Mercurial > repos > iuc > medaka_variant

comparison variant.xml @ 7:103c8b06c95f draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit ed5a3aadbecc0decf9a797447f3ac7700683ea9a"
author iuc
date Mon, 22 Feb 2021 19:56:30 +0000
parents 103a681e82a1
children 849aebec0dd9
comparison
equal deleted inserted replaced
6:103a681e82a1 7:103c8b06c95f
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="medaka_variant" name="medaka variant tool" version="@TOOL_VERSION@+galaxy4" profile="@PROFILE@"> 2 <tool id="medaka_variant" name="medaka variant tool" version="@TOOL_VERSION@+galaxy5" profile="@PROFILE@">
3 <description>Probability decoding</description> 3 <description>Probability decoding</description>
4 <macros> 4 <macros>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements"> 7 <expand macro="requirements">
8 <requirement type="package" version="1.4.1">scipy</requirement> 8 <requirement type="package" version="1.4.1">scipy</requirement>
9 </expand> 9 </expand>
10 10
11 <expand macro="version_command"/> 11 <expand macro="version_command"/>
12
13 <configfiles>
14 <configfile name="convert_fasta">
15 import sys
16 infile = open(sys.argv[1], 'r')
17 outfile = open(sys.argv[2], 'w')
18 for line in infile:
19 if line[0] == '>':
20 outfile.write(line)
21 else:
22 outfile.write(line.upper())
23 infile.close()
24 outfile.close()
25 </configfile>
26 </configfiles>
27
12 <command detect_errors="exit_code"><![CDATA[ 28 <command detect_errors="exit_code"><![CDATA[
13 ## initialize 29 ## initialize
14 @REF_FASTA@ 30 @REF_FASTA@
15 31
16 32
46 '$out_result' ##output 62 '$out_result' ##output
47 2>&1 | tee '$out_log' 63 2>&1 | tee '$out_log'
48 #end if 64 #end if
49 65
50 #if $out_annotated: 66 #if $out_annotated:
67 ## medaka annotate errors out if the reference is lower case at a position it's annotating because it checks vs the ref base in the vcf
68 && python '$convert_fasta' reference.fa upper_reference.fa
51 && ln -s '$output_annotated.in_bam' in.bam 69 && ln -s '$output_annotated.in_bam' in.bam
52 && ln -s '$output_annotated.in_bam.metadata.bam_index' in.bai 70 && ln -s '$output_annotated.in_bam.metadata.bam_index' in.bai
53 && medaka tools annotate --pad $output_annotated.pad '$out_result' reference.fa in.bam tmp.vcf 71 && medaka tools annotate --pad $output_annotated.pad '$out_result' upper_reference.fa in.bam tmp.vcf
54 && '$__tool_directory__/convert_VCF_info_fields.py' tmp.vcf '$out_annotated' 72 && '$__tool_directory__/convert_VCF_info_fields.py' tmp.vcf '$out_annotated'
55 #end if 73 #end if
56 ]]></command> 74 ]]></command>
57 <inputs> 75 <inputs>
58 <conditional name="pool"> 76 <conditional name="pool">
165 </output> 183 </output>
166 <output name="out_annotated"> 184 <output name="out_annotated">
167 <assert_contents> 185 <assert_contents>
168 <has_n_lines n="22"/> 186 <has_n_lines n="22"/>
169 <has_line line="##fileformat=VCFv4.1" /> 187 <has_line line="##fileformat=VCFv4.1" />
170 <has_line line="##medaka_version=1.0.3" /> 188 <has_line_matching expression="##medaka_version=[0-9]+\.[0-9]+\.[0-9]+" />
171 <has_line_matching expression="##medaka_version=[0-9]+\.[0-9]+\.[0-9]+" /> 189 <has_line_matching expression="##convert_VCF_info_fields=[0-9]+\.[0-9]+" />
172 </assert_contents> 190 </assert_contents>
173 </output> 191 </output>
174 <output name="out_log"> 192 <output name="out_log">
175 <assert_contents> 193 <assert_contents>
176 <has_n_lines n="8" /> 194 <has_n_lines n="8" />