Mercurial > repos > jpayne > snp_pipeline
comparison 7_smp_matrix.xml @ 0:eefdd97a6749
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| author | jpayne |
|---|---|
| date | Wed, 24 Jan 2018 14:18:21 -0500 |
| parents | |
| children | 62191abf5426 |
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| -1:000000000000 | 0:eefdd97a6749 |
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| 1 <tool id="snp_matrix" name="7. Create a SNP matrix" version="1.0.1" profile="16.10"> | |
| 2 <description>and associated distance metrics</description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="1.0.1">snp-pipeline</requirement> | |
| 5 <requirement type="package">tabix</requirement> | |
| 6 </requirements> | |
| 7 <command detect_errors="exit_code"><![CDATA[ | |
| 8 $__tool_directory__/snp-wind.py ./ -p "consensus.fasta" | |
| 9 #for $fa in sorted($cons, key=lambda f: f.element_identifier) | |
| 10 -n $fa.element_identifier -f $fa | |
| 11 #end for | |
| 12 > ./file && | |
| 13 cat ./file && | |
| 14 cfsan_snp_pipeline snp_matrix -o $snpma ./file && | |
| 15 cfsan_snp_pipeline distance -p $pairws -m $distma $snpma && | |
| 16 cfsan_snp_pipeline snp_reference -l $snplist -o $referenceSNP $reference | |
| 17 ]]></command> | |
| 18 <inputs> | |
| 19 <param type="data_collection" label="List of FASTA's" name="cons" format="fasta" collection_type="list" /> | |
| 20 <conditional name="reference"> | |
| 21 <param name="ref" type="select" label="Use a curated GalaxyTrakr reference, or a reference from your history" help="Choose whether to use one of our references or your own from your history"> | |
| 22 <option value="curated">Use a GalaxyTrakr reference</option> | |
| 23 <option value="history">Use a reference from your history</option> | |
| 24 </param> | |
| 25 <when value="curated"> | |
| 26 <param name="reference" type="select" label="Select reference fasta"> | |
| 27 <options from_data_table="all_fasta"> | |
| 28 <filter type="sort_by" column="2"/> | |
| 29 <validator type="no_options" message="No assemblies are available for the selected input dataset"/> | |
| 30 </options> | |
| 31 </param> | |
| 32 </when> | |
| 33 <when value="history"> | |
| 34 <param name="reference" type="data" format="fasta" label="Select reference fasta" /> | |
| 35 </when> | |
| 36 </conditional> | |
| 37 <param type="data" format="txt" name="snplist" label="SNP list from your history" /> | |
| 38 </inputs> | |
| 39 <outputs> | |
| 40 <data name="snpma" label="SNP matrix, fasta" format="fasta" /> | |
| 41 <data name="pairws" label="SNP pairwise matrix" format="tsv" /> | |
| 42 <data name="distma" label="SNP distance matrix" format="tsv" /> | |
| 43 <data name="referenceSNP" format="fasta" /> | |
| 44 <data name="metrics" format="tsv" /> | |
| 45 </outputs> | |
| 46 <tests> | |
| 47 <test> | |
| 48 <param name="cons"> | |
| 49 <collection type="list"> | |
| 50 <element name="sample1" value="samples/sample1/consensus.fasta" /> | |
| 51 <element name="sample2" value="samples/sample2/consensus.fasta" /> | |
| 52 <element name="sample3" value="samples/sample3/consensus.fasta" /> | |
| 53 <element name="sample4" value="samples/sample4/consensus.fasta" /> | |
| 54 </collection> | |
| 55 </param> | |
| 56 <param name="ref" value="history" /> | |
| 57 <param name="reference" value="reference/lambda_virus.fasta" /> | |
| 58 <param name="snplist" value="snplist.txt" /> | |
| 59 <output name="snpma" value="snpma.fasta" /> | |
| 60 <output name="pairws" value="snp_distance_pairwise.tsv" /> | |
| 61 <output name="distma" value="snp_distance_matrix.tsv" /> | |
| 62 <output name="referenceSNP" value="referenceSNP.fasta" /> | |
| 63 </test> | |
| 64 </tests> | |
| 65 <help><![CDATA[ | |
| 66 <a href="http://snp-pipeline.readthedocs.io/en/latest/index.html">http://snp-pipeline.readthedocs.io/en/latest/index.html</a> | |
| 67 ]]></help> | |
| 68 <citations> | |
| 69 <citation type="doi">10.7717/peerj-cs.20</citation> | |
| 70 </citations> | |
| 71 </tool> |