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1 <tool id="cfsan_snp_pipeline_snp_matrix" name="CFSAN SNP Pipeline: create SNP matrix" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>and associated matrices</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <command detect_errors="exit_code"><![CDATA[
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8 #if str($reference_cond.reference_source) == 'cached'
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9 set reference = '$reference_cond.reference.fields.path'
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10 #else:
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11 set reference = '$reference_cond.reference'
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12 #end if
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13
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14 python '$__tool_directory__/snp_wind.py' ./ -p 'consensus.fasta'
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15 #for $fa in sorted($input_fasta_collection, key=lambda f: f.element_identifier):
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16 -n '$fa.element_identifier' -f '$fa'
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17 #end for
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18 > ./file &&
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19 cfsan_snp_pipeline snp_matrix -o '$output_snp_matrix_fasta' ./file &&
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20 cfsan_snp_pipeline distance -p '$output_snp_pairwise_matrix_tsv' -m '$output_snp_distance_matrix_tsv' '$output_snp_matrix_fasta' &&
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21 cfsan_snp_pipeline snp_reference -l '$input_merged_snp_sites' -o '$output_snp_reference_fasta' '$reference'
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22 ]]></command>
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23 <inputs>
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24 <param name="input_fasta_collection" type="data_collection" format="fasta" collection_type="list" label="Collection of fasta files"/>
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25 <expand macro="reference_cond"/>
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26 <param name="input_merged_snp_sites" type="data" format="tabular" label="Merged SNP sites tabular file"/>
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27 </inputs>
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28 <outputs>
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29 <data name="output_snp_matrix_fasta" format="fasta" label="SNP matrix (fasta)"/>
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30 <data name="output_snp_pairwise_matrix_tsv" format="tsv" label="SNP pairwise matrix (tsv)"/>
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31 <data name="output_snp_distance_matrix_tsv" format="tsv" label="SNP distance matrix (tsv)"/>
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32 <data name="output_snp_reference_fasta" format="fasta" label="SNP Reference (fasta)"/>
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33 </outputs>
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34 <tests>
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35 <test>
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36 <param name="input_fasta_collection">
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37 <collection type="list">
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38 <element name="sample1" value="input1.fasta"/>
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39 <element name="sample2" value="input2.fasta"/>
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40 <element name="sample3" value="input3.fasta"/>
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41 <element name="sample4" value="input4.fasta"/>
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42 </collection>
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43 </param>
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44 <param name="reference_source" value="history"/>
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45 <param name="reference" value="lambda_virus.fasta"/>
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46 <param name="input_merged_snp_sites" value="input_merged_snp_sites.tabular"/>
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47 <output name="output_snp_matrix_fasta" value="output_snp_matrix.fasta"/>
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48 <output name="output_snp_pairwise_matrix_tsv" value="output_snp_pairwise_matrix.tsv"/>
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49 <output name="output_snp_distance_matrix_tsv" value="output_snp_distance_matrix.tsv"/>
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50 <output name="output_snp_reference_fasta" value="output_snp_reference.fasta"/>
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51 </test>
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52 </tests>
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53 <help><![CDATA[
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54 **What it does**
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55
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56 Create the SNP matrix containing the consensus base for each of the samples at
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57 the positions where high-confidence SNPs were found in any of the samples. The
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58 matrix contains one row per sample and one column per SNP position. Non-SNP
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59 positions are not included in the matrix. The matrix is formatted as a fasta
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60 file, with each sequence (all of identical length) corresponding to the SNPs
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61 in the correspondingly named sequence.
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62
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63 **More information**
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64
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65 CFSAN SNP Pipeline `create SNP matrix documentation <https://snp-pipeline.readthedocs.io/en/latest/cmd_ref.html#snp-matrix>`_
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66 ]]></help>
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67 <expand macro="citations"/>
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68 </tool>
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69
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