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comparison call.xml @ 2:9946bd542898 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
author iuc
date Fri, 22 Jan 2021 14:31:44 +0000
parents 53d90d86fc83
children 6f383714149d
comparison
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1:53d90d86fc83 2:9946bd542898
33 #end if 33 #end if
34 --geno-qual $genotyping.genoqual 34 --geno-qual $genotyping.genoqual
35 #if 'dump' in $oo.out 35 #if 'dump' in $oo.out
36 --dump 'dump.tsv.gz' 36 --dump 'dump.tsv.gz'
37 #end if 37 #end if
38 ## samples 38 ## input
39 #for $i, $current in enumerate($samples) 39 #for $i, $current in enumerate($input)
40 'sample_${i}.bam' 40 'input_${i}.bam'
41 #end for 41 #end for
42 42
43 ## postprocessing 43 ## postprocessing
44 @LOG@ 44 @LOG@
45 @DUMP@
45 @VCF@ 46 @VCF@
46 @DUMP@
47 ]]></command> 47 ]]></command>
48 <inputs> 48 <inputs>
49 <expand macro="samples"/> 49 <expand macro="input" format="bam" multiple="true" label="Select input file(s)"/>
50 <section name="generic" title="Generic options" expanded="true"> 50 <section name="generic" title="Generic options" expanded="true">
51 <expand macro="svtype"/> 51 <expand macro="svtype"/>
52 <expand macro="genome"/> 52 <expand macro="genome"/>
53 <expand macro="exclude"/> 53 <expand macro="exclude"/>
54 </section> 54 </section>
55 <section name="discovery" title="Discovery options" expanded="true"> 55 <section name="discovery" title="Discovery options" expanded="true">
56 <param name="mapqual" type="integer" value="1" label="Set minimum paired-end (PE) mapping quality" help="(--map-qual)"/> 56 <param name="mapqual" type="integer" value="1" label="Set minimum paired-end mapping quality" help="(--map-qual)"/>
57 <param name="qualtra" type="integer" value="20" label="Set minimum PE quality for translocation" help="(--qual-tra)"/> 57 <param name="qualtra" type="integer" value="20" label="Set minimum paired-end quality for translocation" help="(--qual-tra)"/>
58 <param name="madcutoff" type="integer" value="9" label="Set insert size cutoff" help="median+s*MAD, deletions only (--mad-cutoff)"/> 58 <param name="madcutoff" type="integer" value="9" label="Set insert size cutoff" help="median+s*MAD, deletions only (--mad-cutoff)"/>
59 <expand macro="minclip"/> 59 <expand macro="minclip"/>
60 <expand macro="mincliquesize"/> 60 <expand macro="mincliquesize"/>
61 <expand macro="minrefsep"/> 61 <expand macro="minrefsep" default="25"/>
62 <expand macro="maxreadsep"/> 62 <expand macro="maxreadsep" default="40"/>
63 </section> 63 </section>
64 <section name="genotyping" title="Genotyping options" expanded="true"> 64 <section name="genotyping" title="Genotyping options" expanded="true">
65 <expand macro="vcffile"/> 65 <expand macro="vcffile"/>
66 <expand macro="genoqual"/> 66 <expand macro="genoqual"/>
67 </section> 67 </section>
68 <section name="oo" title="Output options"> 68 <section name="oo" title="Output options" expanded="true">
69 <param name="out" type="select" multiple="true" optional="false" label="Select output file(s)"> 69 <param name="out" type="select" multiple="true" optional="false" label="Select output file(s)">
70 <option value="bcf" selected="true">BCF</option> 70 <option value="bcf" selected="true">BCF</option>
71 <option value="log">Log</option>
72 <option value="dump">SV-reads (--dump)</option>
71 <option value="vcf">VCF</option> 73 <option value="vcf">VCF</option>
72 <option value="dump">SV-reads (--dump)</option>
73 <option value="log">Log</option>
74 </param> 74 </param>
75 </section> 75 </section>
76 </inputs> 76 </inputs>
77 <outputs> 77 <outputs>
78 <expand macro="vcf"/>
79 <expand macro="bcf"/> 78 <expand macro="bcf"/>
80 <expand macro="dump"/> 79 <expand macro="dump"/>
81 <expand macro="log"/> 80 <expand macro="log"/>
81 <expand macro="vcf"/>
82 </outputs> 82 </outputs>
83 <tests> 83 <tests>
84 <!-- no test implemented for parameter vcffile --> 84 <!-- no test implemented for parameter vcffile -->
85 85
86 <!-- #1 default, single --> 86 <!-- #1 default, single -->
87 <test expect_num_outputs="2"> 87 <test expect_num_outputs="2">
88 <param name="samples" value="normal.bam"/> 88 <param name="input" value="normal.bam"/>
89 <section name="generic"> 89 <section name="generic">
90 <param name="genome" value="genome.fasta"/> 90 <param name="genome" value="genome.fasta"/>
91 </section> 91 </section>
92 <section name="oo"> 92 <section name="oo">
93 <param name="out" value="vcf,bcf"/> 93 <param name="out" value="vcf,bcf"/>
94 </section> 94 </section>
95 <output name="out_bcf">
96 <assert_contents>
97 <has_size value="1184" delta="10"/>
98 </assert_contents>
99 </output>
95 <output name="out_vcf"> 100 <output name="out_vcf">
96 <assert_contents> 101 <assert_contents>
97 <has_size value="3661" delta="10"/> 102 <has_size value="3661" delta="10"/>
98 <has_line line="#CHROM&#009;POS&#009;ID&#009;REF&#009;ALT&#009;QUAL&#009;FILTER&#009;INFO&#009;FORMAT&#009;normal"/> 103 <has_line line="#CHROM&#009;POS&#009;ID&#009;REF&#009;ALT&#009;QUAL&#009;FILTER&#009;INFO&#009;FORMAT&#009;normal"/>
99 </assert_contents> 104 </assert_contents>
100 </output> 105 </output>
101 <output name="out_bcf">
102 <assert_contents>
103 <has_size value="1184" delta="10"/>
104 </assert_contents>
105 </output>
106 </test> 106 </test>
107 <!-- #2 default, multi; test data to small, results are empty --> 107 <!-- #2 default, multi; test data to small, results are empty -->
108 <test expect_num_outputs="3"> 108 <test expect_num_outputs="3">
109 <param name="samples" value="normal.bam,tumor.bam"/> 109 <param name="input" value="normal.bam,tumor.bam"/>
110 <section name="generic"> 110 <section name="generic">
111 <param name="genome" value="genome.fasta"/> 111 <param name="genome" value="genome.fasta"/>
112 </section> 112 </section>
113 <section name="oo"> 113 <section name="oo">
114 <param name="out" value="vcf,bcf,log"/> 114 <param name="out" value="vcf,bcf,log"/>
115 </section> 115 </section>
116 <output name="out_vcf">
117 <assert_contents>
118 <has_size value="0"/>
119 </assert_contents>
120 </output>
121 <output name="out_bcf"> 116 <output name="out_bcf">
122 <assert_contents> 117 <assert_contents>
123 <has_size value="0"/> 118 <has_size value="0"/>
124 </assert_contents> 119 </assert_contents>
125 </output> 120 </output>
126 <output name="out_log"> 121 <output name="out_log">
127 <assert_contents> 122 <assert_contents>
128 <has_text_matching expression="Sample has not enough data to estimate library parameters.+"/> 123 <has_text_matching expression="Sample has not enough data to estimate library parameters.+"/>
129 </assert_contents> 124 </assert_contents>
130 </output> 125 </output>
131 </test> 126 <output name="out_vcf">
132 <!-- #3; results are empty due to exclude file --> 127 <assert_contents>
128 <has_size value="0"/>
129 </assert_contents>
130 </output>
131 </test>
132 <!-- #3; results are empty due to exclude file -->
133 <test expect_num_outputs="4"> 133 <test expect_num_outputs="4">
134 <param name="samples" value="normal.bam"/> 134 <param name="input" value="normal.bam"/>
135 <section name="generic"> 135 <section name="generic">
136 <param name="genome" value="genome.fasta"/> 136 <param name="genome" value="genome.fasta"/>
137 <param name="exclude" value="exclude.tsv"/> 137 <param name="exclude" value="exclude.tsv"/>
138 </section> 138 </section>
139 <section name="oo"> 139 <section name="oo">
140 <param name="out" value="vcf,bcf,dump,log"/> 140 <param name="out" value="vcf,bcf,dump,log"/>
141 </section> 141 </section>
142 <output name="out_vcf">
143 <assert_contents>
144 <has_size value="0"/>
145 </assert_contents>
146 </output>
147 <output name="out_bcf"> 142 <output name="out_bcf">
148 <assert_contents> 143 <assert_contents>
149 <has_size value="0"/> 144 <has_size value="0"/>
150 </assert_contents> 145 </assert_contents>
151 </output> 146 </output>
157 <output name="out_log"> 152 <output name="out_log">
158 <assert_contents> 153 <assert_contents>
159 <has_text_matching expression="Sample has not enough data to estimate library parameters.+"/> 154 <has_text_matching expression="Sample has not enough data to estimate library parameters.+"/>
160 </assert_contents> 155 </assert_contents>
161 </output> 156 </output>
157 <output name="out_vcf">
158 <assert_contents>
159 <has_size value="0"/>
160 </assert_contents>
161 </output>
162 </test> 162 </test>
163 <!-- #4 --> 163 <!-- #4 -->
164 <test expect_num_outputs="1"> 164 <test expect_num_outputs="1">
165 <param name="samples" value="normal.bam"/> 165 <param name="input" value="normal.bam"/>
166 <section name="generic"> 166 <section name="generic">
167 <param name="svtype" value="ALL"/> 167 <param name="svtype" value="ALL"/>
168 <param name="genome" value="genome.fasta"/> 168 <param name="genome" value="genome.fasta"/>
169 </section> 169 </section>
170 <section name="discovery"> 170 <section name="discovery">
189 </assert_contents> 189 </assert_contents>
190 </output> 190 </output>
191 </test> 191 </test>
192 <!-- #5 --> 192 <!-- #5 -->
193 <test expect_num_outputs="1"> 193 <test expect_num_outputs="1">
194 <param name="samples" value="normal.bam"/> 194 <param name="input" value="normal.bam"/>
195 <section name="generic"> 195 <section name="generic">
196 <param name="svtype" value="DEL"/> 196 <param name="svtype" value="DEL"/>
197 <param name="genome" value="genome.fasta"/> 197 <param name="genome" value="genome.fasta"/>
198 </section> 198 </section>
199 <section name="oo"> 199 <section name="oo">
205 </assert_contents> 205 </assert_contents>
206 </output> 206 </output>
207 </test> 207 </test>
208 <!-- #6 --> 208 <!-- #6 -->
209 <test expect_num_outputs="1"> 209 <test expect_num_outputs="1">
210 <param name="samples" value="normal.bam"/> 210 <param name="input" value="normal.bam"/>
211 <section name="generic"> 211 <section name="generic">
212 <param name="svtype" value="INS"/> 212 <param name="svtype" value="INS"/>
213 <param name="genome" value="genome.fasta"/> 213 <param name="genome" value="genome.fasta"/>
214 </section> 214 </section>
215 <section name="oo"> 215 <section name="oo">
221 </assert_contents> 221 </assert_contents>
222 </output> 222 </output>
223 </test> 223 </test>
224 <!-- #7 --> 224 <!-- #7 -->
225 <test expect_num_outputs="1"> 225 <test expect_num_outputs="1">
226 <param name="samples" value="normal.bam"/> 226 <param name="input" value="normal.bam"/>
227 <section name="generic"> 227 <section name="generic">
228 <param name="svtype" value="INV"/> 228 <param name="svtype" value="INV"/>
229 <param name="genome" value="genome.fasta"/> 229 <param name="genome" value="genome.fasta"/>
230 </section> 230 </section>
231 <section name="oo"> 231 <section name="oo">
237 </assert_contents> 237 </assert_contents>
238 </output> 238 </output>
239 </test> 239 </test>
240 <!-- #8 --> 240 <!-- #8 -->
241 <test expect_num_outputs="2"> 241 <test expect_num_outputs="2">
242 <param name="samples" value="normal.bam"/> 242 <param name="input" value="normal.bam"/>
243 <section name="generic"> 243 <section name="generic">
244 <param name="svtype" value="BND"/> 244 <param name="svtype" value="BND"/>
245 <param name="genome" value="genome.fasta"/> 245 <param name="genome" value="genome.fasta"/>
246 </section> 246 </section>
247 <section name="oo"> 247 <section name="oo">
267 267
268 @WID@ 268 @WID@
269 269
270 **Input** 270 **Input**
271 271
272 Delly *call* needs a sorted, indexed and duplicate marked BAM file for every input sample. An indexed reference genome is required to identify split-reads. Additionally a VCF/BCF file for genotyping can be applied. 272 Delly *call* requires a sorted, indexed and duplicate marked BAM file for every input sample. An indexed reference genome is required to identify split-reads. Additionally a BCF/VCF file for genotyping can be applied.
273 273
274 **Output** 274 **Output**
275 275
276 The output is available in BCF and VCF format. Additionally an output file for SV-reads is provided. 276 The output is available in BCF and VCF format. Additionally an output file for SV-reads and a log file are provided.
277 277
278 .. class:: infomark 278 .. class:: infomark
279 279
280 **References** 280 **References**
281 281