Mercurial > repos > iuc > medaka_variant

comparison variant.xml @ 6:aabb4e1c0b7b draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
author iuc
date Wed, 10 Feb 2021 08:28:04 +0000
parents 19f3b583a9b3
children 28c13c42de01
comparison
equal deleted inserted replaced
5:19f3b583a9b3 6:aabb4e1c0b7b
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="medaka_variant" name="medaka variant tool" version="@TOOL_VERSION@+galaxy3" profile="@PROFILE@"> 2 <tool id="medaka_variant" name="medaka variant tool" version="@TOOL_VERSION@+galaxy4" 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">
45 '$pool.input' 45 '$pool.input'
46 '$out_result' ##output 46 '$out_result' ##output
47 2>&1 | tee '$out_log' 47 2>&1 | tee '$out_log'
48 #end if 48 #end if
49 49
50 #if $out_annotated 50 #if $out_annotated:
51 && samtools faidx reference.fa 51 && ln -s '$output_annotated.in_bam' in.bam
52 && grep -v "^#" '$out_result' > tmp.txt 52 && ln -s '$output_annotated.in_bam.metadata.bam_index' in.bai
53 && cut -f 1,2 tmp.txt > positions.txt 53 && medaka tools annotate --pad $output_annotated.pad '$out_result' reference.fa in.bam tmp.vcf
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 54 && '$__tool_directory__/convert_VCF_info_fields.py' tmp.vcf '$out_annotated'
55 && python '$__tool_directory__/annotateVCF.py' '$out_result' mpileup.txt '$out_annotated'
56 #end if 55 #end if
57 ]]></command> 56 ]]></command>
58 <inputs> 57 <inputs>
59 <conditional name="pool"> 58 <conditional name="pool">
60 <param name="pool_mode" type="select" label="Are you pooling HDF5 datasets?"> 59 <param name="pool_mode" type="select" label="Are you pooling HDF5 datasets?">
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)"> 82 <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)">
84 <option value="true" selected="true">Output annotated VCF</option> 83 <option value="true" selected="true">Output annotated VCF</option>
85 <option value="false">Don't output annotated VCF</option> 84 <option value="false">Don't output annotated VCF</option>
86 </param> 85 </param>
87 <when value="true"> 86 <when value="true">
88 <param name="in_bam" type="data" format="bam" optional="false" label="BAM to annotate the VCF" /> 87 <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)" /> 88 <param name="pad" type="integer" min="1" value="25" label="Padding width on either side of variant for realignment in medaka tools anntotate, used to calculate DPSP, DPSPS, AF, FAF, RAF, SB, DP4, and AS in the output annotated VCF"/>
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)" />
91 </when> 89 </when>
92 <when value="false"/> 90 <when value="false"/>
93 </conditional> 91 </conditional>
94 <param name="output_log_bool" type="boolean" label="Output log file?" checked="true"/> 92 <param name="output_log_bool" type="boolean" label="Output log file?" checked="true"/>
95 </inputs> 93 </inputs>
96 <outputs> 94 <outputs>
97 <!-- standard --> 95 <!-- standard -->
98 <data name="out_result" format="vcf" label="${tool.name} on ${on_string}: Result"/> 96 <data name="out_result" format="vcf" label="${tool.name} on ${on_string}: Result"/>
99 <!-- optional --> 97 <!-- optional -->
100 <data name="out_annotated" format="vcf" label="${tool.name} on ${on_string}: Annotated"> 98 <data name="out_annotated" format="vcf" label="${tool.name} on ${on_string}: Annotated">
101 <filter>output_annotated_select</filter> 99 <filter>output_annotated['output_annotated_select']!='false'</filter>
102 </data> 100 </data>
103 <data name="out_log" format="tabular" label="${tool.name} on ${on_string}: Log"> 101 <data name="out_log" format="tabular" label="${tool.name} on ${on_string}: Log">
104 <filter>output_log_bool</filter> 102 <filter>output_log_bool</filter>
105 </data> 103 </data>
106 </outputs> 104 </outputs>
123 121
124 <output name="out_result"> 122 <output name="out_result">
125 <assert_contents> 123 <assert_contents>
126 <has_n_lines n="9"/> 124 <has_n_lines n="9"/>
127 <has_line line="##fileformat=VCFv4.1" /> 125 <has_line line="##fileformat=VCFv4.1" />
128 <has_line line="##medaka_version=1.0.3" /> 126 <has_line_matching expression="##medaka_version=[0-9]+\.[0-9]+\.[0-9]+" />
129 </assert_contents> 127 </assert_contents>
130 </output> 128 </output>
131 <output name="out_annotated"> 129 <output name="out_annotated">
132 <assert_contents> 130 <assert_contents>
133 <has_n_lines n="16"/> 131 <has_n_lines n="22"/>
134 <has_line line="##fileformat=VCFv4.1" /> 132 <has_line line="##fileformat=VCFv4.1" />
135 <has_line line="##medaka_version=1.0.3" /> 133 <has_line_matching expression="##medaka_version=[0-9]+\.[0-9]+\.[0-9]+" />
136 <has_line line="##annotateVCFVersion=0.2" /> 134 <has_line_matching expression="##convert_VCF_info_fields=[0-9]+\.[0-9]+" />
137 </assert_contents> 135 </assert_contents>
138 </output> 136 </output>
139 <output name="out_log"> 137 <output name="out_log">
140 <assert_contents> 138 <assert_contents>
141 <has_n_lines n="10" /> 139 <has_n_lines n="10" />
160 158
161 <output name="out_result"> 159 <output name="out_result">
162 <assert_contents> 160 <assert_contents>
163 <has_n_lines n="9"/> 161 <has_n_lines n="9"/>
164 <has_line line="##fileformat=VCFv4.1" /> 162 <has_line line="##fileformat=VCFv4.1" />
163 <has_line_matching expression="##medaka_version=[0-9]+\.[0-9]+\.[0-9]+" />
164 </assert_contents>
165 </output>
166 <output name="out_annotated">
167 <assert_contents>
168 <has_n_lines n="22"/>
169 <has_line line="##fileformat=VCFv4.1" />
165 <has_line line="##medaka_version=1.0.3" /> 170 <has_line line="##medaka_version=1.0.3" />
166 </assert_contents> 171 <has_line_matching expression="##medaka_version=[0-9]+\.[0-9]+\.[0-9]+" />
167 </output>
168 <output name="out_annotated">
169 <assert_contents>
170 <has_n_lines n="16"/>
171 <has_line line="##fileformat=VCFv4.1" />
172 <has_line line="##medaka_version=1.0.3" />
173 <has_line line="##annotateVCFVersion=0.2" />
174 </assert_contents> 172 </assert_contents>
175 </output> 173 </output>
176 <output name="out_log"> 174 <output name="out_log">
177 <assert_contents> 175 <assert_contents>
178 <has_n_lines n="8" /> 176 <has_n_lines n="8" />
177 </assert_contents>
178 </output>
179 </test>
180 <!--No annotation or log-->
181 <test expect_num_outputs="1">
182 <conditional name="pool">
183 <param name="pool_mode" value="No"/>
184 <param name="input" value="medaka_test.hdf"/>
185 </conditional>
186 <conditional name="reference_source">
187 <param name="reference_source_selector" value="history"/>
188 <param name="ref_file" value="ref.fasta"/>
189 </conditional>
190 <conditional name="output_annotated">
191 <param name="output_annotated_select" value="false"/>
192 </conditional>
193 <param name="output_log_bool" value="false"/>
194
195 <output name="out_result">
196 <assert_contents>
197 <has_n_lines n="9"/>
198 <has_line line="##fileformat=VCFv4.1" />
199 <has_line_matching expression="##medaka_version=[0-9]+\.[0-9]+\.[0-9]+" />
179 </assert_contents> 200 </assert_contents>
180 </output> 201 </output>
181 </test> 202 </test>
182 </tests> 203 </tests>
183 <help><![CDATA[ 204 <help><![CDATA[