | Fri, 14 Sep 2018 04:52:55 -0400 |
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| -1:000000000000 | 0:7fbff19b4485 |
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| 1 <tool id="zerone_damid" name="Discretize DamID experiments with Zerone" version="1.0"> | |
| 2 <requirements> | |
| 3 <requirement type="package" version="1.0">r-zerone</requirement> | |
| 4 <requirement type="package" version="2.9.3">rpy2</requirement> | |
| 5 <requirement type="package" version="0.23">pandas</requirement> | |
| 6 <requirement type="package" version="6.7">click</requirement> | |
| 7 </requirements> | |
| 8 <command detect_errors="exit_code"><![CDATA[ | |
| 9 python '$__tool_directory__/r-zerone.py' | |
| 10 #for c in $control_files: | |
| 11 --control_files '$c' | |
| 12 #end for | |
| 13 #for d in $fusion_files: | |
| 14 --fusion_files '$d' | |
| 15 #end for | |
| 16 --output '$output' | |
| 17 ]]></command> | |
| 18 <inputs> | |
| 19 <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"/> | |
| 20 <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"/> | |
| 21 </inputs> | |
| 22 <outputs> | |
| 23 <data name="output" label="Discretized DamID profile for ${on_string}" format="bed"/> | |
| 24 </outputs> | |
| 25 <tests> | |
| 26 <test> | |
| 27 <param name="control_files" value="c1.bed,c2.bed" ftype="bed"/> | |
| 28 <param name="damid_files" value="d1.bed,d2.bed" ftype="bed"/> | |
| 29 <output name="output" value="discrete.bed" ftype="bed"/> | |
| 30 </test> | |
| 31 </tests> | |
| 32 <help><![CDATA[ | |
| 33 | |
| 34 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. | |
| 35 | |
| 36 This wrapper uses the zerone R package to discretize quantified GATC counts. | |
| 37 ]]></help> | |
| 38 <citations> | |
| 39 <citation type="doi">10.1093/bioinformatics/btw336</citation> | |
| 40 </citations> | |
| 41 </tool> |