annotate snp.xml @ 0:179342c7b86c draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
author iuc
date Wed, 12 Oct 2022 07:43:59 +0000
parents
children 630e6aeeb7e8
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
1 <tool id="medaka_snp" name="medaka SNP tool" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
2 <description>decodes probabilities to SNPs</description>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
3 <macros>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
4 <import>macros.xml</import>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
5 </macros>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
6 <expand macro="requirements"/>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
7 <expand macro="version_command"/>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
8 <command detect_errors="exit_code"><![CDATA[
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
9 ## initialize
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
10 @REF_FASTA@
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
11
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
12
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
13 #if $pool.pool_mode == "Yes":
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
14 ## run
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
15 medaka snp
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
16 ## optional
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
17 --debug
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
18 #if $regions
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
19 --regions '${regions}'
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
20 #end if
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
21 --threshold $threshold
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
22 #if $ref_vcf
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
23 --ref_vcf '$ref_vcf'
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
24 #end if
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
25 $verbose
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
26 ## required
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
27 reference.fa
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
28 #for $current in $pool.inputs
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
29 '$current'
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
30 #end for
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
31 #elif $pool.pool_mode == "No":
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
32 ## run
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
33 medaka snp
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
34 ## optional
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
35 --debug
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
36 #if $regions
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
37 --regions '${regions}'
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
38 #end if
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
39 --threshold $threshold
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
40 #if $ref_vcf
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
41 --ref_vcf '$ref_vcf'
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
42 #end if
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
43 $verbose
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
44 ## required
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
45 reference.fa
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
46 '$pool.input'
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
47 #end if
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
48 #if str($output_annotated.output_annotated_select) == 'false':
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
49 '$out_SNPs' ##output
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
50 2>&1 | tee '$out_log'
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
51 #else
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
52 raw.vcf ##output of medaka snp
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
53 2>&1 | tee '$out_log'
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
54 && ln -s '$output_annotated.in_bam' in.bam
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
55 && ln -s '$output_annotated.in_bam.metadata.bam_index' in.bai
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
56 && medaka tools annotate --dpsp --pad $output_annotated.pad raw.vcf reference.fa in.bam tmp.vcf
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
57 && python '$__tool_directory__/convert_VCF_info_fields.py' tmp.vcf '$out_SNPs'
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
58 #end if
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
59 ]]></command>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
60 <inputs>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
61 <conditional name="pool">
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
62 <param name="pool_mode" type="select" label="Are you pooling HDF5 datasets?">
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
63 <option value="No" selected="true">No</option>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
64 <option value="Yes">Yes</option>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
65 </param>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
66 <when value="Yes">
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
67 <param name="inputs" type="data" format="h5" multiple="true" label="Select consensus file(s)"/>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
68 </when>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
69 <when value="No">
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
70 <param name="input" type="data" format="h5" label="Select consensus file(s)"/>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
71 </when>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
72 </conditional>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
73 <expand macro="reference"/>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
74 <param argument="--regions" type="text" value="" optional="true" label="Set reference names to limit SNP calling" help="Separated by ','.">
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
75 <sanitizer invalid_char="">
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
76 <valid initial="string.ascii_letters,string.digits">
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
77 <add value="_"/>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
78 <add value=","/>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
79 <add value="."/>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
80 </valid>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
81 </sanitizer>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
82 </param>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
83 <param argument="--threshold" type="float" label="Threshold for considering secondary calls" value="0.04" min="0" max="1" help="A value of 1 will result in haploid decoding" optional="true"/>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
84 <param name="ref_vcf" type="data" format="vcf" optional="true" label="Reference vcf"/>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
85 <param argument="--verbose" type="boolean" truevalue="--verbose" falsevalue="" label="Populate VCF info fields?"/>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
86 <conditional name="output_annotated">
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
87 <param name="output_annotated_select" type="select"
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
88 label="Type of VCF to generate"
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
89 help="SNP INFO fields in the VCF can be extended to include allele frequency, depth of coverage, etc., but this requires a BAM dataset to calculate those values from.">
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
90 <option value="true" selected="true">Write annotated VCF with extended INFO</option>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
91 <option value="false">Write original decoded VCF with minimal INFO field</option>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
92 </param>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
93 <when value="true">
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
94 <param name="in_bam" type="data" format="bam" optional="false" label="BAM to caclulate additional INFO fields from"/>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
95 <param name="pad" type="integer" min="1" value="25"
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
96 label="Padding width on either side of SNP for realignment"
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
97 help="To calculate the additional INFO fields the tool will run medaka tools anntotate, which performs local realignment of the region +- this width around each SNP. All calculated new fields will depend on the width chosen, so only change this value if you know what you are doing." />
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
98 </when>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
99 <when value="false"/>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
100 </conditional>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
101 <param name="output_log_bool" type="boolean" label="Output log file?" checked="true"/>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
102 </inputs>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
103 <outputs>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
104 <data name="out_SNPs" format="vcf" label="${tool.name} on ${on_string}: called SNPs"/>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
105 <data name="out_log" format="tabular" label="${tool.name} on ${on_string}: Log">
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
106 <filter>output_log_bool</filter>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
107 </data>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
108 </outputs>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
109 <tests>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
110 <!--No annotation or log-->
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
111 <test expect_num_outputs="1">
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
112 <conditional name="pool">
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
113 <param name="pool_mode" value="No"/>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
114 <param name="input" value="medaka_test.hdf"/>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
115 </conditional>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
116 <conditional name="reference_source">
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
117 <param name="reference_source_selector" value="history"/>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
118 <param name="ref_file" value="ref.fasta"/>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
119 </conditional>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
120 <conditional name="output_annotated">
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
121 <param name="output_annotated_select" value="false"/>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
122 </conditional>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
123 <param name="output_log_bool" value="false"/>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
124 <output name="out_SNPs">
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
125 <assert_contents>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
126 <has_n_lines n="7"/>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
127 <has_line line="##fileformat=VCFv4.1" />
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
128 <has_line_matching expression="##medaka_version=[0-9]+\.[0-9]+\.[0-9]+" />
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
129 </assert_contents>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
130 </output>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
131 </test>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
132 </tests>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
133 <help><![CDATA[
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
134 .. class:: infomark
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
135
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
136 **What it does**
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
137
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
138 @WID@
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
139
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
140 This module decodes probabilities to SNPs but NOT indels.
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
141
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
142 For a more general solution see the medaka *variant* tool.
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
143 ----
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
144
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
145 .. class:: infomark
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
146
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
147 **Input**
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
148
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
149 - reference sequence (FASTA)
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
150 - (several) consensus files (H5/HDF)
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
151
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
152 ----
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
153
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
154 .. class:: infomark
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
155
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
156 **Output**
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
157
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
158 - decoded SNP probabilities (VCF)
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
159
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
160 ----
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
161
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
162 .. class:: infomark
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
163
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
164 **References**
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
165
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
166 @REFERENCES@
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
167 ]]></help>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
168 <expand macro="citations"/>
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
iuc
parents:
diff changeset
169 </tool>