Mercurial > repos > iuc > medaka_variant_pipeline

comparison medaka_variant.xml @ 10:7623e5888be9 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 0faf0ade3f13d7c78d93869823ea9fdf25c21b13"
author iuc
date Thu, 22 Apr 2021 20:24:49 +0000
parents 336b3def9b2b
children 3fbefde449bc
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9:336b3def9b2b 10:7623e5888be9
1 <tool id="medaka_variant_pipeline" name="medaka variant pipeline" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@"> 1 <tool id="medaka_variant_pipeline" name="medaka variant pipeline" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
2 <description>via neural networks</description> 2 <description>via neural networks</description>
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"/>
39 <expand macro="reference"/> 39 <expand macro="reference"/>
40 <param argument="-r" type="text" value="" optional="true" label="Set region string(s)" help="If not provided, will process all contigs."/> 40 <param argument="-r" type="text" value="" optional="true" label="Set region string(s)" help="If not provided, will process all contigs."/>
41 <expand macro="model" argument="-s" label="Select model for initial SNP calling from mixed reads prior to phasing"/> 41 <expand macro="model" argument="-s" label="Select model for initial SNP calling from mixed reads prior to phasing"/>
42 <expand macro="model" argument="-m" label="Select model for final variant calling from phased reads"/> 42 <expand macro="model" argument="-m" label="Select model for final variant calling from phased reads"/>
43 <expand macro="b"/> 43 <expand macro="b"/>
44 <param argument="-N" type="integer" value="14" label="Set threshold for filtering indels in final VCF"/> 44 <param argument="-N" type="integer" value="9" label="Set threshold for filtering indels in final VCF"/>
45 <param argument="-P" type="integer" value="12" label="Set threshold for filtering SNPs in final VCF"/> 45 <param argument="-P" type="integer" value="8" label="Set threshold for filtering SNPs in final VCF"/>
46 <param argument="-U" type="boolean" truevalue="-U" falsevalue="" label="Avoid filtering of final VCF?"/> 46 <param argument="-U" type="boolean" truevalue="-U" falsevalue="" label="Avoid filtering of final VCF?"/>
47 <param argument="-S" type="boolean" truevalue="-S" falsevalue="" label="Stop after initial SNP calling from mixed reads prior to phasing?"/> 47 <param argument="-S" type="boolean" truevalue="-S" falsevalue="" label="Stop after initial SNP calling from mixed reads prior to phasing?"/>
48 <param name="out" type="select" multiple="true" optional="false" label="Select out file(s)5"> 48 <param name="out" type="select" multiple="true" optional="false" label="Select out file(s)5">
49 <option value="round_0_hap_mixed_phased_bam">round_0_hap_mixed_phased.bam</option> 49 <option value="round_0_hap_mixed_phased_bam">round_0_hap_mixed_phased.bam</option>
50 <option value="round_0_hap_mixed_phased_vcf">round_0_hap_mixed_phased.vcf</option> 50 <option value="round_0_hap_mixed_phased_vcf">round_0_hap_mixed_phased.vcf</option>
103 </data> 103 </data>
104 </outputs> 104 </outputs>
105 <tests> 105 <tests>
106 <!-- #1 default --> 106 <!-- #1 default -->
107 <test> 107 <test>
108 <param name="i" value="alignment.bam"/> 108 <param name="i" value="medaka_test.bam"/>
109 <conditional name="reference_source"> 109 <conditional name="reference_source">
110 <param name="reference_source_selector" value="cached"/> 110 <param name="reference_source_selector" value="cached"/>
111 <param name="ref_file" value="bwa-mem-mt-genome"/> 111 <param name="ref_file" value="ref_fasta"/>
112 </conditional> 112 </conditional>
113 <param name="out" value="round_0_hap_mixed_probs.hdf,round_0_hap_mixed_unphased.vcf,log"/> 113 <param name="out" value="round_0_hap_mixed_probs.hdf,round_0_hap_mixed_unphased.vcf,log"/>
114 <output name="out_round_0_hap_mixed_unphased_vcf"> 114 <output name="out_round_0_hap_mixed_unphased_vcf">
115 <assert_contents> 115 <assert_contents>
116 <has_n_lines n="6"/> 116 <has_n_lines n="7"/>
117 <has_line line="##fileformat=VCFv4.1"/> 117 <has_line line="##fileformat=VCFv4.1"/>
118 </assert_contents> 118 </assert_contents>
119 </output> 119 </output>
120 <output name="out_round_0_hap_mixed_probs_hdf"> 120 <output name="out_round_0_hap_mixed_probs_hdf">
121 <assert_contents> 121 <assert_contents>
122 <has_size value="32624"/> 122 <has_size value="108753" delta="100"/>
123 </assert_contents> 123 </assert_contents>
124 </output> 124 </output>
125 <output name="out_log"> 125 <output name="out_log">
126 <assert_contents> 126 <assert_contents>
127 <has_line line="++ Preparing data"/> 127 <has_line line="++ Preparing data"/>