comparison bcftools_roh.xml @ 16:6a636d58dfc2 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
author iuc
date Tue, 20 Sep 2022 12:59:01 +0000
parents fb3af223ff33
children fa65af07ce7d
comparison
equal deleted inserted replaced
15:78cd8b69da4c 16:6a636d58dfc2
1 <?xml version='1.0' encoding='utf-8'?> 1 <?xml version='1.0' encoding='utf-8'?>
2 <tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@"> 2 <tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
3 <description>HMM model for detecting runs of homo/autozygosity</description> 3 <description>HMM model for detecting runs of homo/autozygosity</description>
4 <macros> 4 <macros>
5 <token name="@EXECUTABLE@">roh</token> 5 <token name="@EXECUTABLE@">roh</token>
6 <import>macros.xml</import> 6 <import>macros.xml</import>
7 </macros> 7 </macros>
46 --buffer-size "${section.buffer_size},${section.buffer_overlap}" 46 --buffer-size "${section.buffer_size},${section.buffer_overlap}"
47 #else: 47 #else:
48 --buffer-size "${section.buffer_size}" 48 --buffer-size "${section.buffer_size}"
49 #end if 49 #end if
50 #end if 50 #end if
51 $section.ignore_homref
52 $section.include_noalt
51 53
52 ## HMM section 54 ## HMM section
53 #set $section = $sec_hmm 55 #set $section = $sec_hmm
54 #if $section.hw_to_az: 56 #if $section.hw_to_az:
55 --hw-to-az "${section.hw_to_az}" 57 --hw-to-az "${section.hw_to_az}"
102 <param name="buffer_overlap" type="integer" min="0" label="Sliding Buffer Overlap" optional="True"> 104 <param name="buffer_overlap" type="integer" min="0" label="Sliding Buffer Overlap" optional="True">
103 <help> 105 <help>
104 The number of overlapping sites for the sliding buffer. The default overlap is set to roughly 1% of the buffer size. 106 The number of overlapping sites for the sliding buffer. The default overlap is set to roughly 1% of the buffer size.
105 </help> 107 </help>
106 </param> 108 </param>
109 <param argument="--ignore-homref" type="boolean" truevalue="--ignore-homref" falsevalue="" checked="false" label="Ignore homo-ref" help="skip hom-ref genotypes (0/0)" />
110 <param argument="--include-noalt" type="boolean" truevalue="--include-noalt" falsevalue="" checked="false" label="Include sites with no ALT allele" help="Ignored by default" />
107 </section> 111 </section>
108 <section name="sec_hmm" expanded="true" title="HMM Options"> 112 <section name="sec_hmm" expanded="true" title="HMM Options">
109 <param name="hw_to_az" type="float" label="Hw To Az" value="6.7e-8" optional="True" help="P(AZ|HW) transition probability from HW (Hardy-Weinberg) to AZ (autozygous) state" /> 113 <param name="hw_to_az" type="float" label="Hw To Az" value="6.7e-8" optional="True" help="P(AZ|HW) transition probability from HW (Hardy-Weinberg) to AZ (autozygous) state" />
110 <param name="az_to_hw" type="float" label="Az To Hw" value="5e-9" optional="True" help="P(HW|AZ) transition probability from AZ to HW state" /> 114 <param name="az_to_hw" type="float" label="Az To Hw" value="5e-9" optional="True" help="P(HW|AZ) transition probability from AZ to HW state" />
111 <param name="viterbi_training" type="boolean" truevalue="--viterbi-training" falsevalue="" label="Viterbi Training" help="Perform Viterbi training to estimate transition probabilities" /> 115 <param name="viterbi_training" type="boolean" truevalue="--viterbi-training" falsevalue="" label="Viterbi Training" help="Perform Viterbi training to estimate transition probabilities" />
140 <not_has_text text="ST"/> 144 <not_has_text text="ST"/>
141 <has_text_matching expression="RG\tsample\t1"/> 145 <has_text_matching expression="RG\tsample\t1"/>
142 </assert_contents> 146 </assert_contents>
143 </output> 147 </output>
144 </test> 148 </test>
149 <!-- Test ignore homref and include noalt-->
150 <test>
151 <param name="input_file" ftype="vcf" value="roh.vcf" />
152 <param name="AF_dflt" value="0.4" />
153 <param name="GTs_only" value="30" />
154 <param name="output_type" value="r" />
155 <param name="ignore_homref" value="true"/>
156 <param name="include_noalt" value="true"/>
157 <output name="output_file">
158 <assert_contents>
159 <not_has_text text="ST"/>
160 <has_text_matching expression="RG\tsample\t1"/>
161 </assert_contents>
162 </output>
163 <assert_command>
164 <has_text text="--ignore-homref" />
165 <has_text text="--include-noalt" />
166 </assert_command>
167 </test>
168 <!-- Test region overlap-->
169 <test>
170 <param name="input_file" ftype="vcf" value="roh.vcf" />
171 <section name="sec_general">
172 <param name="AF_dflt" value="0.4" />
173 <param name="GTs_only" value="30" />
174 </section>
175 <section name="sec_restrict">
176 <param name="regions_overlap" value="1"/>
177 </section>
178 <output name="output_file">
179 <assert_contents>
180 <has_text_matching expression="ST\tsample\t1"/>
181 <has_text_matching expression="RG\tsample\t1"/>
182 </assert_contents>
183 </output>
184 <assert_command>
185 <has_text text="--regions-overlap" />
186 </assert_command>
187 </test>
145 </tests> 188 </tests>
146 <help><![CDATA[ 189 <help><![CDATA[
147 ===================================== 190 =====================================
148 bcftools @EXECUTABLE@ 191 bcftools @EXECUTABLE@
149 ===================================== 192 =====================================