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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 03ac2f3182f9e72db31297fa9e2fd5f0802343ea
author drosofff
date Sun, 18 Dec 2016 10:35:43 -0500
parents ecbc563571ea
children 02adb61c0246
comparison
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11:ecbc563571ea 12:b3fb23bbca8e
1 <tool id="lumpy" name="lumpy-sv" version="0.2.1"> 1 <tool id="lumpy" name="lumpy-sv" version="0.3.0">
2 <description>find structural variants</description> 2 <description>find structural variants</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.2.12">lumpy-sv</requirement> 4 <requirement type="package" version="0.2.12">lumpy-sv</requirement>
5 <requirement type="package" version="1.3.1">samtools</requirement> 5 <requirement type="package" version="1.3.1">samtools</requirement>
6 <requirement type="package" version="1.11.2">numpy</requirement> 6 <requirement type="package" version="1.11.2">numpy</requirement>
7 </requirements> 7 </requirements>
8 <stdio> 8 <stdio>
9 <exit_code range="1:" level="fatal" description="Tool exception" /> 9 <exit_code range="1:" level="fatal" description="Tool exception" />
10 </stdio> 10 </stdio>
11 <command detect_errors="exit_code"><![CDATA[ 11 <command detect_errors="exit_code"><![CDATA[
12 #import re
13 #set one_sample_bam = re.sub('[^\w\-]', '_', str($analysis_type.input_file.element_identifier))
12 #if $analysis_type.analysis_type_list == "one_sample": 14 #if $analysis_type.analysis_type_list == "one_sample":
13 ln -f -s '$analysis_type.input_file' input.bam && 15 ln -f -s '$analysis_type.input_file' '$one_sample_bam' &&
14 #else: 16 #else:
15 ln -f -s '$analysis_type.input_file' input.A.bam && 17 #set sample_a_bam = re.sub('[^\w\-]', '_', str($analysis_type.input_file.element_identifier))
16 ln -f -s '$analysis_type.input_fileB' input.B.bam && 18 #set sample_b_bam = re.sub('[^\w\-]', '_', str($analysis_type.input_fileB.element_identifier))
19 #if $sample_a_bam == $sample_b_bam:
20 #set sample_a_bam = "%s_a" % str($sample_a_bam)
21 #set sample_b_bam = "%s_b" % str($sample_b_bam)
22 #end if
23 ln -f -s '$analysis_type.input_file' '$sample_a_bam' &&
24 ln -f -s '$analysis_type.input_fileB' '$sample_b_bam' &&
17 #end if 25 #end if
18 26
19 #if $analysis_type.analysis_type_list == "one_sample": 27 #if $analysis_type.analysis_type_list == "one_sample":
20 28
21 #if $seq_method.seq_method_list == "paired-end": 29 #if $seq_method.seq_method_list == "paired-end":
22 samtools view -b -F 1294 input.bam > "input.discordants.unsorted.bam" && 30 samtools view -u -F 1294 '$one_sample_bam' | samtools sort -O bam -o input.discordants.bam &&
23 samtools view -h input.bam | python $__tool_directory__/extractSplitReads_BwaMem.py -i stdin | samtools view -Sb - > "input.splitters.unsorted.bam" && 31 samtools view -h '$one_sample_bam' | python $__tool_directory__/extractSplitReads_BwaMem.py -i stdin | samtools sort -O bam -o input.splitters.bam &&
24 samtools sort input.discordants.unsorted.bam > input.discordants.bam && 32 samtools view '$one_sample_bam'
25 samtools sort input.splitters.unsorted.bam > input.splitters.bam &&
26 samtools view input.bam
27 |tail -n +1
28 |python $__tool_directory__/pairend_distro.py -r $analysis_type.readLength -X 4 -N $seq_method.additional_params.samplingValue -o input.lib.histo > meandev.txt && 33 |python $__tool_directory__/pairend_distro.py -r $analysis_type.readLength -X 4 -N $seq_method.additional_params.samplingValue -o input.lib.histo > meandev.txt &&
29 mean=\$(cat meandev.txt | sed s/mean:// | sed -r s/stdev:.+//) && 34 mean=\$(cat meandev.txt | sed s/mean:// | sed -r s/stdev:.+//) &&
30 stdev=\$(cat meandev.txt | sed -r s/mean:.+stdev://) && 35 stdev=\$(cat meandev.txt | sed -r s/mean:.+stdev://) &&
31 lumpy -mw $seq_method.additional_params.mw -tt $seq_method.additional_params.tt 36 lumpy $seq_method.additional_params.evidence $seq_method.additional_params.probability_curve -mw $seq_method.additional_params.mw -tt $seq_method.additional_params.tt
32 #if $output_format == "BEDPE": 37 #if $output_format == "BEDPE":
33 -b 38 -b
34 #end if 39 #end if
35 -pe id:input.bam,bam_file:input.discordants.bam,histo_file:input.lib.histo,mean:"\$mean",stdev:"\$stdev",read_length:$analysis_type.readLength,min_non_overlap:$seq_method.additional_params.min_non_overlap,discordant_z:$seq_method.additional_params.discordant_z,back_distance:$seq_method.additional_params.back_distance,weight:$seq_method.additional_params.weight,min_mapping_threshold:$seq_method.additional_params.min_mapping_threshold 40 -pe id:'$one_sample_bam',bam_file:input.discordants.bam,histo_file:input.lib.histo,mean:"\$mean",stdev:"\$stdev",read_length:$analysis_type.readLength,min_non_overlap:$seq_method.additional_params.min_non_overlap,discordant_z:$seq_method.additional_params.discordant_z,back_distance:$seq_method.additional_params.back_distance,weight:$seq_method.additional_params.weight,min_mapping_threshold:$seq_method.additional_params.min_mapping_threshold
36 -sr id:input.bam,bam_file:input.splitters.bam,back_distance:$seq_method.additional_params.back_distance,weight:$seq_method.additional_params.weight,min_mapping_threshold:$seq_method.additional_params.min_mapping_threshold > output.vcf && 41 -sr id:'$one_sample_bam',bam_file:input.splitters.bam,back_distance:$seq_method.additional_params.back_distance,weight:$seq_method.additional_params.weight,min_mapping_threshold:$seq_method.additional_params.min_mapping_threshold > '$vcf_call'
37 mv input.discordants.bam $discordants && 42 #elif $seq_method.seq_method_list == "single-read":
38 mv input.splitters.bam $splits && 43 samtools view -h '$one_sample_bam' | python $__tool_directory__/extractSplitReads_BwaMem.py -i stdin | samtools sort -O bam -o input.splitters.bam &&
39 mv input.lib.histo $histogram && 44 lumpy $seq_method.additional_params.evidence $seq_method.additional_params.probability_curve -mw $seq_method.additional_params.mw -tt $seq_method.additional_params.tt
40 mv output.vcf $vcf_call && 45 #if $output_format == "BEDPE":
41 rm input.discordants.unsorted.bam input.splitters.unsorted.bam meandev.txt 46 -b
47 #end if
48 -sr id:'$one_sample_bam',bam_file:input.splitters.bam,back_distance:$seq_method.additional_params.back_distance,weight:$seq_method.additional_params.weight,min_mapping_threshold:$seq_method.additional_params.min_mapping_threshold > '$vcf_call'
42 #end if 49 #end if
43 #if $seq_method.seq_method_list == "single-read":
44 samtools view -h input.bam | python $__tool_directory__/extractSplitReads_BwaMem.py -i stdin | samtools view -Sb - > "input.splitters.unsorted.bam" &&
45 lumpy -mw $seq_method.additional_params.mw -tt $seq_method.additional_params.tt
46 #if $output_format == "BEDPE":
47 -b
48 #end if
49 -sr id:input.bam,bam_file:input.splitters.unsorted.bam,back_distance:$seq_method.additional_params.back_distance,weight:$seq_method.additional_params.weight,min_mapping_threshold:$seq_method.additional_params.min_mapping_threshold > output.vcf &&
50 mv input.splitters.unsorted.bam $splits &&
51 mv output.vcf $vcf_call
52 #end if
53
54 #else: 50 #else:
55
56 #if $seq_method.seq_method_list == "paired-end": 51 #if $seq_method.seq_method_list == "paired-end":
57 samtools view -b -F 1294 input.A.bam > "input.A.discordants.unsorted.bam" && 52 samtools view -u -F 1294 '$sample_a_bam' | samtools sort -O bam -o input.discordants.bam &&
58 samtools view -b -F 1294 input.B.bam > "input.B.discordants.unsorted.bam" && 53 samtools view -u -F 1294 '$sample_b_bam' | samtools sort -O bam -o input.B.discordants.bam &&
59 samtools view -h input.A.bam | python $__tool_directory__/extractSplitReads_BwaMem.py -i stdin | samtools view -Sb - > "input.A.splitters.unsorted.bam" && 54 samtools view -h '$sample_a_bam' | python $__tool_directory__/extractSplitReads_BwaMem.py -i stdin | samtools sort -O bam -o input.splitters.bam &&
60 samtools view -h input.B.bam | python $__tool_directory__/extractSplitReads_BwaMem.py -i stdin | samtools view -Sb - > "input.B.splitters.unsorted.bam" && 55 samtools view -h '$sample_b_bam' | python $__tool_directory__/extractSplitReads_BwaMem.py -i stdin | samtools sort -O bam -o input.B.splitters.bam &&
61 samtools sort input.A.discordants.unsorted.bam > input.A.discordants.bam && 56 samtools view '$sample_a_bam'
62 samtools sort input.B.discordants.unsorted.bam > input.B.discordants.bam && 57 |python $__tool_directory__/pairend_distro.py -r $analysis_type.readLength -X 4 -N $seq_method.additional_params.samplingValue -o input.lib.histo > meandevA.txt &&
63 samtools sort input.A.splitters.unsorted.bam > input.A.splitters.bam && 58 samtools view '$sample_b_bam'
64 samtools sort input.B.splitters.unsorted.bam > input.B.splitters.bam &&
65 samtools view input.A.bam
66 |tail -n +1
67 |python $__tool_directory__/pairend_distro.py -r $analysis_type.readLength -X 4 -N $seq_method.additional_params.samplingValue -o input.A.lib.histo > meandevA.txt &&
68 samtools view input.B.bam
69 |tail -n +1
70 |python $__tool_directory__/pairend_distro.py -r $analysis_type.readLengthB -X 4 -N $seq_method.additional_params.samplingValue -o input.B.lib.histo > meandevB.txt && 59 |python $__tool_directory__/pairend_distro.py -r $analysis_type.readLengthB -X 4 -N $seq_method.additional_params.samplingValue -o input.B.lib.histo > meandevB.txt &&
71 meanA=\$(cat meandevA.txt | sed s/mean:// | sed -r s/stdev:.+//) && 60 meanA=\$(cat meandevA.txt | sed s/mean:// | sed -r s/stdev:.+//) &&
72 meanB=\$(cat meandevB.txt | sed s/mean:// | sed -r s/stdev:.+//) && 61 meanB=\$(cat meandevB.txt | sed s/mean:// | sed -r s/stdev:.+//) &&
73 stdevA=\$(cat meandevA.txt | sed -r s/mean:.+stdev://) && 62 stdevA=\$(cat meandevA.txt | sed -r s/mean:.+stdev://) &&
74 stdevB=\$(cat meandevB.txt | sed -r s/mean:.+stdev://) && 63 stdevB=\$(cat meandevB.txt | sed -r s/mean:.+stdev://) &&
75 lumpy -mw $seq_method.additional_params.mw -tt $seq_method.additional_params.tt 64 lumpy $seq_method.additional_params.evidence $seq_method.additional_params.probability_curve -mw $seq_method.additional_params.mw -tt $seq_method.additional_params.tt
76 #if $output_format == "BEDPE": 65 #if $output_format == "BEDPE":
77 -b 66 -b
78 #end if 67 #end if
79 -pe id:inputA.bam,bam_file:input.A.discordants.bam,histo_file:input.A.lib.histo,mean:"\$meanA",stdev:"\$stdevA",read_length:$analysis_type.readLength,min_non_overlap:$seq_method.additional_params.min_non_overlap,discordant_z:$seq_method.additional_params.discordant_z,back_distance:$seq_method.additional_params.back_distance,weight:$seq_method.additional_params.weight,min_mapping_threshold:$seq_method.additional_params.min_mapping_threshold 68 -pe id:inputA.bam,bam_file:input.discordants.bam,histo_file:input.lib.histo,mean:"\$meanA",stdev:"\$stdevA",read_length:$analysis_type.readLength,min_non_overlap:$seq_method.additional_params.min_non_overlap,discordant_z:$seq_method.additional_params.discordant_z,back_distance:$seq_method.additional_params.back_distance,weight:$seq_method.additional_params.weight,min_mapping_threshold:$seq_method.additional_params.min_mapping_threshold
80 -pe id:inputB.bam,bam_file:input.B.discordants.bam,histo_file:input.B.lib.histo,mean:"\$meanB",stdev:"\$stdevA",read_length:$analysis_type.readLengthB,min_non_overlap:$seq_method.additional_params.min_non_overlap,discordant_z:$seq_method.additional_params.discordant_z,back_distance:$seq_method.additional_params.back_distance,weight:$seq_method.additional_params.weight,min_mapping_threshold:$seq_method.additional_params.min_mapping_threshold 69 -pe id:inputB.bam,bam_file:input.B.discordants.bam,histo_file:input.B.lib.histo,mean:"\$meanB",stdev:"\$stdevA",read_length:$analysis_type.readLengthB,min_non_overlap:$seq_method.additional_params.min_non_overlap,discordant_z:$seq_method.additional_params.discordant_z,back_distance:$seq_method.additional_params.back_distance,weight:$seq_method.additional_params.weight,min_mapping_threshold:$seq_method.additional_params.min_mapping_threshold
81 -sr id:inputA.bam,bam_file:input.A.splitters.bam,back_distance:$seq_method.additional_params.back_distance,weight:$seq_method.additional_params.weight,min_mapping_threshold:$seq_method.additional_params.min_mapping_threshold 70 -sr id:inputA.bam,bam_file:input.splitters.bam,back_distance:$seq_method.additional_params.back_distance,weight:$seq_method.additional_params.weight,min_mapping_threshold:$seq_method.additional_params.min_mapping_threshold
82 -sr id:inputB.bam,bam_file:input.B.splitters.bam,back_distance:$seq_method.additional_params.back_distance,weight:$seq_method.additional_params.weight,min_mapping_threshold:$seq_method.additional_params.min_mapping_threshold > output.vcf && 71 -sr id:inputB.bam,bam_file:input.B.splitters.bam,back_distance:$seq_method.additional_params.back_distance,weight:$seq_method.additional_params.weight,min_mapping_threshold:$seq_method.additional_params.min_mapping_threshold > '$vcf_call'
83 mv input.A.discordants.bam $discordants && 72 #elif $seq_method.seq_method_list == "single-read":
84 mv input.B.discordants.bam $discordantsB && 73 samtools view -h '$sample_a_bam' | python $__tool_directory__/extractSplitReads_BwaMem.py -i stdin | samtools sort -O bam -o input.splitters.bam &&
85 mv input.A.splitters.bam $splits && 74 samtools view -h '$sample_b_bam' | python $__tool_directory__/extractSplitReads_BwaMem.py -i stdin | samtools sort -O bam -o input.B.splitters.bam &&
86 mv input.B.splitters.bam $splitsB && 75 lumpy $seq_method.additional_params.evidence $seq_method.additional_params.probability_curve -mw $seq_method.additional_params.mw -tt $seq_method.additional_params.tt
87 mv input.A.lib.histo $histogram && 76 #if $output_format == "BEDPE":
88 mv input.B.lib.histo $histogramB && 77 -b
89 mv output.vcf $vcf_call && 78 #end if
90 rm input.A.discordants.unsorted.bam input.B.discordants.unsorted.bam input.A.splitters.unsorted.bam input.B.splitters.unsorted.bam meandevA.txt meandevB.txt 79 -sr id:'$sample_a_bam',bam_file:input.splitters.bam,back_distance:$seq_method.additional_params.back_distance,weight:$seq_method.additional_params.weight,min_mapping_threshold:$seq_method.additional_params.min_mapping_threshold
80 -sr id:'$sample_b_bam',bam_file:input.B.splitters.bam,back_distance:$seq_method.additional_params.back_distance,weight:$seq_method.additional_params.weight,min_mapping_threshold:$seq_method.additional_params.min_mapping_threshold > '$vcf_call'
91 #end if 81 #end if
92 #if $seq_method.seq_method_list == "single-read":
93 samtools view -h input.A.bam | python $__tool_directory__/extractSplitReads_BwaMem.py -i stdin | samtools view -Sb - > "input.A.splitters.unsorted.bam" &&
94 samtools view -h input.B.bam | python $__tool_directory__/extractSplitReads_BwaMem.py -i stdin | samtools view -Sb - > "input.B.splitters.unsorted.bam" &&
95 lumpy -mw $seq_method.additional_params.mw -tt $seq_method.additional_params.tt
96 #if $output_format == "BEDPE":
97 -b
98 #end if
99 -sr id:input.A.bam,bam_file:input.A.splitters.unsorted.bam,back_distance:$seq_method.additional_params.back_distance,weight:$seq_method.additional_params.weight,min_mapping_threshold:$seq_method.additional_params.min_mapping_threshold
100 -sr id:input.B.bam,bam_file:input.B.splitters.unsorted.bam,back_distance:$seq_method.additional_params.back_distance,weight:$seq_method.additional_params.weight,min_mapping_threshold:$seq_method.additional_params.min_mapping_threshold > output.vcf &&
101 mv input.A.splitters.unsorted.bam $splits &&
102 mv input.B.splitters.unsorted.bam $splitsB &&
103 mv output.vcf $vcf_call
104 #end if
105
106
107 #end if 82 #end if
108 83
109 ]]></command> 84 ]]></command>
110 <!-- basic error handling --> 85 <!-- basic error handling -->
111 <inputs> 86 <inputs>
138 <param name="min_non_overlap" value="101" type="integer" label="min_non_overlap" help="e.g. 101" /> 113 <param name="min_non_overlap" value="101" type="integer" label="min_non_overlap" help="e.g. 101" />
139 <param name="discordant_z" value="5" type="integer" label="discordant_z" help="e.g. 5" /> 114 <param name="discordant_z" value="5" type="integer" label="discordant_z" help="e.g. 5" />
140 <param name="back_distance" value="10" type="integer" label="back_distance" help="e.g. 10" /> 115 <param name="back_distance" value="10" type="integer" label="back_distance" help="e.g. 10" />
141 <param name="weight" value="1" type="integer" label="weight" help="e.g. 1" /> 116 <param name="weight" value="1" type="integer" label="weight" help="e.g. 1" />
142 <param name="min_mapping_threshold" value="20" type="integer" label="min_mapping_threshold" help="e.g. 20" /> 117 <param name="min_mapping_threshold" value="20" type="integer" label="min_mapping_threshold" help="e.g. 20" />
118 <param name="probability_curve" argument="-P" type="boolean" truevalue="-P" falsevalue="" checked="true" label="output probability curve for each variant"/>
119 <param name="evidence" argument="-e" type="boolean" truevalue="-e" falsevalue="" checked="true" label="show evidence for each call"/>
143 </section> 120 </section>
144 </when> 121 </when>
145 <when value="single-read"> 122 <when value="single-read">
146 <section name="additional_params" title="Additional Options" expanded="False"> 123 <section name="additional_params" title="Additional Options" expanded="False">
147 <param name="mw" value="4" type="integer" label="-mw" help="minimum weight across all samples for a call (default: 4)" /> 124 <param name="mw" value="4" type="integer" label="-mw" help="minimum weight across all samples for a call (default: 4)" />
148 <param name="tt" value="0" type="integer" label="-tt" help="trim threshold (default: 0)" /> 125 <param name="tt" value="0" type="integer" label="-tt" help="trim threshold (default: 0)" />
149 <param name="back_distance" value="10" type="integer" label="back_distance" help="e.g. 10" /> 126 <param name="back_distance" value="10" type="integer" label="back_distance" help="e.g. 10" />
150 <param name="weight" value="1" type="integer" label="weight" help="e.g. 1" /> 127 <param name="weight" value="1" type="integer" label="weight" help="e.g. 1" />
151 <param name="min_mapping_threshold" value="20" type="integer" label="min_mapping_threshold" help="e.g. 20" /> 128 <param name="min_mapping_threshold" value="20" type="integer" label="min_mapping_threshold" help="e.g. 20" />
129 <param name="probability_curve" argument="-P" type="boolean" truevalue="-P" falsevalue="" checked="false" label="output probability curve for each variant"/>
130 <param name="evidence" argument="-e" type="boolean" truevalue="-e" falsevalue="" checked="false" label="show evidence for each call"/>
152 </section> 131 </section>
153 </when> 132 </when>
154 133
155 </conditional> 134 </conditional>
156 <param help="get variant calling in vcf or BEDPE format" label="variant calling format" name="output_format" type="select"> 135 <param help="get variant calling in vcf or BEDPE format" label="variant calling format" name="output_format" type="select">
158 <option value="BEDPE">BEDPE</option> 137 <option value="BEDPE">BEDPE</option>
159 </param> 138 </param>
160 </inputs> 139 </inputs>
161 140
162 <outputs> 141 <outputs>
163 <data format="tabular" name="histogram" label="Lumpy on ${on_string}: Fragment size distribution"> 142 <data format="tabular" name="histogram" label="Lumpy on ${on_string}: Fragment size distribution" from_work_dir="input.lib.histo">
164 <filter>seq_method['seq_method_list'] == "paired-end"</filter> 143 <filter>seq_method['seq_method_list'] == "paired-end"</filter>
165 </data> 144 </data>
166 <data format="tabular" name="histogramB" label="Lumpy on ${on_string}: Fragment size distribution"> 145 <data format="tabular" name="histogramB" label="Lumpy on ${on_string}: Fragment size distribution" from_work_dir="input.B.lib.histo">
167 <filter>seq_method['seq_method_list'] == "paired-end"</filter> 146 <filter>seq_method['seq_method_list'] == "paired-end"</filter>
168 <filter>analysis_type['analysis_type_list'] == "two_sample"</filter> 147 <filter>analysis_type['analysis_type_list'] == "two_sample"</filter>
169 </data> 148 </data>
170 <data format="bam" name="splits" label="Lumpy on ${on_string}: Split Reads (Bam format)"/> 149 <data format="bam" name="splits" label="Lumpy on ${on_string}: Split Reads (Bam format)" from_work_dir="input.splitters.bam"/>
171 <data format="bam" name="splitsB" label="Lumpy on ${on_string}: Split Reads (Bam format)"> 150 <data format="bam" name="splitsB" label="Lumpy on ${on_string}: Split Reads (Bam format)" from_work_dir="input.B.splitters.bam">
172 <filter>analysis_type['analysis_type_list'] == "two_sample"</filter> 151 <filter>analysis_type['analysis_type_list'] == "two_sample"</filter>
173 </data> 152 </data>
174 <data format="bam" name="discordants" label="Lumpy on ${on_string}: Discordant Pairs (Bam format)"> 153 <data format="bam" name="discordants" label="Lumpy on ${on_string}: Discordant Pairs (Bam format)" from_work_dir="input.discordants.bam">
175 <filter>seq_method['seq_method_list'] == "paired-end"</filter> 154 <filter>seq_method['seq_method_list'] == "paired-end"</filter>
176 </data> 155 </data>
177 <data format="bam" name="discordantsB" label="Lumpy on ${on_string}: Discordant Pairs (Bam format)"> 156 <data format="bam" name="discordantsB" label="Lumpy on ${on_string}: Discordant Pairs (Bam format)" from_work_dir="input.discordants.B.bam">
178 <filter>seq_method['seq_method_list'] == "paired-end"</filter> 157 <filter>seq_method['seq_method_list'] == "paired-end"</filter>
179 <filter>analysis_type['analysis_type_list'] == "two_sample"</filter> 158 <filter>analysis_type['analysis_type_list'] == "two_sample"</filter>
180 </data> 159 </data>
181 <data format="vcf" name="vcf_call" label="Lumpy Variant Calling"> 160 <data format="vcf" name="vcf_call" label="Lumpy Variant Calling">
182 <change_format> 161 <change_format>
185 </data> 164 </data>
186 </outputs> 165 </outputs>
187 166
188 <tests> 167 <tests>
189 <test> 168 <test>
190 <param name="analysis_type" value="one_sample" /> 169 <param name="analysis_type_list" value="one_sample" />
191 <param name="input_file" value="sr.input.bam" ftype="bam"/> 170 <param name="input_file" value="sr.input.bam" ftype="bam"/>
192 <param name="seq_method_list" value="single-read" /> 171 <param name="seq_method_list" value="single-read" />
193 <param name="mw" value="4"/> 172 <param name="mw" value="4"/>
194 <param name="tt" value="0"/> 173 <param name="tt" value="0"/>
195 <param name="back_distance" value="10"/> 174 <param name="back_distance" value="10"/>
196 <param name="weight" value="1" /> 175 <param name="weight" value="1" />
197 <param name="min_mapping_threshold" value="20" /> 176 <param name="min_mapping_threshold" value="20" />
198 <output name="vcf_call" file="output.vcf" ftype="vcf"/> 177 <output name="vcf_call" file="output.vcf" ftype="vcf"/>
178 </test>
179 <test>
180 <param name="analysis_type_list" value="one_sample" />
181 <param name="input_file" value="sr.input.bam" ftype="bam"/>
182 <param name="seq_method_list" value="single-read" />
183 <param name="mw" value="4"/>
184 <param name="tt" value="0"/>
185 <param name="back_distance" value="10"/>
186 <param name="weight" value="1" />
187 <param name="min_mapping_threshold" value="20" />
188 <param name="evidence" value="true" />
189 <param name="probability_curve" value="true" />
190 <output name="vcf_call" file="output_extended.vcf" ftype="vcf" compare="sim_size"/>
191 </test>
192 <test>
193 <param name="analysis_type_list" value="two_sample" />
194 <param name="input_file" value="sr.input.bam" ftype="bam"/>
195 <param name="input_fileB" value="sr.input.bam" ftype="bam"/>
196 <param name="seq_method_list" value="single-read" />
197 <param name="mw" value="4"/>
198 <param name="tt" value="0"/>
199 <param name="back_distance" value="10"/>
200 <param name="weight" value="1" />
201 <param name="min_mapping_threshold" value="20" />
202 <output name="vcf_call" file="output_two.vcf" ftype="vcf"/>
199 </test> 203 </test>
200 </tests> 204 </tests>
201 205
202 <help> 206 <help>
203 207