Mercurial > repos > iuc > nanocompore_db
comparison nanocompore_db.xml @ 0:ace1c453a190 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 652a872061324ba1073bfa286777ffeefa352671"
| author | iuc |
|---|---|
| date | Mon, 08 Jun 2020 18:33:20 +0000 |
| parents | |
| children | 97a6b3f9a98d |
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| -1:000000000000 | 0:ace1c453a190 |
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| 1 <tool id="nanocompore_db" name="NanoComporeDB" version="@TOOL_VERSION@+@WRAPPER_VERSION@"> | |
| 2 <description>Process SampComp results database</description> | |
| 3 <macros> | |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="requirements"/> | |
| 7 <command detect_errors="exit_code"><![CDATA[ | |
| 8 mkdir results && | |
| 9 tar -xf $db --strip-components 1 -C results/ && | |
| 10 python '$__tool_directory__/NanocomporeDB_process.py' | |
| 11 --db-path 'results/out_SampComp.db' | |
| 12 --ref-fasta '$reference' | |
| 13 --annotation-bed '$annotation' | |
| 14 ]]></command> | |
| 15 <inputs> | |
| 16 <param name="reference" type="data" format="fasta" label="The reference genome used for read alignment."/> | |
| 17 <param name="annotation" format="bed" type="data" label="BED file containing the annotation of the transcriptome used as reference when mapping"/> | |
| 18 <param name="db" type="data" format="tar" label="SampComp Database" /> | |
| 19 </inputs> | |
| 20 <outputs> | |
| 21 <data name="GMM_logit" format="bedgraph" from_work_dir="GMM_logit_pvalue.bedgraph" /> | |
| 22 <data name="KS_dwell" format="bedgraph" from_work_dir="KS_dwell_pvalue.bedgraph" /> | |
| 23 <data name="KS_intensity" format="bedgraph" from_work_dir="KS_intensity_pvalue.bedgraph" /> | |
| 24 </outputs> | |
| 25 <tests> | |
| 26 <test> | |
| 27 <param name="reference" value="reference.fa"/> | |
| 28 <param name="annotation" value="annot.bed"/> | |
| 29 <param name="db" value="DB.tar"/> | |
| 30 <output name="GMM_logit" file="GMM_logit_pvalue.bedgraph"/> | |
| 31 <output name="KS_dwell" file="KS_dwell_pvalue.bedgraph"/> | |
| 32 <output name="KS_intensity" file="KS_intensity_pvalue.bedgraph"/> | |
| 33 </test> | |
| 34 </tests> | |
| 35 <help><![CDATA[ | |
| 36 Produces interval bed and bedgraph outputs from NanoCompore SampComp results as input using NaonComporeDB API. | |
| 37 | |
| 38 **References** | |
| 39 | |
| 40 @REFERENCES@ | |
| 41 ]]></help> | |
| 42 <expand macro="citations"/> | |
| 43 </tool> |