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comparison variant.xml @ 17:16fc9856b20a draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka commit 450d1acaa1feae57e288d7cefb5a20cfca025fe4
author iuc
date Tue, 28 Oct 2025 09:58:30 +0000
parents ec699520444c
children
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equal deleted inserted replaced
16:eb746fa6f514 17:16fc9856b20a
1 <tool id="medaka_variant" name="medaka variant tool" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> 1 <tool id="medaka_variant" name="medaka vcf tool" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>decodes variant calls from medaka consensus output</description> 2 <description>decodes variant calls from medaka consensus output</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"/>
10 @REF_FASTA@ 10 @REF_FASTA@
11 11
12 12
13 #if $pool.pool_mode == "Yes": 13 #if $pool.pool_mode == "Yes":
14 ## run 14 ## run
15 medaka variant 15 medaka vcf
16 ## optional 16 ## optional
17 --debug 17 --debug
18 #if $regions 18 #if $regions
19 --regions '${regions}' 19 --regions '${regions}'
20 #end if 20 #end if
21 $verbose 21 $verbose
22 ${ambig_ref} 22 ${ambig_ref}
23 ${gvcf} 23 ${gvcf}
24 ## required 24 ## required
25 reference.fa
26 #for $current in $pool.inputs 25 #for $current in $pool.inputs
27 '$current' 26 '$current'
28 #end for 27 #end for
28 reference.fa
29 #elif $pool.pool_mode == "No": 29 #elif $pool.pool_mode == "No":
30 ## run 30 ## run
31 medaka variant 31 medaka vcf
32 ## optional 32 ## optional
33 --debug 33 --debug
34 #if $regions 34 #if $regions
35 --regions '${regions}' 35 --regions '${regions}'
36 #end if 36 #end if
37 $verbose 37 $verbose
38 ${ambig_ref} 38 ${ambig_ref}
39 ${gvcf} 39 ${gvcf}
40 ## required 40 ## required
41 '$pool.input'
41 reference.fa 42 reference.fa
42 '$pool.input'
43 #end if 43 #end if
44 #if str($output_annotated.output_annotated_select) == 'false': 44 #if str($output_annotated.output_annotated_select) == 'false':
45 '$out_variants' ##output 45 '$out_variants' 2>&1 | tee log.txt
46 2>&1 | tee '$out_log'
47 #else 46 #else
48 raw.vcf ##output of medaka variant 47 raw.vcf 2>&1 | tee log.txt
49 2>&1 | tee '$out_log'
50 && ln -s '$output_annotated.in_bam' in.bam 48 && ln -s '$output_annotated.in_bam' in.bam
51 && ln -s '$output_annotated.in_bam.metadata.bam_index' in.bai 49 && ln -s '$output_annotated.in_bam.metadata.bam_index' in.bai
52 && medaka tools annotate --dpsp --pad $output_annotated.pad raw.vcf reference.fa in.bam tmp.vcf 50 && medaka tools annotate --dpsp --pad $output_annotated.pad raw.vcf reference.fa in.bam tmp.vcf
53 && python '$__tool_directory__/convert_VCF_info_fields.py' tmp.vcf '$out_variants' 51 && python '$__tool_directory__/convert_VCF_info_fields.py' tmp.vcf '$out_variants'
54 #end if 52 #end if
96 </conditional> 94 </conditional>
97 <param name="output_log_bool" type="boolean" label="Output log file?" checked="true"/> 95 <param name="output_log_bool" type="boolean" label="Output log file?" checked="true"/>
98 </inputs> 96 </inputs>
99 <outputs> 97 <outputs>
100 <data name="out_variants" format="vcf" label="${tool.name} on ${on_string}: called variants"/> 98 <data name="out_variants" format="vcf" label="${tool.name} on ${on_string}: called variants"/>
101 <data name="out_log" format="tabular" label="${tool.name} on ${on_string}: Log"> 99 <data name="out_log" format="tabular" from_work_dir="log.txt" label="${tool.name} on ${on_string}: Log">
102 <filter>output_log_bool</filter> 100 <filter>output_log_bool</filter>
103 </data> 101 </data>
104 </outputs> 102 </outputs>
105 <tests> 103 <tests>
106 <!-- #1 default --> 104 <!-- #1 default -->