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1 <tool id="snp_matrix" name="7. Create a SNP matrix" version="1.0.1" profile="16.10">
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2 <description>and associated distance metrics</description>
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3 <requirements>
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4 <requirement type="package" version="1.6">bcftools</requirement>
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5 <requirement type="package" version="1.0.6">bzip2</requirement>
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6 <requirement type="package" version="1.0.1">snp-pipeline</requirement>
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7 <requirement type="package" version="0.2.5">tabix</requirement>
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8 <!-- <requirement type="package" version="3.5">python</requirement> -->
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9 </requirements>
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10 <command detect_errors="exit_code"><![CDATA[
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11 export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" &&
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12 env &&
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13 python $__tool_directory__/snp-wind.py ./ -p "consensus.fasta"
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14 #for $fa in sorted($cons, key=lambda f: f.element_identifier)
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15 -n $fa.element_identifier -f $fa
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16 #end for
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17 > ./file &&
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18 cat ./file &&
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19 cfsan_snp_pipeline snp_matrix -o $snpma ./file &&
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20 cfsan_snp_pipeline distance -p $pairws -m $distma $snpma &&
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21 cfsan_snp_pipeline snp_reference -l $snplist -o $referenceSNP $reference
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22 ]]></command>
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23 <inputs>
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24 <param type="data_collection" label="List of FASTA's" name="cons" format="fasta" collection_type="list" />
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25 <conditional name="reference">
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26 <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">
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27 <option value="curated">Use a GalaxyTrakr reference</option>
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28 <option value="history">Use a reference from your history</option>
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29 </param>
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30 <when value="curated">
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31 <param name="reference" type="select" label="Select reference fasta">
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32 <options from_data_table="all_fasta">
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33 <filter type="sort_by" column="2"/>
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34 <validator type="no_options" message="No assemblies are available for the selected input dataset"/>
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35 </options>
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36 </param>
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37 </when>
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38 <when value="history">
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39 <param name="reference" type="data" format="fasta" label="Select reference fasta" />
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40 </when>
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41 </conditional>
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42 <param type="data" format="txt" name="snplist" label="SNP list from your history" />
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43 </inputs>
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44 <outputs>
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45 <data name="snpma" label="SNP matrix, fasta" format="fasta" />
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46 <data name="pairws" label="SNP pairwise matrix" format="tsv" />
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47 <data name="distma" label="SNP distance matrix" format="tsv" />
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48 <data name="referenceSNP" label="SNP Reference (FASTA)" format="fasta" />
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49 <data name="metrics" label="SNP matrix metrics" hidden="true" format="tsv" />
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50 </outputs>
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51 <tests>
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52 <test>
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53 <param name="cons">
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54 <collection type="list">
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55 <element name="sample1" value="samples/sample1/consensus.fasta" />
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56 <element name="sample2" value="samples/sample2/consensus.fasta" />
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57 <element name="sample3" value="samples/sample3/consensus.fasta" />
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58 <element name="sample4" value="samples/sample4/consensus.fasta" />
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59 </collection>
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60 </param>
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61 <param name="ref" value="history" />
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62 <param name="reference" value="reference/lambda_virus.fasta" />
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63 <param name="snplist" value="snplist.txt" />
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64 <output name="snpma" value="snpma.fasta" />
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65 <output name="pairws" value="snp_distance_pairwise.tsv" />
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66 <output name="distma" value="snp_distance_matrix.tsv" />
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67 <output name="referenceSNP" value="referenceSNP.fasta" />
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68 </test>
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69 </tests>
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70 <help><![CDATA[
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71 <a href="http://snp-pipeline.readthedocs.io/en/latest/index.html">http://snp-pipeline.readthedocs.io/en/latest/index.html</a>
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72 ]]></help>
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73 <citations>
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74 <citation type="doi">10.7717/peerj-cs.20</citation>
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75 </citations>
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76 </tool> |
