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comparison stacks_gstacks.xml @ 2:30efa5dfbaf6 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
author iuc
date Wed, 15 Jul 2020 21:10:16 +0000
parents 8b6aa27346b7
children 14544fb17871
comparison
equal deleted inserted replaced
1:8b6aa27346b7 2:30efa5dfbaf6
88 ## exit codes and stderr output) this adds the samtools requirement 88 ## exit codes and stderr output) this adds the samtools requirement
89 ## for later versions where this is fixed the output bam files could just be moved 89 ## for later versions where this is fixed the output bam files could just be moved
90 ## to stacks_outputs if this is still necessary 90 ## to stacks_outputs if this is still necessary
91 #if $mode_cond.mode_select == "denovo" and $mode_cond.advanced_cond.advanced_select == "yes" and $mode_cond.advanced_cond.write_alignments != "" 91 #if $mode_cond.mode_select == "denovo" and $mode_cond.advanced_cond.advanced_select == "yes" and $mode_cond.advanced_cond.write_alignments != ""
92 #if $popmap: 92 #if $popmap:
93 && for b in bam_inputs/*alns.bam; do (samtools view -b "\$b" || true) 2> /dev/null > stacks_outputs/\$(basename "\$b"); done 93 && for b in stacks_outputs/*alns.bam; do (samtools view -b "\$b" || true) 2> /dev/null > tmp && mv tmp "\$b"; done
94 #else 94 #else
95 && (samtools view -b bam_inputs/alignments.bam || true) 2> /dev/null > stacks_outputs/alignments.bam 95 && (samtools view -b stacks_outputs/alignments.bam || true) 2> /dev/null > tmp && mv tmp stacks_outputs/alignments.bam
96 #end if 96 #end if
97 #end if 97 #end if
98 98
99 @EXTRACT_VCF@ 99 @EXTRACT_VCF@
100 100
107 ## TODO make optional output collection 107 ## TODO make optional output collection
108 ]]></command> 108 ]]></command>
109 109
110 <inputs> 110 <inputs>
111 <expand macro="bam_input_macro"/> 111 <expand macro="bam_input_macro"/>
112 <param name="popmap" type="data" format="tabular,txt" label="Population map" help="If set, matching will be done only for samples listed in this file" optional="true" argument="-M" /> 112 <param name="popmap" type="data" format="tabular,txt" label="Population map" help="If set, matching will be done only for samples listed in this file" optional="true" argument="-M"/>
113 113
114 <conditional name="mode_cond"> 114 <conditional name="mode_cond">
115 <param name="mode_select" type="select" label="Mode"> 115 <param name="mode_select" type="select" label="Mode">
116 <option value="denovo" selected="true">De novo mode</option> 116 <option value="denovo" selected="true">De novo mode</option>
117 <option value="refbased">Reference-based</option> 117 <option value="refbased">Reference-based</option>
118 </param> 118 </param>
119 <when value="denovo"> 119 <when value="denovo">
120 <param argument="--ignore-pe-reads" name="ignore_pe_reads" type="boolean" checked="false" truevalue="--ignore-pe-reads" falsevalue="" label="Ignore paired-end reads" help="ignore paired-end reads even if present in the input" /> 120 <param argument="--ignore-pe-reads" name="ignore_pe_reads" type="boolean" checked="false" truevalue="--ignore-pe-reads" falsevalue="" label="Ignore paired-end reads" help="ignore paired-end reads even if present in the input"/>
121 <conditional name="advanced_cond"> 121 <conditional name="advanced_cond">
122 <param name="advanced_select" type="select" label="Advanced options"> 122 <param name="advanced_select" type="select" label="Advanced options">
123 <option value="no">No</option> 123 <option value="no">No</option>
124 <option value="yes">Yes</option> 124 <option value="yes">Yes</option>
125 </param> 125 </param>
126 <when value="yes"> 126 <when value="yes">
127 <param argument="--kmer-length" name="kmer_length" type="integer" value="31" min="2" max="31" label="K-mer length for the de Bruijn graph" /> 127 <param argument="--kmer-length" name="kmer_length" type="integer" value="31" min="2" max="31" label="K-mer length for the de Bruijn graph"/>
128 <param argument="--max-debruijn-reads" name="max_debruijn_reads" type="integer" value="1000" min="1" label="Maximum number of reads to use in the de Bruijn graph" /> 128 <param argument="--max-debruijn-reads" name="max_debruijn_reads" type="integer" value="1000" min="1" label="Maximum number of reads to use in the de Bruijn graph"/>
129 <param argument="--min-kmer-cov" name="min_kmer_cov" type="integer" value="2" label="Minimum coverage to consider a kmer" /> 129 <param argument="--min-kmer-cov" name="min_kmer_cov" type="integer" value="2" label="Minimum coverage to consider a kmer"/>
130 <param argument="--write-alignments" name="write_alignments" type="boolean" checked="false" truevalue="--write-alignments" falsevalue="" label="save read alignments" help="heavy BAM files"/> 130 <param argument="--write-alignments" name="write_alignments" type="boolean" checked="false" truevalue="--write-alignments" falsevalue="" label="save read alignments" help="heavy BAM files"/>
131 </when> 131 </when>
132 <when value="no"/> 132 <when value="no"/>
133 </conditional> 133 </conditional>
134 </when> 134 </when>
138 <option value="" selected="true">single/paired</option> 138 <option value="" selected="true">single/paired</option>
139 <option value="--unpaired" selected="true">ignore read pairing (--unpaired)</option> 139 <option value="--unpaired" selected="true">ignore read pairing (--unpaired)</option>
140 <option value="--ignore-pe-reads" selected="true">ignore paired-end reads (--ignore-pe-reads)</option> 140 <option value="--ignore-pe-reads" selected="true">ignore paired-end reads (--ignore-pe-reads)</option>
141 </param> 141 </param>
142 <when value=""> 142 <when value="">
143 <param argument="--rm-unpaired-reads" name="rm_unpaired_reads" type="boolean" checked="false" truevalue="--rm-unpaired-reads" falsevalue="" label="Discard unpaired reads" /> 143 <param argument="--rm-unpaired-reads" name="rm_unpaired_reads" type="boolean" checked="false" truevalue="--rm-unpaired-reads" falsevalue="" label="Discard unpaired reads"/>
144 <param argument="--rm-pcr-duplicates" name="rm_pcr_duplicates" type="boolean" checked="false" truevalue="--rm-pcr-duplicates" falsevalue="" label="Remove read pairs of the same sample that have the same insert length" help="implies --rm-unpaired-reads" /> 144 <param argument="--rm-pcr-duplicates" name="rm_pcr_duplicates" type="boolean" checked="false" truevalue="--rm-pcr-duplicates" falsevalue="" label="Remove read pairs of the same sample that have the same insert length" help="implies --rm-unpaired-reads"/>
145 </when> 145 </when>
146 <when value="--unpaired"/> 146 <when value="--unpaired"/>
147 <when value="--ignore-pe-reads"/> 147 <when value="--ignore-pe-reads"/>
148 </conditional> 148 </conditional>
149 <conditional name="advanced_cond"> 149 <conditional name="advanced_cond">
150 <param name="advanced_select" type="select" label="Advanced options"> 150 <param name="advanced_select" type="select" label="Advanced options">
151 <option value="no">No</option> 151 <option value="no">No</option>
152 <option value="yes">Yes</option> 152 <option value="yes">Yes</option>
153 </param> 153 </param>
154 <when value="yes"> 154 <when value="yes">
155 <param argument="--min-mapq" name="min_mapq" type="integer" value="10" min="0" max="255" label="Minimum PHRED-scaled mapping quality to consider a read" /> 155 <param argument="--min-mapq" name="min_mapq" type="integer" value="10" min="0" max="255" label="Minimum PHRED-scaled mapping quality to consider a read"/>
156 <param argument="--max-clipped" name="max_clipped" type="float" value="0.2" min="0.0" max="1.1" label="Maximum soft-clipping level" help="in fraction of read length" /> 156 <param argument="--max-clipped" name="max_clipped" type="float" value="0.2" min="0.0" max="1.1" label="Maximum soft-clipping level" help="in fraction of read length"/>
157 <param argument="--max-insert-len" name="max_insert_len" type="integer" value="1000" min="0" label="Maximum allowed sequencing insert length" /> 157 <param argument="--max-insert-len" name="max_insert_len" type="integer" value="1000" min="0" label="Maximum allowed sequencing insert length"/>
158 <param argument="--details" type="boolean" checked="false" truevalue="--details" falsevalue="" label="Write a heaview output" /> 158 <param argument="--details" type="boolean" checked="false" truevalue="--details" falsevalue="" label="Write a heaview output"/>
159 <param name="phasing_cooccurrences_thr_min" type="integer" value="1" min="0" label="Edge coverage min" help="(--phasing-cooccurrences-thr-range)" /> 159 <param name="phasing_cooccurrences_thr_min" type="integer" value="1" min="0" label="Edge coverage min" help="(--phasing-cooccurrences-thr-range)"/>
160 <param name="phasing_cooccurrences_thr_max" type="integer" value="2" min="0" label="Edge coverage max" help="range of edge coverage thresholds to iterate over when building the graph of allele cooccurrences for SNP phasing (--phasing-cooccurrences-thr-range)"/> 160 <param name="phasing_cooccurrences_thr_max" type="integer" value="2" min="0" label="Edge coverage max" help="range of edge coverage thresholds to iterate over when building the graph of allele cooccurrences for SNP phasing (--phasing-cooccurrences-thr-range)"/>
161 <param argument="--phasing-dont-prune-hets" name="phasing_dont_prune_hets" type="boolean" checked="false" truevalue="--phasing-dont-prune-hets" falsevalue="" label="Don't try to ignore dubious heterozygote genotypes during phasing" /> 161 <param argument="--phasing-dont-prune-hets" name="phasing_dont_prune_hets" type="boolean" checked="false" truevalue="--phasing-dont-prune-hets" falsevalue="" label="Don't try to ignore dubious heterozygote genotypes during phasing"/>
162 </when> 162 </when>
163 <when value="no"/> 163 <when value="no"/>
164 </conditional> 164 </conditional>
165 </when> 165 </when>
166 </conditional> 166 </conditional>
179 </when> 179 </when>
180 <when value="snp"> 180 <when value="snp">
181 <expand macro="variant_calling_options_vg"/> 181 <expand macro="variant_calling_options_vg"/>
182 </when> 182 </when>
183 </conditional> 183 </conditional>
184 <param name="add_log_distribs" type="boolean" checked="false" truevalue="yes" falsevalue="no" label="Add log distribs output as dataset" /> 184 <param name="add_log_distribs" type="boolean" checked="false" truevalue="yes" falsevalue="no" label="Add log distribs output as dataset"/>
185 <expand macro="in_log"/> 185 <expand macro="in_log"/>
186 </inputs> 186 </inputs>
187 <outputs> 187 <outputs>
188 <expand macro="out_log"/> 188 <expand macro="out_log"/>
189 <expand macro="gstacks_outputs_full_macro"/> 189 <expand macro="gstacks_outputs_full_macro"/>
191 191
192 <tests> 192 <tests>
193 <!-- denovomode, w popmap --> 193 <!-- denovomode, w popmap -->
194 <test expect_num_outputs="3"> 194 <test expect_num_outputs="3">
195 <param name="input_bam" ftype="bam" value="tsv2bam/PopA_01.matches.bam,tsv2bam/PopA_02.matches.bam"/> 195 <param name="input_bam" ftype="bam" value="tsv2bam/PopA_01.matches.bam,tsv2bam/PopA_02.matches.bam"/>
196 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" /> 196 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv"/>
197 <conditional name="mode_cond"> 197 <conditional name="mode_cond">
198 <param name="mode_select" value="denovo"/> 198 <param name="mode_select" value="denovo"/>
199 </conditional> 199 </conditional>
200 <param name="add_log" value="yes" /> 200 <param name="add_log" value="yes"/>
201 <param name="add_log_distribs" value="yes" /> 201 <param name="add_log_distribs" value="yes"/>
202 <output name="output_log" ftype="txt" file="gstacks/gstacks.log" lines_diff="8"/> 202 <output name="output_log" ftype="txt" file="gstacks/gstacks.log" lines_diff="8"/>
203 <output name="distribs" ftype="txt" file="gstacks/gstacks.log.distribs" compare="sim_size"/> 203 <output name="distribs" ftype="txt" file="gstacks/gstacks.log.distribs" compare="sim_size" delta="10"/>
204 <output_collection name="gstacks_out" type="list" count="2"> 204 <output_collection name="gstacks_out" type="list" count="2">
205 <element name="catalog.calls.vcf" file="gstacks/catalog.calls.vcf" ftype="vcf" lines_diff="2"/> 205 <element name="catalog.calls.vcf" file="gstacks/catalog.calls.vcf" ftype="vcf" lines_diff="4"/>
206 <element name="catalog.fa.gz" file="gstacks/catalog.fa.gz" ftype="fasta.gz"/> 206 <element name="catalog.fa.gz" file="gstacks/catalog.fa.gz" ftype="fasta.gz" compare="sim_size" delta_frac="0.01"/>
207 </output_collection> 207 </output_collection>
208 </test> 208 </test>
209 <!-- denovomode, w popmap, write alignments --> 209 <!-- denovomode, w popmap, write alignments -->
210 <test expect_num_outputs="3"> 210 <test expect_num_outputs="3">
211 <param name="input_bam" ftype="bam" value="tsv2bam/PopA_01.matches.bam,tsv2bam/PopA_02.matches.bam"/> 211 <param name="input_bam" ftype="bam" value="tsv2bam/PopA_01.matches.bam,tsv2bam/PopA_02.matches.bam"/>
212 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" /> 212 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv"/>
213 <conditional name="mode_cond"> 213 <conditional name="mode_cond">
214 <param name="mode_select" value="denovo"/> 214 <param name="mode_select" value="denovo"/>
215 <conditional name="advanced_cond"> 215 <conditional name="advanced_cond">
216 <param name="advanced_select" value="yes"/> 216 <param name="advanced_select" value="yes"/>
217 <param name="write_alignments" value="--write-alignments" /> 217 <param name="write_alignments" value="--write-alignments"/>
218 </conditional> 218 </conditional>
219 </conditional> 219 </conditional>
220 <param name="add_log" value="yes" /> 220 <param name="add_log" value="yes"/>
221 <assert_command> 221 <assert_command>
222 <has_text text="--write-alignments" /> 222 <has_text text="--write-alignments"/>
223 </assert_command> 223 </assert_command>
224 <output name="output_log" ftype="txt"><assert_contents><has_text text="done." /></assert_contents></output> 224 <output name="output_log" ftype="txt"><assert_contents><has_text text="done."/></assert_contents></output>
225 <output_collection name="gstacks_out" type="list" count="2"/> 225 <output_collection name="gstacks_out" type="list" count="2"/>
226 <output_collection name="gstacks_alns_out" type="list" count="2"> 226 <output_collection name="gstacks_alns_out" type="list" count="2">
227 <element name="PopA_01" file="gstacks/PopA_01.alns.bam" ftype="bam" /> 227 <element name="PopA_01" file="gstacks/PopA_01.alns.bam" ftype="bam"/>
228 <element name="PopA_02" file="gstacks/PopA_02.alns.bam" ftype="bam" /> 228 <element name="PopA_02" file="gstacks/PopA_02.alns.bam" ftype="bam"/>
229 </output_collection> 229 </output_collection>
230 </test> 230 </test>
231 <!-- denovomode, wo popmap (allows for only one input), ignore PE, advanced, alt model --> 231 <!-- denovomode, wo popmap (allows for only one input), ignore PE, advanced, alt model -->
232 <test expect_num_outputs="3"> 232 <test expect_num_outputs="3">
233 <param name="input_bam" value="tsv2bam/PopA_01.matches.bam" ftype="bam"/> 233 <param name="input_bam" value="tsv2bam/PopA_01.matches.bam" ftype="bam"/>
234 <conditional name="mode_cond"> 234 <conditional name="mode_cond">
235 <param name="mode_select" value="denovo" /> 235 <param name="mode_select" value="denovo"/>
236 <param name="ignore_pe_reads" value="--ignore-pe-reads" /> 236 <param name="ignore_pe_reads" value="--ignore-pe-reads"/>
237 <conditional name="advanced_cond"> 237 <conditional name="advanced_cond">
238 <param name="advanced_select" value="yes"/> 238 <param name="advanced_select" value="yes"/>
239 <param name="kmer_length" value="23" /> 239 <param name="kmer_length" value="23"/>
240 <param name="max_debruijn_reads" value="666"/> 240 <param name="max_debruijn_reads" value="666"/>
241 <param name="min_kmer_cov" value="3" /> 241 <param name="min_kmer_cov" value="3"/>
242 <param name="write_alignments" value="--write-alignments" /> 242 <param name="write_alignments" value="--write-alignments"/>
243 </conditional> 243 </conditional>
244 </conditional> 244 </conditional>
245 <conditional name="model_cond"> 245 <conditional name="model_cond">
246 <param name="model" value="marukihigh"/> 246 <param name="model" value="marukihigh"/>
247 <param name="var_alpha" value="0.1" /> 247 <param name="var_alpha" value="0.1"/>
248 <param name="gt_alpha" value="0.1" /> 248 <param name="gt_alpha" value="0.1"/>
249 </conditional> 249 </conditional>
250 <param name="add_log" value="yes" /> 250 <param name="add_log" value="yes"/>
251 <assert_command> 251 <assert_command>
252 <has_text text="--ignore-pe-reads" /> 252 <has_text text="--ignore-pe-reads"/>
253 <has_text text="--kmer-length 23" /> 253 <has_text text="--kmer-length 23"/>
254 <has_text text="--max-debruijn-reads 666" /> 254 <has_text text="--max-debruijn-reads 666"/>
255 <has_text text="--min-kmer-cov 3" /> 255 <has_text text="--min-kmer-cov 3"/>
256 <has_text text="--write-alignments" /> 256 <has_text text="--write-alignments"/>
257 <has_text text="--model marukihigh" /> 257 <has_text text="--model marukihigh"/>
258 <has_text text="--var-alpha 0.1" /> 258 <has_text text="--var-alpha 0.1"/>
259 <has_text text="--gt-alpha 0.1" /> 259 <has_text text="--gt-alpha 0.1"/>
260 </assert_command> 260 </assert_command>
261 <output name="output_log" ftype="txt"><assert_contents><has_text text="done." /></assert_contents></output> 261 <output name="output_log" ftype="txt"><assert_contents><has_text text="done."/></assert_contents></output>
262 <output_collection name="gstacks_out" type="list" count="2"/> 262 <output_collection name="gstacks_out" type="list" count="2"/>
263 <output name="gstacks_aln_out" ftype="bam" file="gstacks/alignments.bam" /> 263 <output name="gstacks_aln_out" ftype="bam" file="gstacks/alignments.bam"/>
264 </test> 264 </test>
265 <!-- refbased wo popmap, paired options, removing all unpaired reads results in an error --> 265 <!-- refbased wo popmap, paired options, removing all unpaired reads results in an error -->
266 <test expect_failure="true" expect_exit_code="1"> 266 <test expect_failure="true" expect_exit_code="1">
267 <param name="input_bam" value="tsv2bam/PopA_01.bam,tsv2bam/PopA_02.bam"/> 267 <param name="input_bam" value="tsv2bam/PopA_01.bam,tsv2bam/PopA_02.bam"/>
268 <conditional name="mode_cond"> 268 <conditional name="mode_cond">
269 <param name="mode_select" value="refbased"/> 269 <param name="mode_select" value="refbased"/>
270 <conditional name="paired_cond"> 270 <conditional name="paired_cond">
271 <param name="paired_select" value=""/> 271 <param name="paired_select" value=""/>
272 <!--<param name="rm_unpaired_reads" value="\-\-rm-unpaired-reads" /> removes too much of the test data and gstacks fails--> 272 <!--<param name="rm_unpaired_reads" value="\-\-rm-unpaired-reads"/> removes too much of the test data and gstacks fails-->
273 <param name="rm_pcr_duplicates" value="--rm-pcr-duplicates" /> 273 <param name="rm_pcr_duplicates" value="--rm-pcr-duplicates"/>
274 </conditional> 274 </conditional>
275 </conditional> 275 </conditional>
276 <param name="add_log" value="yes" /> 276 <param name="add_log" value="yes"/>
277 <assert_command> 277 <assert_command>
278 <not_has_text text="-I bam_inputs" /> 278 <not_has_text text="-I bam_inputs"/>
279 <has_text text="-B " /> 279 <has_text text="-B "/>
280 <not_has_text text="--rm-unpaired-reads" /> 280 <not_has_text text="--rm-unpaired-reads"/>
281 <has_text text="--rm-pcr-duplicates" /> 281 <has_text text="--rm-pcr-duplicates"/>
282 </assert_command> 282 </assert_command>
283 </test> 283 </test>
284 <!-- refbased w popmap (here bam names need to be equal to sample names in popmap), \-\-unpaired, advanced, snp model --> 284 <!-- refbased w popmap (here bam names need to be equal to sample names in popmap), \-\-unpaired, advanced, snp model -->
285 <test expect_num_outputs="2"> 285 <test expect_num_outputs="2">
286 <param name="input_bam" ftype="bam" value="tsv2bam/PopA_01.bam,tsv2bam/PopA_02.bam"/> 286 <param name="input_bam" ftype="bam" value="tsv2bam/PopA_01.bam,tsv2bam/PopA_02.bam"/>
287 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" /> 287 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv"/>
288 <conditional name="mode_cond"> 288 <conditional name="mode_cond">
289 <param name="mode_select" value="refbased"/> 289 <param name="mode_select" value="refbased"/>
290 <conditional name="paired_cond"> 290 <conditional name="paired_cond">
291 <param name="paired_select" value="--unpaired"/> 291 <param name="paired_select" value="--unpaired"/>
292 </conditional> 292 </conditional>
293 <conditional name="advanced_cond"> 293 <conditional name="advanced_cond">
294 <param name="advanced_select" value="yes" /> 294 <param name="advanced_select" value="yes"/>
295 <param name="min_mapq" value="23" /> 295 <param name="min_mapq" value="23"/>
296 <param name="max_clipped" value="0.23" /> 296 <param name="max_clipped" value="0.23"/>
297 <param name="max_insert_len" value="666" /> 297 <param name="max_insert_len" value="666"/>
298 <param name="details" value="--details"/> 298 <param name="details" value="--details"/>
299 <param name="phasing_cooccurrences_thr_min" value="2"/> 299 <param name="phasing_cooccurrences_thr_min" value="2"/>
300 <param name="phasing_cooccurrences_thr_max" value="3"/> 300 <param name="phasing_cooccurrences_thr_max" value="3"/>
301 <param name="phasing_dont_prune_hets" value="--phasing-dont-prune-hets" /> 301 <param name="phasing_dont_prune_hets" value="--phasing-dont-prune-hets"/>
302 </conditional> 302 </conditional>
303 </conditional> 303 </conditional>
304 <param name="model_cond|model" value="snp"/> 304 <param name="model_cond|model" value="snp"/>
305 <param name="model_cond|gt_alpha" value="0.1" /> 305 <param name="model_cond|gt_alpha" value="0.1"/>
306 <param name="model_cond|var_alpha" value="0.1" /> 306 <param name="model_cond|var_alpha" value="0.1"/>
307 <param name="add_log" value="yes" /> 307 <param name="add_log" value="yes"/>
308 <assert_command> 308 <assert_command>
309 <has_text text="-I bam_inputs" /> 309 <has_text text="-I bam_inputs"/>
310 <not_has_text text="-B " /> 310 <not_has_text text="-B "/>
311 <has_text text="--unpaired" /> 311 <has_text text="--unpaired"/>
312 <has_text text="--min-mapq 23" /> 312 <has_text text="--min-mapq 23"/>
313 <has_text text="--max-clipped 0.23" /> 313 <has_text text="--max-clipped 0.23"/>
314 <has_text text="--max-insert-len 666" /> 314 <has_text text="--max-insert-len 666"/>
315 <has_text text="--details" /> 315 <has_text text="--details"/>
316 <has_text text="--phasing-cooccurrences-thr-range 2,3" /> 316 <has_text text="--phasing-cooccurrences-thr-range 2,3"/>
317 <has_text text="--phasing-dont-prune-hets" /> 317 <has_text text="--phasing-dont-prune-hets"/>
318 <has_text text="--model snp" /> 318 <has_text text="--model snp"/>
319 <has_text text="--gt-alpha 0.1" /> 319 <has_text text="--gt-alpha 0.1"/>
320 </assert_command> 320 </assert_command>
321 <output name="output_log" ftype="txt"><assert_contents><has_text text="done." /></assert_contents></output> 321 <output name="output_log" ftype="txt"><assert_contents><has_text text="done."/></assert_contents></output>
322 <output_collection name="gstacks_out" type="list" count="2"/> 322 <output_collection name="gstacks_out" type="list" count="2"/>
323 </test> 323 </test>
324 <!-- refbased wo popmap (here bam names don't matter), \-\-ignorepe --> 324 <!-- refbased wo popmap (here bam names don't matter), \-\-ignorepe -->
325 <test expect_num_outputs="2"> 325 <test expect_num_outputs="2">
326 <param name="input_bam" ftype="bam" value="tsv2bam/PopA_01.bam,tsv2bam/PopA_02.bam"/> 326 <param name="input_bam" ftype="bam" value="tsv2bam/PopA_01.bam,tsv2bam/PopA_02.bam"/>
328 <param name="mode_select" value="refbased"/> 328 <param name="mode_select" value="refbased"/>
329 <conditional name="paired_cond"> 329 <conditional name="paired_cond">
330 <param name="paired_select" value="--ignore-pe-reads"/> 330 <param name="paired_select" value="--ignore-pe-reads"/>
331 </conditional> 331 </conditional>
332 </conditional> 332 </conditional>
333 <param name="add_log" value="yes" /> 333 <param name="add_log" value="yes"/>
334 <assert_command> 334 <assert_command>
335 <not_has_text text="-I bam_inputs" /> 335 <not_has_text text="-I bam_inputs"/>
336 <has_text text="-B " /> 336 <has_text text="-B "/>
337 <has_text text="--ignore-pe-reads" /> 337 <has_text text="--ignore-pe-reads"/>
338 </assert_command> 338 </assert_command>
339 <output name="output_log"><assert_contents><has_text text="gstacks is done." /></assert_contents></output> 339 <output name="output_log"><assert_contents><has_text text="gstacks is done."/></assert_contents></output>
340 <output_collection name="gstacks_out" type="list" count="2"/> 340 <output_collection name="gstacks_out" type="list" count="2"/>
341 </test> 341 </test>
342 </tests> 342 </tests>
343 343
344 <help> 344 <help>
375 - Optional outputs: Read alignments and log.distribs 375 - Optional outputs: Read alignments and log.distribs
376 376
377 @STACKS_INFOS@ 377 @STACKS_INFOS@
378 ]]> 378 ]]>
379 </help> 379 </help>
380 <expand macro="citation" /> 380 <expand macro="citation"/>
381 </tool> 381 </tool>