Mercurial > repos > greg > cfsan_snp_pipeline_filter_snp_regions
comparison cfsan_snp_pipeline_filter_snp_regions.xml @ 0:be8994ce4fb6 draft
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author | greg |
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date | Thu, 12 Oct 2023 19:55:24 +0000 |
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children | bbf17f071638 |
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1 <tool id="cfsan_snp_pipeline_filter_snp_regions" name="CFSAN SNP Pipeline: filter SNP Regions" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> | |
2 <description>based on location</description> | |
3 <macros> | |
4 <import>macros.xml</import> | |
5 </macros> | |
6 <expand macro="requirements"/> | |
7 <command detect_errors="exit_code"><![CDATA[ | |
8 #if str($reference_cond.reference_source) == 'cached' | |
9 #set reference = $reference_cond.reference.fields.path | |
10 #else: | |
11 #set reference = $reference_cond.reference | |
12 #end if | |
13 mkdir -p ./samples/sample/ && | |
14 ln -s '$calls' ./samples/sample/var.flt.vcf && | |
15 echo "\$PWD/samples/sample" > ./alignment.txt && | |
16 cfsan_snp_pipeline filter_regions ./alignment.txt '$reference' && | |
17 cp ./samples/sample/var.flt_preserved.vcf '$filcalls' && | |
18 cp ./samples/sample/var.flt_removed.vcf '$excludes' | |
19 ]]></command> | |
20 <inputs> | |
21 <param name="calls" type="data" format="vcf" label="Unfiltered SNP calls from your history"/> | |
22 <expand macro="reference_cond"/> | |
23 </inputs> | |
24 <outputs> | |
25 <data name="filcalls" format="vcf" label="Filtered SNPs"/> | |
26 <data name="excludes" format="vcf" label="SNPs excluded by filtering"/> | |
27 </outputs> | |
28 <tests> | |
29 <test> | |
30 <param name="calls" value="input.vcf" /> | |
31 <param name="reference_source" value="history"/> | |
32 <param name="reference" value="lambda_virus.fasta"/> | |
33 <output name="filcalls" value="output_preserved.vcf" lines_diff="6"/> | |
34 <output name="excludes" value="output_removed.vcf" lines_diff="6"/> | |
35 </test> | |
36 </tests> | |
37 <help><![CDATA[ | |
38 **What it does** | |
39 | |
40 Remove abnormally dense SNPs from the input VCF file, save the reserved SNPs | |
41 into a new VCF file, and save the removed SNPs into another VCF file. | |
42 | |
43 **Optional parameters** | |
44 | |
45 * **force** - Force processing even when result files already exist and are newer than inputs (default: False) | |
46 * **vcfname** - File name of the input VCF files which must exist in each of the sample directories (default: var.flt.vcf) | |
47 * **edge_length** - The length of the edge regions in a contig, in which all SNPs will be removed. (default: 500) | |
48 * **window_size** - The length of the window in which the number of SNPs should be no more than max_num_snp. (default: [1000]) | |
49 * **max_snp** - The maximum number of SNPs allowed in a window. (default: [3]) | |
50 * **out_group** - Relative or absolute path to the file indicating outgroup samples, one sample ID per line. (default: None) | |
51 | |
52 **More information** | |
53 | |
54 [CFSAN SNP Pipeline documentation](http://snp-pipeline.readthedocs.io/en/latest/index.html">http://snp-pipeline.readthedocs.io/en/latest/index.html) | |
55 ]]></help> | |
56 <expand macro="citations"/> | |
57 </tool> |