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comparison cfsan_snp_pipeline_snp_matrix.xml @ 1:f3485a9e51a3 draft

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author greg
date Wed, 22 Nov 2023 20:04:57 +0000
parents 6b0a13deae92
children f959d99d1758
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0:6b0a13deae92 1:f3485a9e51a3
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 python '$__tool_directory__/snp_wind.py' ./ 8 #if str($reference_cond.reference_source) == 'cached'
9 #if str($input_type_cond.input_type) == 'single': 9 set reference = '$reference_cond.reference.fields.path'
10 -n '$input_fasta.element_identifier'
11 -f '$input_fasta'
12 #else: 10 #else:
13 #for $fa in sorted($input_fasta_collection, key=lambda f: f.element_identifier) 11 set reference = '$reference_cond.reference'
14 -n '$fa.element_identifier'
15 -f '$fa'
16 #end for
17 #end if 12 #end if
18 -p 'consensus.fasta' > ./file && 13
14 python '$__tool_directory__/snp_wind.py' ./ -p 'consensus.fasta'
15 #for $fa in sorted($input_fasta_collection, key=lambda f: f.element_identifier):
16 -n '$fa.element_identifier' -f '$fa'
17 #end for
18 > ./file &&
19 cfsan_snp_pipeline snp_matrix -o '$output_snp_matrix_fasta' ./file && 19 cfsan_snp_pipeline snp_matrix -o '$output_snp_matrix_fasta' ./file &&
20 cfsan_snp_pipeline distance -p '$output_snp_pairwise_matrix_tsv' -m '$output_snp_distance_matrix_tsv' '$output_snp_matrix_fasta' && 20 cfsan_snp_pipeline distance -p '$output_snp_pairwise_matrix_tsv' -m '$output_snp_distance_matrix_tsv' '$output_snp_matrix_fasta' &&
21 cfsan_snp_pipeline snp_reference 21 cfsan_snp_pipeline snp_reference -l '$input_merged_snp_sites' -o '$output_snp_reference_fasta' '$reference'
22 -l '$input_merged_snp_sites'
23 -o '$output_snp_reference_fasta'
24 #if str($reference_cond.reference_source) == 'cached'
25 '$reference_cond.reference.fields.path'
26 #else:
27 '$reference_cond.reference'
28 #end if
29 ]]></command> 22 ]]></command>
30 <inputs> 23 <inputs>
31 <expand macro="input_type_cond"/> 24 <param name="input_fasta_collection" type="data_collection" format="fasta" collection_type="list" label="Collection of fasta files"/>
32 <expand macro="reference_cond"/> 25 <expand macro="reference_cond"/>
33 <param name="input_merged_snp_sites" type="data" format="tabular" label="Merged SNP sites tabular file"/> 26 <param name="input_merged_snp_sites" type="data" format="tabular" label="Merged SNP sites tabular file"/>
34 </inputs> 27 </inputs>
35 <outputs> 28 <outputs>
36 <data name="output_snp_matrix_fasta" format="fasta" label="SNP matrix (fasta)"/> 29 <data name="output_snp_matrix_fasta" format="fasta" label="SNP matrix (fasta)"/>
38 <data name="output_snp_distance_matrix_tsv" format="tsv" label="SNP distance matrix (tsv)"/> 31 <data name="output_snp_distance_matrix_tsv" format="tsv" label="SNP distance matrix (tsv)"/>
39 <data name="output_snp_reference_fasta" format="fasta" label="SNP Reference (fasta)"/> 32 <data name="output_snp_reference_fasta" format="fasta" label="SNP Reference (fasta)"/>
40 </outputs> 33 </outputs>
41 <tests> 34 <tests>
42 <test> 35 <test>
43 <param name="input_type" value="collection"/>
44 <param name="input_fasta_collection"> 36 <param name="input_fasta_collection">
45 <collection type="list"> 37 <collection type="list">
46 <element name="sample1" value="input1.fasta"/> 38 <element name="sample1" value="input1.fasta"/>
47 <element name="sample2" value="input2.fasta"/> 39 <element name="sample2" value="input2.fasta"/>
48 <element name="sample3" value="input3.fasta"/> 40 <element name="sample3" value="input3.fasta"/>