Mercurial > repos > iuc > nanocompore_db
view nanocompore_db.xml @ 2:ca9e70c0fef8 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit c2985b5c91a932e175cbfaf9b54a76e23beff9e9"
author | iuc |
---|---|
date | Thu, 09 Jul 2020 02:39:10 -0400 |
parents | 2af554112418 |
children | 35d3618b124b |
line wrap: on
line source
<tool id="nanocompore_db" name="NanoComporeDB" version="@TOOL_VERSION@+galaxy2"> <description>Process SampComp results database</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ mkdir -p results plots && 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' --pvalue-types '$pvalue_types' --pvalue-threshold $pvalue_threshold --out-dir ./plots/ $bedgraph ]]></command> <inputs> <param name="reference" type="data" format="fasta" label="The reference genome used for read alignment."/> <param name="annotation" format="bed" type="data" label="BED file containing the annotation of the transcriptome used as reference when mapping"/> <param name="db" type="data" format="tar" label="SampComp Database" /> <param argument="--pvalue-types" type="text" value="GMM_logit_pvalue,KS_dwell_pvalue,KS_intensity_pvalue" label="pvalue field names" help="Comma-separated values."> <validator type="regex" message="No valid pvalue field name list.">^(\w+(,\w+)*)?$</validator> </param> <param argument="pvalue-threshold" type="float" value="1.0" min="0.0" label="Maximum reported p-value"/> <param argument="--bedgraph" type="boolean" truevalue="--bedgraph" falsevalue="" label="Write output in BedGraph format instead of BED"/> </inputs> <outputs> <collection name="pvalue_output" type="list"> <discover_datasets pattern="__name_and_ext__" directory="plots" /> </collection> </outputs> <tests> <test> <param name="reference" value="reference.fa"/> <param name="annotation" value="annot.bed"/> <param name="db" value="DB.tar" ftype="tar" /> <output_collection name="pvalue_output" type="list" count="3"> <element name="GMM_logit_pvalue" file="GMM_logit_pvalue.bed" ftype="bed"/> <element name="KS_dwell_pvalue" file="KS_dwell_pvalue.bed" ftype="bed"/> <element name="KS_intensity_pvalue" file="KS_intensity_pvalue.bed" ftype="bed"/> </output_collection> </test> <test> <param name="reference" value="reference.fa"/> <param name="annotation" value="annot.bed"/> <param name="db" value="DB.tar" ftype="tar" /> <param name="bedgraph" value="true"/> <param name="pvalue_types" value="GMM_logit_pvalue,KS_dwell_pvalue"/> <output_collection name="pvalue_output" type="list" count="2"> <element name="GMM_logit_pvalue" file="GMM_logit_pvalue.bedgraph" ftype="bedgraph"/> <element name="KS_dwell_pvalue" file="KS_dwell_pvalue.bedgraph" ftype="bedgraph"/> </output_collection> </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>