Mercurial > repos > iuc > medaka_variant

comparison variant.xml @ 4:43bc582c0556 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
author iuc
date Tue, 13 Oct 2020 15:58:18 +0000
parents 009673c8ac31
children 294565bd47cd
comparison
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3:009673c8ac31 4:43bc582c0556
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="medaka_variant" name="medaka: Variant" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@"> 2 <tool id="medaka_variant" name="medaka variant tool" version="@TOOL_VERSION@+galaxy2" 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>
9 </expand>
10
8 <expand macro="version_command"/> 11 <expand macro="version_command"/>
9 <command detect_errors="exit_code"><![CDATA[ 12 <command detect_errors="exit_code"><![CDATA[
10 ## initialize 13 ## initialize
11 @REF_FASTA@ 14 @REF_FASTA@
12 15
13 ## run 16
14 medaka variant 17 #if $pool.pool_mode == "Yes":
15 ## optional 18 ## run
16 --debug 19 medaka variant
17 #if $region 20 ## optional
18 --region '${region}' 21 --debug
22 #if $regions
23 --regions '${regions}'
24 #end if
25 $verbose
26 ## required
27 reference.fa
28 #for $current in $pool.inputs
29 '$current'
30 #end for
31 '$out_result' ## output
32
33 2>&1 | tee '$out_log'
34 #elif $pool.pool_mode == "No":
35 ## run
36 medaka variant
37 ## optional
38 --debug
39 #if $regions
40 --regions '${regions}'
41 #end if
42 $verbose
43 ## required
44 reference.fa
45 '$pool.input'
46 '$out_result' ##output
47 2>&1 | tee '$out_log'
19 #end if 48 #end if
20 $verbose
21 ## required
22 reference.fa
23 #for $current in $inputs
24 '$current'
25 #end for
26 '$out_result' ## output
27
28 2>&1 | tee '$out_log'
29 49
30 #if $out_annotated 50 #if $out_annotated
31 && python '$__tool_directory__/annotateVCF.py' '$out_result' '$in_mpileup' '$out_annotated' 51 && samtools faidx reference.fa
52 && grep -v "^#" '$out_result' > tmp.txt
53 && cut -f 1,2 tmp.txt > positions.txt
54 && samtools mpileup -d 0 --positions positions.txt -Q $output_annotated.min_basequal -q $output_annotated.min_mapqual -f reference.fa '$output_annotated.in_bam' > mpileup.txt
55 && python '$__tool_directory__/annotateVCF.py' '$out_result' mpileup.txt '$out_annotated'
32 #end if 56 #end if
33 ]]></command> 57 ]]></command>
34 <inputs> 58 <inputs>
35 <param argument="inputs" type="data" format="h5" multiple="true" label="Select consensus file(s)"/> 59 <conditional name="pool">
60 <param name="pool_mode" type="select" label="Are you pooling HDF5 datasets?">
61 <option value="No" selected="True">No</option>
62 <option value="Yes">Yes</option>
63 </param>
64 <when value="Yes">
65 <param name="inputs" type="data" format="h5" multiple="true" label="Select consensus file(s)"/>
66 </when>
67 <when value="No">
68 <param name="input" type="data" format="h5" label="Select consensus file(s)"/>
69 </when>
70 </conditional>
36 <expand macro="reference"/> 71 <expand macro="reference"/>
37 <param argument="--region" type="text" value="" optional="true" label="Set reference names to limit variant calling" help="Separated by ','."> 72 <param argument="--regions" type="text" value="" optional="true" label="Set reference names to limit variant calling" help="Separated by ','.">
38 <sanitizer invalid_char=""> 73 <sanitizer invalid_char="">
39 <valid initial="string.ascii_letters,string.digits"> 74 <valid initial="string.ascii_letters,string.digits">
40 <add value="_"/> 75 <add value="_"/>
41 <add value=","/> 76 <add value=","/>
42 <add value="."/> 77 <add value="."/>
43 </valid> 78 </valid>
44 </sanitizer> 79 </sanitizer>
45 </param> 80 </param>
46 <param argument="--verbose" type="boolean" truevalue="--verbose" falsevalue="" label="Populate VCF info fields?"/> 81 <param argument="--verbose" type="boolean" truevalue="--verbose" falsevalue="" label="Populate VCF info fields?"/>
47
48 <conditional name="output_annotated"> 82 <conditional name="output_annotated">
49 <param name="output_annotated_select" type="select" label="Output annotated VCF?" help="Annotate allele frequency, depth of coverage, etc for each variant (requires pileup file)"> 83 <param name="output_annotated_select" type="select" label="Output annotated VCF?" help="Annotate allele frequency, depth of coverage, etc for each variant (requires BAM file)">
50 <option value="true" selected="true">Output annotated VCF</option> 84 <option value="true" selected="true">Output annotated VCF</option>
51 <option value="false">Don't output annotated VCF</option> 85 <option value="false">Don't output annotated VCF</option>
52 </param> 86 </param>
53 <when value="true"> 87 <when value="true">
54 <param name="in_mpileup" type = "data" format="pileup" optional="false" label="Mpileup to annotate the VCF"/> 88 <param name="in_bam" type="data" format="bam" optional="false" label="BAM to annotate the VCF" />
89 <param name="min_basequal" type="integer" value="0" min="0" max="50" label="Minimum base quality" help="The minimum base quality (default: 0) at a given variant position required to include a read in the calculation of variant statistics (samtools mpileup -Q)" />
90 <param name="min_mapqual" type="integer" value="0" min="0" max="60" label="Minimum mapping quality" help="The minimum mapping quality (default: 0) required for a read to be considered in calculation of variant statistics (samtools mpileup -q)" />
55 </when> 91 </when>
92 <when value="false"/>
56 </conditional> 93 </conditional>
57 <param name="output_log_bool" type="boolean" label="Output log file?" checked="true"/> 94 <param name="output_log_bool" type="boolean" label="Output log file?" checked="true"/>
58 </inputs> 95 </inputs>
59 <outputs> 96 <outputs>
60 <!-- standard --> 97 <!-- standard -->
68 </data> 105 </data>
69 </outputs> 106 </outputs>
70 <tests> 107 <tests>
71 <!-- #1 default --> 108 <!-- #1 default -->
72 <test expect_num_outputs="3"> 109 <test expect_num_outputs="3">
73 <param name="inputs" value="medaka_test.hdf"/> 110 <conditional name="pool">
111 <param name="pool_mode" value="Yes"/>
112 <param name="inputs" value="medaka_test.hdf,medaka_test.hdf"/>
113 </conditional>
74 <conditional name="reference_source"> 114 <conditional name="reference_source">
75 <param name="reference_source_selector" value="history"/> 115 <param name="reference_source_selector" value="history"/>
76 <param name="ref_file" value="ref.fasta"/> 116 <param name="ref_file" value="ref.fasta"/>
77 </conditional> 117 </conditional>
78 <conditional name="output_annotated"> 118 <conditional name="output_annotated">
79 <param name="output_annotated_select" value="true"/> 119 <param name="output_annotated_select" value="true"/>
80 <param name="in_mpileup" value="annotate_vcf_test.pileup"/> 120 <param name="in_bam" value="medaka_test.bam"/>
121 </conditional>
122 <param name="output_log_bool" value="true"/>
123
124 <output name="out_result">
125 <assert_contents>
126 <has_n_lines n="9"/>
127 <has_line line="##fileformat=VCFv4.1" />
128 <has_line line="##medaka_version=1.0.3" />
129 </assert_contents>
130 </output>
131 <output name="out_annotated">
132 <assert_contents>
133 <has_n_lines n="16"/>
134 <has_line line="##fileformat=VCFv4.1" />
135 <has_line line="##medaka_version=1.0.3" />
136 <has_line line="##annotateVCFVersion=0.1" />
137 </assert_contents>
138 </output>
139 <output name="out_log">
140 <assert_contents>
141 <has_n_lines n="10" />
142 </assert_contents>
143 </output>
144 </test>
145 <!--No pooling-->
146 <test expect_num_outputs="3">
147 <conditional name="pool">
148 <param name="pool_mode" value="No"/>
149 <param name="input" value="medaka_test.hdf"/>
150 </conditional>
151 <conditional name="reference_source">
152 <param name="reference_source_selector" value="history"/>
153 <param name="ref_file" value="ref.fasta"/>
154 </conditional>
155 <conditional name="output_annotated">
156 <param name="output_annotated_select" value="true"/>
157 <param name="in_bam" value="medaka_test.bam"/>
81 </conditional> 158 </conditional>
82 <param name="output_log_bool" value="true"/> 159 <param name="output_log_bool" value="true"/>
83 160
84 <output name="out_result"> 161 <output name="out_result">
85 <assert_contents> 162 <assert_contents>