Mercurial > repos > iuc > nanocompore_db
view nanocompore_db.xml @ 0:b6eeea872fd2 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 652a872061324ba1073bfa286777ffeefa352671"
author | iuc |
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date | Mon, 08 Jun 2020 14:41:41 -0400 |
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children | 2af554112418 |
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<tool id="nanocompore_db" name="NanoComporeDB" version="@TOOL_VERSION@+@WRAPPER_VERSION@"> <description>Process SampComp results database</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ mkdir results && tar -xf $db --strip-components 1 -C results/ && python '$__tool_directory__/NanocomporeDB_process.py' --db-path 'results/out_SampComp.db' --ref-fasta '$reference' --annotation-bed '$annotation' ]]></command> <inputs> <param name="reference" type="data" format="fasta" label="The reference genome used for read alignment."/> <param name="annotation" format="bed" type="data" label="BED file containing the annotation of the transcriptome used as reference when mapping"/> <param name="db" type="data" format="tar" label="SampComp Database" /> </inputs> <outputs> <data name="GMM_logit" format="bedgraph" from_work_dir="GMM_logit_pvalue.bedgraph" /> <data name="KS_dwell" format="bedgraph" from_work_dir="KS_dwell_pvalue.bedgraph" /> <data name="KS_intensity" format="bedgraph" from_work_dir="KS_intensity_pvalue.bedgraph" /> </outputs> <tests> <test> <param name="reference" value="reference.fa"/> <param name="annotation" value="annot.bed"/> <param name="db" value="DB.tar"/> <output name="GMM_logit" file="GMM_logit_pvalue.bedgraph"/> <output name="KS_dwell" file="KS_dwell_pvalue.bedgraph"/> <output name="KS_intensity" file="KS_intensity_pvalue.bedgraph"/> </test> </tests> <help><![CDATA[ Produces interval bed and bedgraph outputs from NanoCompore SampComp results as input using NaonComporeDB API. **References** @REFERENCES@ ]]></help> <expand macro="citations"/> </tool>