Mercurial > repos > greg > cfsan_snp_pipeline_merge_sites
comparison cfsan_snp_pipeline_merge_sites.xml @ 3:bb483baa0e50 draft
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author | greg |
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date | Wed, 22 Nov 2023 19:41:49 +0000 |
parents | b64c03573271 |
children | 36e984464e12 |
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2:b64c03573271 | 3:bb483baa0e50 |
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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 '$__tool_directory__/snp_wind.py' ./ | 8 python '$__tool_directory__/snp_wind.py' ./ |
9 #if str($input_type_cond.input_type) == 'single': | 9 #for $input_vcf in $input_vcf_collection: |
10 -n '$input_type_cond.input_vcf.element_identifier' | 10 -n '$input_vcf.element_identifier' -f '$input_vcf' |
11 -f '$input_type_cond.input_vcf' | 11 #end for |
12 #else: | |
13 #for $input_vcf in $input_type_cond.input_vcf_collection: | |
14 -n '$input_vcf.element_identifier' | |
15 -f '$input_vcf' | |
16 #end for | |
17 #end if | |
18 -p 'var.fit.vcf' > ./file | 12 -p 'var.fit.vcf' > ./file |
19 && cfsan_snp_pipeline merge_sites -v 4 -n 'var.fit.vcf' ./file ./filtered_snps -o '$output' | 13 && cfsan_snp_pipeline merge_sites -v 4 -n 'var.fit.vcf' ./file ./filtered_snps -o '$output' |
20 ]]></command> | 14 ]]></command> |
21 <inputs> | 15 <inputs> |
22 <expand macro="input_type_cond"/> | 16 <param name="input_vcf_collection" type="data_collection" format="vcf" collection_type="list" label="Collection of VCF files"/> |
23 </inputs> | 17 </inputs> |
24 <outputs> | 18 <outputs> |
25 <data name="output" format="tabular"/> | 19 <data name="output" format="tabular"/> |
26 </outputs> | 20 </outputs> |
27 <tests> | 21 <tests> |
28 <test> | |
29 <param name="input_vcf" value="input1.vcf"/> | |
30 <output name="output" value="output.tabular"/> | |
31 </test> | |
32 <test> | 22 <test> |
33 <param name="input_type" value="collection"/> | 23 <param name="input_type" value="collection"/> |
34 <param name="input_vcf_collection"> | 24 <param name="input_vcf_collection"> |
35 <collection type="list"> | 25 <collection type="list"> |
36 <element name="input1" value="input1.vcf" ftype="vcf"/> | 26 <element name="input1" value="input1.vcf" ftype="vcf"/> |