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comparison samtools_stats.xml @ 12:8fecc86e574a draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
author iuc
date Sun, 08 Sep 2024 03:23:56 +0000
parents a95f78faca04
children
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11:a95f78faca04 12:8fecc86e574a
1 <tool id="samtools_stats" name="Samtools stats" version="2.0.4" profile="@PROFILE@"> 1 <tool id="samtools_stats" name="Samtools stats" version="2.0.5" profile="@PROFILE@">
2 <description>generate statistics for BAM dataset</description> 2 <description>generate statistics for BAM dataset</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
43 #end if 43 #end if
44 44
45 #if $use_ref: 45 #if $use_ref:
46 --ref-seq "\$reffa" 46 --ref-seq "\$reffa"
47 #end if 47 #end if
48 ## TODO currently not implemented in Galaxy 48 ## currently not implemented in Galaxy
49 ## generates STR_VALUE.bamstat where STR is given by -P and VALUE is a value of the TAG given by -S 49 ## generates STR_VALUE.bamstat where STR is given by -P and VALUE is a value of the TAG given by -S
50 ## needs some discover data sets action... 50 ## needs some discover data sets action...
51 ## -P, --split-prefix STR 51 ## -P, --split-prefix STR
52 ## -S, --split TAG 52 ## -S, --split TAG
53 $sparse 53 $sparse
82 <param name="coverage_min" type="integer" value="1" label="Minimum coverage" help="Minimum coverage" /> 82 <param name="coverage_min" type="integer" value="1" label="Minimum coverage" help="Minimum coverage" />
83 <param name="coverage_max" type="integer" value="1000" label="Maximum coverage" help="Maximum coverage" /> 83 <param name="coverage_max" type="integer" value="1000" label="Maximum coverage" help="Maximum coverage" />
84 <param name="coverage_step" type="integer" value="1" label="Coverage step" help="Step value for coverage" /> 84 <param name="coverage_step" type="integer" value="1" label="Coverage step" help="Step value for coverage" />
85 </when> 85 </when>
86 </conditional> 86 </conditional>
87 <param name="remove_dups" argument="--remove-dups" type="boolean" truevalue="--remove-dups" falsevalue="" checked="False" label="Exclude reads marked as duplicates" /> 87 <param argument="--remove-dups" type="boolean" truevalue="--remove-dups" falsevalue="" checked="False" label="Exclude reads marked as duplicates" />
88 <conditional name="split_output_cond"> 88 <conditional name="split_output_cond">
89 <param name="split_output_selector" type="select" label="Output" help="Select between one single output or separate outputs for each statistics"> 89 <param name="split_output_selector" type="select" label="Output" help="Select between one single output or separate outputs for each statistics">
90 <option value="no" selected="True">One single summary file</option> 90 <option value="no" selected="True">One single summary file</option>
91 <option value="yes">Separate datasets for each statistic</option> 91 <option value="yes">Separate datasets for each statistic</option>
92 </param> 92 </param>
129 <when value="nofilter" /> 129 <when value="nofilter" />
130 130
131 </conditional> 131 </conditional>
132 <!-- TODO I would like to set the default values of float and int parameters as on the samtools stats help page, but then the tests don't work. Hence I leave the optional and give the defaults in the help --> 132 <!-- TODO I would like to set the default values of float and int parameters as on the samtools stats help page, but then the tests don't work. Hence I leave the optional and give the defaults in the help -->
133 <param name="gc_depth" argument="--GC-depth" type="float" optional="True" label="Size of GC-depth bins" help="Decreasing bin size increases memory requirement. default=2e4" /> 133 <param name="gc_depth" argument="--GC-depth" type="float" optional="True" label="Size of GC-depth bins" help="Decreasing bin size increases memory requirement. default=2e4" />
134 <param name="insert_size" argument="--insert-size" type="integer" optional="True" label="Maximum insert size" help="default=8000" /> 134 <param argument="--insert-size" type="integer" optional="True" label="Maximum insert size" help="default=8000" />
135 <!-- TOOD https://github.com/samtools/samtools/issues/1489 --> 135 <!-- TOOD https://github.com/samtools/samtools/issues/1489 -->
136 <param name="read_group" argument="--id" type="select" optional="true" label="Limit to a specific read group name" > 136 <param name="read_group" argument="--id" type="select" optional="true" label="Limit to a specific read group name" >
137 <options> 137 <options>
138 <filter type="data_meta" ref="input" key="read_groups" /> 138 <filter type="data_meta" ref="input" key="read_groups" />
139 </options> 139 </options>
140 </param> 140 </param>
141 <param name="read_length" argument="--read-length" type="integer" optional="true" label="Minimum read length to generate statistics for" help="No cutoff if left empty" /> 141 <param argument="--read-length" type="integer" optional="true" label="Minimum read length to generate statistics for" help="No cutoff if left empty" />
142 <param name="most_inserts" argument="--most-inserts" type="float" optional="true" label="Report only the main part of inserts" help="default=0.99" /> 142 <param argument="--most-inserts" type="float" optional="true" label="Report only the main part of inserts" help="default=0.99" />
143 <param name="trim_quality" argument="--trim-quality" type="integer" optional="true" label="BWA trim parameter" help="default=0" /> 143 <param argument="--trim-quality" type="integer" optional="true" label="BWA trim parameter" help="default=0" />
144 144
145 <expand macro="optional_reference" argument="--ref-seq" help="Required for GC-depth and mismatches-per-cycle calculation"/> 145 <expand macro="optional_reference" argument="--ref-seq" help="Required for GC-depth and mismatches-per-cycle calculation"/>
146 <!-- unfortunately -t takes tabular and not bed like view (otherwise a macro might have simplified this) --> 146 <!-- unfortunately -t takes tabular and not bed like view (otherwise a macro might have simplified this) -->
147 147
148 <expand macro="regions_macro"/> 148 <expand macro="regions_macro"/>
151 <param name="remove_overlaps" argument="-p/--remove-overlaps" type="boolean" truevalue="-p" falsevalue="" checked="False" label="Remove overlaps of paired-end reads from coverage and base count computations" /> 151 <param name="remove_overlaps" argument="-p/--remove-overlaps" type="boolean" truevalue="-p" falsevalue="" checked="False" label="Remove overlaps of paired-end reads from coverage and base count computations" />
152 <param name="cov_threshold" argument="-g/--cov-threshold" optional="true" type="integer" label="Only bases with coverage above this value will be included in the target percentage computation" /> 152 <param name="cov_threshold" argument="-g/--cov-threshold" optional="true" type="integer" label="Only bases with coverage above this value will be included in the target percentage computation" />
153 </inputs> 153 </inputs>
154 154
155 <outputs> 155 <outputs>
156 <data name="output" format="tabular" label="${tool.name} on ${on_string}"> 156 <data name="output" format="tabular">
157 <discover_datasets directory="split" pattern="(?P&lt;designation&gt;.+)\.tab" format="tabular" visible="true" assign_primary_output="true"/>
158 <filter>split_output_cond['split_output_selector'] == 'no'</filter> 157 <filter>split_output_cond['split_output_selector'] == 'no'</filter>
159 </data> 158 </data>
160 <collection name="output_collection" type="list" label="${tool.name} on ${on_string}"> 159 <collection name="output_collection" type="list" label="${tool.name} on ${on_string}: separate statistics">
161 <discover_datasets directory="split" pattern="(?P&lt;designation&gt;.+)\.tab" format="tabular" visible="false"/> 160 <discover_datasets directory="split" pattern="(?P&lt;designation&gt;.+)\.tab" format="tabular" visible="false"/>
162 <filter>split_output_cond['split_output_selector'] == 'yes'</filter> 161 <filter>split_output_cond['split_output_selector'] == 'yes'</filter>
163 </collection> 162 </collection>
164 </outputs> 163 </outputs>
165 <tests> 164 <tests>
166 <!-- https://github.com/samtools/samtools/blob/9ce8c64493f7ea3fa69bc5c1ac980b1a8e3dcf1f/test/test.pl#L2402 --> 165 <!-- https://github.com/samtools/samtools/blob/9ce8c64493f7ea3fa69bc5c1ac980b1a8e3dcf1f/test/test.pl#L2402 -->
167 <test> 166 <test expect_num_outputs="1">
168 <param name="input" value="1_map_cigar.sam" ftype="sam" /> 167 <param name="input" value="1_map_cigar.sam" ftype="sam" />
169 <conditional name="addref_cond"> 168 <conditional name="addref_cond">
170 <param name="addref_select" value="history" /> 169 <param name="addref_select" value="history" />
171 <param name="ref" value="test.fa" ftype="fasta" /> 170 <param name="ref" value="test.fa" ftype="fasta" />
172 </conditional> 171 </conditional>
173 <output name="output" file="1.stats.expected" ftype="tabular" lines_diff="4" /> 172 <output name="output" file="1.stats.expected" ftype="tabular" lines_diff="4" />
174 </test> 173 </test>
175 <!-- test_cmd($opts,out=>'stat/1.stats.expected',cmd=>"$$opts{bin}/samtools stats -r $$opts{path}/stat/test.fa $$opts{path}/stat/1_map_cigar.sam | tail -n+4", exp_fix=>$efix);--> 174 <!-- test_cmd($opts,out=>'stat/1.stats.expected',cmd=>"$$opts{bin}/samtools stats -r $$opts{path}/stat/test.fa $$opts{path}/stat/1_map_cigar.sam | tail -n+4", exp_fix=>$efix);-->
176 <test> 175 <test expect_num_outputs="1">
177 <param name="input" value="2_equal_cigar_full_seq.sam" ftype="sam" /> 176 <param name="input" value="2_equal_cigar_full_seq.sam" ftype="sam" />
178 <conditional name="addref_cond"> 177 <conditional name="addref_cond">
179 <param name="addref_select" value="history" /> 178 <param name="addref_select" value="history" />
180 <param name="ref" value="test.fa" ftype="fasta" /> 179 <param name="ref" value="test.fa" ftype="fasta" />
181 </conditional> 180 </conditional>
183 </test> 182 </test>
184 <!-- test_cmd($opts,out=>'stat/2.stats.expected',cmd=>"$$opts{bin}/samtools stats -r $$opts{path}/stat/test.fa $$opts{path}/stat/2_equal_cigar_full_seq.sam | tail -n+4", exp_fix=>$efix);--> 183 <!-- test_cmd($opts,out=>'stat/2.stats.expected',cmd=>"$$opts{bin}/samtools stats -r $$opts{path}/stat/test.fa $$opts{path}/stat/2_equal_cigar_full_seq.sam | tail -n+4", exp_fix=>$efix);-->
185 <!-- test_cmd($opts,out=>'stat/3.stats.expected',cmd=>"$$opts{bin}/samtools stats -r $$opts{path}/stat/test.fa $$opts{path}/stat/3_map_cigar_equal_seq.sam | tail -n+4", exp_fix=>$efix);--> 184 <!-- test_cmd($opts,out=>'stat/3.stats.expected',cmd=>"$$opts{bin}/samtools stats -r $$opts{path}/stat/test.fa $$opts{path}/stat/3_map_cigar_equal_seq.sam | tail -n+4", exp_fix=>$efix);-->
186 <!-- test_cmd($opts,out=>'stat/4.stats.expected',cmd=>"$$opts{bin}/samtools stats -r $$opts{path}/stat/test.fa $$opts{path}/stat/4_X_cigar_full_seq.sam | tail -n+4", exp_fix=>$efix);--> 185 <!-- test_cmd($opts,out=>'stat/4.stats.expected',cmd=>"$$opts{bin}/samtools stats -r $$opts{path}/stat/test.fa $$opts{path}/stat/4_X_cigar_full_seq.sam | tail -n+4", exp_fix=>$efix);-->
187 <!-- test_cmd($opts,out=>'stat/5.stats.expected',cmd=>"$$opts{bin}/samtools stats -r $$opts{path}/stat/test.fa $$opts{path}/stat/5_insert_cigar.sam | tail -n+4", exp_fix=>$efix); --> 186 <!-- test_cmd($opts,out=>'stat/5.stats.expected',cmd=>"$$opts{bin}/samtools stats -r $$opts{path}/stat/test.fa $$opts{path}/stat/5_insert_cigar.sam | tail -n+4", exp_fix=>$efix); -->
188 <test> 187 <test expect_num_outputs="1">
189 <param name="input" value="5_insert_cigar.sam" ftype="sam" /> 188 <param name="input" value="5_insert_cigar.sam" ftype="sam" />
190 <param name="insert_size" value="0" /> 189 <param name="insert_size" value="0" />
191 <conditional name="addref_cond"> 190 <conditional name="addref_cond">
192 <param name="addref_select" value="history" /> 191 <param name="addref_select" value="history" />
193 <param name="ref" value="test.fa" ftype="fasta" /> 192 <param name="ref" value="test.fa" ftype="fasta" />
197 <!-- test_cmd($opts,out=>'stat/6.stats.expected',cmd=>"$$opts{bin}/samtools stats -r $$opts{path}/stat/test.fa -i 0 $$opts{path}/stat/5_insert_cigar.sam | tail -n+4", exp_fix=>$efix); --> 196 <!-- test_cmd($opts,out=>'stat/6.stats.expected',cmd=>"$$opts{bin}/samtools stats -r $$opts{path}/stat/test.fa -i 0 $$opts{path}/stat/5_insert_cigar.sam | tail -n+4", exp_fix=>$efix); -->
198 <!-- test_cmd($opts,out=>'stat/7.stats.expected',cmd=>"$$opts{bin}/samtools stats -r $$opts{path}/stat/test.fa $$opts{path}/stat/7_supp.sam | tail -n+4", exp_fix=>$efix); --> 197 <!-- test_cmd($opts,out=>'stat/7.stats.expected',cmd=>"$$opts{bin}/samtools stats -r $$opts{path}/stat/test.fa $$opts{path}/stat/7_supp.sam | tail -n+4", exp_fix=>$efix); -->
199 <!-- test_cmd($opts,out=>'stat/8.stats.expected',cmd=>"$$opts{bin}/samtools stats -r $$opts{path}/stat/test.fa $$opts{path}/stat/8_secondary.sam | tail -n+4", exp_fix=>$efix);--> 198 <!-- test_cmd($opts,out=>'stat/8.stats.expected',cmd=>"$$opts{bin}/samtools stats -r $$opts{path}/stat/test.fa $$opts{path}/stat/8_secondary.sam | tail -n+4", exp_fix=>$efix);-->
200 <!-- test_cmd($opts,out=>'stat/9.stats.expected',cmd=>"$$opts{bin}/samtools stats -S RG -r $$opts{path}/stat/test.fa $$opts{path}/stat/1_map_cigar.sam | tail -n+4", exp_fix=>$efix,out_map=>{"stat/1_map_cigar.sam_s1_a_1.bamstat"=>"stat/1_map_cigar.sam_s1_a_1.expected.bamstat"},hskip=>3);--> 199 <!-- test_cmd($opts,out=>'stat/9.stats.expected',cmd=>"$$opts{bin}/samtools stats -S RG -r $$opts{path}/stat/test.fa $$opts{path}/stat/1_map_cigar.sam | tail -n+4", exp_fix=>$efix,out_map=>{"stat/1_map_cigar.sam_s1_a_1.bamstat"=>"stat/1_map_cigar.sam_s1_a_1.expected.bamstat"},hskip=>3);-->
201 <!-- test_cmd($opts,out=>'stat/10.stats.expected',cmd=>"$$opts{bin}/samtools stats -S RG -r $$opts{path}/stat/test.fa $$opts{path}/stat/10_map_cigar.sam | tail -n+4", exp_fix=>$efix,out_map=>{"stat/10_map_cigar.sam_s1_a_1.bamstat"=>"stat/10_map_cigar.sam_s1_a_1.expected.bamstat", "stat/10_map_cigar.sam_s1_b_1.bamstat"=>"stat/10_map_cigar.sam_s1_b_1.expected.bamstat"},hskip=>3);--> 200 <!-- test_cmd($opts,out=>'stat/10.stats.expected',cmd=>"$$opts{bin}/samtools stats -S RG -r $$opts{path}/stat/test.fa $$opts{path}/stat/10_map_cigar.sam | tail -n+4", exp_fix=>$efix,out_map=>{"stat/10_map_cigar.sam_s1_a_1.bamstat"=>"stat/10_map_cigar.sam_s1_a_1.expected.bamstat", "stat/10_map_cigar.sam_s1_b_1.bamstat"=>"stat/10_map_cigar.sam_s1_b_1.expected.bamstat"},hskip=>3);-->
202 <test> 201 <test expect_num_outputs="1">
203 <param name="input" value="11_target.sam" ftype="sam" /> 202 <param name="input" value="11_target.sam" ftype="sam" />
204 <conditional name="addref_cond"> 203 <conditional name="addref_cond">
205 <param name="addref_select" value="no" /> 204 <param name="addref_select" value="no" />
206 </conditional> 205 </conditional>
207 <conditional name="cond_region"> 206 <conditional name="cond_region">
210 </conditional> 209 </conditional>
211 <output name="output" file="11.stats.expected" ftype="tabular" lines_diff="4" /> 210 <output name="output" file="11.stats.expected" ftype="tabular" lines_diff="4" />
212 </test> 211 </test>
213 <!-- test_cmd($opts,out=>'stat/11.stats.expected',cmd=>"$$opts{bin}/samtools stats -t $$opts{path}/stat/11.stats.targets $$opts{path}/stat/11_target.sam | tail -n+4", exp_fix=>$efix); --> 212 <!-- test_cmd($opts,out=>'stat/11.stats.expected',cmd=>"$$opts{bin}/samtools stats -t $$opts{path}/stat/11.stats.targets $$opts{path}/stat/11_target.sam | tail -n+4", exp_fix=>$efix); -->
214 213
215 <test> 214 <test expect_num_outputs="1">
216 <param name="input" value="11_target.bam" ftype="bam" /> 215 <param name="input" value="11_target.bam" ftype="bam" />
217 <conditional name="addref_cond"> 216 <conditional name="addref_cond">
218 <param name="addref_select" value="no" /> 217 <param name="addref_select" value="no" />
219 </conditional> 218 </conditional>
220 <conditional name="cond_region"> 219 <conditional name="cond_region">
225 </conditional> 224 </conditional>
226 <output name="output" file="11.stats.expected" ftype="tabular" lines_diff="4" /> 225 <output name="output" file="11.stats.expected" ftype="tabular" lines_diff="4" />
227 </test> 226 </test>
228 <!-- test_cmd($opts,out=>'stat/11.stats.expected',cmd=>"$$opts{bin}/samtools stats $$opts{path}/stat/11_target.bam ref1:10-24 ref1:30-46 ref1:39-56 | tail -n+4", exp_fix=>$efix); 227 <!-- test_cmd($opts,out=>'stat/11.stats.expected',cmd=>"$$opts{bin}/samtools stats $$opts{path}/stat/11_target.bam ref1:10-24 ref1:30-46 ref1:39-56 | tail -n+4", exp_fix=>$efix);
229 --> 228 -->
230 <test> 229 <test expect_num_outputs="1">
231 <param name="input" value="11_target.sam" ftype="sam" /> 230 <param name="input" value="11_target.sam" ftype="sam" />
232 <conditional name="addref_cond"> 231 <conditional name="addref_cond">
233 <param name="addref_select" value="no" /> 232 <param name="addref_select" value="no" />
234 </conditional> 233 </conditional>
235 <conditional name="cond_region"> 234 <conditional name="cond_region">
238 </conditional> 237 </conditional>
239 <param name="cov_threshold" value="4" /> 238 <param name="cov_threshold" value="4" />
240 <output name="output" file="11.stats.g4.expected" ftype="tabular" lines_diff="4" /> 239 <output name="output" file="11.stats.g4.expected" ftype="tabular" lines_diff="4" />
241 </test> 240 </test>
242 <!-- test_cmd($opts,out=>'stat/11.stats.g4.expected',cmd=>"$$opts{bin}/samtools stats -g 4 -t $$opts{path}/stat/11.stats.targets $$opts{path}/stat/11_target.sam | tail -n+4", exp_fix=>$efix);--> 241 <!-- test_cmd($opts,out=>'stat/11.stats.g4.expected',cmd=>"$$opts{bin}/samtools stats -g 4 -t $$opts{path}/stat/11.stats.targets $$opts{path}/stat/11_target.sam | tail -n+4", exp_fix=>$efix);-->
243 <test> 242 <test expect_num_outputs="1">
244 <param name="input" value="11_target.bam" ftype="bam" /> 243 <param name="input" value="11_target.bam" ftype="bam" />
245 <conditional name="addref_cond"> 244 <conditional name="addref_cond">
246 <param name="addref_select" value="no" /> 245 <param name="addref_select" value="no" />
247 </conditional> 246 </conditional>
248 <conditional name="cond_region"> 247 <conditional name="cond_region">
253 </conditional> 252 </conditional>
254 <param name="cov_threshold" value="4" /> 253 <param name="cov_threshold" value="4" />
255 <output name="output" file="11.stats.g4.expected" ftype="tabular" lines_diff="4" /> 254 <output name="output" file="11.stats.g4.expected" ftype="tabular" lines_diff="4" />
256 </test> 255 </test>
257 <!-- test_cmd($opts,out=>'stat/11.stats.g4.expected',cmd=>"$$opts{bin}/samtools stats -g 4 $$opts{path}/stat/11_target.bam ref1:10-24 ref1:30-46 ref1:39-56 | tail -n+4", exp_fix=>$efix); --> 256 <!-- test_cmd($opts,out=>'stat/11.stats.g4.expected',cmd=>"$$opts{bin}/samtools stats -g 4 $$opts{path}/stat/11_target.bam ref1:10-24 ref1:30-46 ref1:39-56 | tail -n+4", exp_fix=>$efix); -->
258 <test> 257 <test expect_num_outputs="1">
259 <param name="input" value="12_overlaps.bam" ftype="bam" /> 258 <param name="input" value="12_overlaps.bam" ftype="bam" />
260 <conditional name="addref_cond"> 259 <conditional name="addref_cond">
261 <param name="addref_select" value="no" /> 260 <param name="addref_select" value="no" />
262 </conditional> 261 </conditional>
263 <conditional name="cond_region"> 262 <conditional name="cond_region">
265 <param name="targetregions" value="12_3reads.bed" ftype="tabular" /> 264 <param name="targetregions" value="12_3reads.bed" ftype="tabular" />
266 </conditional> 265 </conditional>
267 <output name="output" file="12.3reads.overlap.expected" ftype="tabular" lines_diff="4" /> 266 <output name="output" file="12.3reads.overlap.expected" ftype="tabular" lines_diff="4" />
268 </test> 267 </test>
269 <!-- test_cmd($opts,out=>'stat/12.3reads.overlap.expected',cmd=>"$$opts{bin}/samtools stats $$opts{path}/stat/12_overlaps.bam -t $$opts{path}/stat/12_3reads.bed | tail -n+4", exp_fix=>$efix);--> 268 <!-- test_cmd($opts,out=>'stat/12.3reads.overlap.expected',cmd=>"$$opts{bin}/samtools stats $$opts{path}/stat/12_overlaps.bam -t $$opts{path}/stat/12_3reads.bed | tail -n+4", exp_fix=>$efix);-->
270 <test> 269 <test expect_num_outputs="1">
271 <param name="input" value="12_overlaps.bam" ftype="bam" /> 270 <param name="input" value="12_overlaps.bam" ftype="bam" />
272 <conditional name="addref_cond"> 271 <conditional name="addref_cond">
273 <param name="addref_select" value="no" /> 272 <param name="addref_select" value="no" />
274 </conditional> 273 </conditional>
275 <conditional name="cond_region"> 274 <conditional name="cond_region">
278 </conditional> 277 </conditional>
279 <param name="remove_overlaps" value="-p"/> 278 <param name="remove_overlaps" value="-p"/>
280 <output name="output" file="12.3reads.nooverlap.expected" ftype="tabular" lines_diff="4" /> 279 <output name="output" file="12.3reads.nooverlap.expected" ftype="tabular" lines_diff="4" />
281 </test> 280 </test>
282 <!-- test_cmd($opts,out=>'stat/12.3reads.nooverlap.expected',cmd=>"$$opts{bin}/samtools stats $$opts{path}/stat/12_overlaps.bam -p -t $$opts{path}/stat/12_3reads.bed | tail -n+4", exp_fix=>$efix);--> 281 <!-- test_cmd($opts,out=>'stat/12.3reads.nooverlap.expected',cmd=>"$$opts{bin}/samtools stats $$opts{path}/stat/12_overlaps.bam -p -t $$opts{path}/stat/12_3reads.bed | tail -n+4", exp_fix=>$efix);-->
283 <test> 282 <test expect_num_outputs="1">
284 <param name="input" value="12_overlaps.bam" ftype="bam" /> 283 <param name="input" value="12_overlaps.bam" ftype="bam" />
285 <conditional name="addref_cond"> 284 <conditional name="addref_cond">
286 <param name="addref_select" value="no" /> 285 <param name="addref_select" value="no" />
287 </conditional> 286 </conditional>
288 <conditional name="cond_region"> 287 <conditional name="cond_region">
290 <param name="targetregions" value="12_2reads.bed" ftype="tabular" /> 289 <param name="targetregions" value="12_2reads.bed" ftype="tabular" />
291 </conditional> 290 </conditional>
292 <output name="output" file="12.2reads.overlap.expected" ftype="tabular" lines_diff="4" /> 291 <output name="output" file="12.2reads.overlap.expected" ftype="tabular" lines_diff="4" />
293 </test> 292 </test>
294 <!-- test_cmd($opts,out=>'stat/12.2reads.overlap.expected',cmd=>"$$opts{bin}/samtools stats $$opts{path}/stat/12_overlaps.bam -t $$opts{path}/stat/12_2reads.bed | tail -n+4", exp_fix=>$efix);--> 293 <!-- test_cmd($opts,out=>'stat/12.2reads.overlap.expected',cmd=>"$$opts{bin}/samtools stats $$opts{path}/stat/12_overlaps.bam -t $$opts{path}/stat/12_2reads.bed | tail -n+4", exp_fix=>$efix);-->
295 <test> 294 <test expect_num_outputs="1">
296 <param name="input" value="12_overlaps.bam" ftype="bam" /> 295 <param name="input" value="12_overlaps.bam" ftype="bam" />
297 <conditional name="addref_cond"> 296 <conditional name="addref_cond">
298 <param name="addref_select" value="no" /> 297 <param name="addref_select" value="no" />
299 </conditional> 298 </conditional>
300 <conditional name="cond_region"> 299 <conditional name="cond_region">
303 </conditional> 302 </conditional>
304 <param name="remove_overlaps" value="-p"/> 303 <param name="remove_overlaps" value="-p"/>
305 <output name="output" file="12.2reads.nooverlap.expected" ftype="tabular" lines_diff="4" /> 304 <output name="output" file="12.2reads.nooverlap.expected" ftype="tabular" lines_diff="4" />
306 </test> 305 </test>
307 <!-- test_cmd($opts,out=>'stat/12.2reads.nooverlap.expected',cmd=>"$$opts{bin}/samtools stats $$opts{path}/stat/12_overlaps.bam -p -t $$opts{path}/stat/12_2reads.bed | tail -n+4", exp_fix=>$efix);--> 306 <!-- test_cmd($opts,out=>'stat/12.2reads.nooverlap.expected',cmd=>"$$opts{bin}/samtools stats $$opts{path}/stat/12_overlaps.bam -p -t $$opts{path}/stat/12_2reads.bed | tail -n+4", exp_fix=>$efix);-->
308 <test> 307 <test expect_num_outputs="1">
309 <param name="input" value="samtools_stats_input.bam" ftype="bam" /> 308 <param name="input" value="samtools_stats_input.bam" ftype="bam" />
310 <conditional name="addref_cond"> 309 <conditional name="addref_cond">
311 <param name="addref_select" value="history" /> 310 <param name="addref_select" value="history" />
312 <param name="ref" value="samtools_stats_ref.fa" ftype="fasta" /> 311 <param name="ref" value="samtools_stats_ref.fa" ftype="fasta" />
313 </conditional> 312 </conditional>
314 <output name="output" file="samtools_stats_out1.tab" ftype="tabular" lines_diff="4" /> 313 <output name="output" file="samtools_stats_out1.tab" ftype="tabular" lines_diff="4" />
315 </test> 314 </test>
316 <test> 315 <test expect_num_outputs="1">
317 <param name="input" value="samtools_stats_input.bam" ftype="bam" /> 316 <param name="input" value="samtools_stats_input.bam" ftype="bam" />
318 <conditional name="addref_cond"> 317 <conditional name="addref_cond">
319 <param name="addref_select" value="history" /> 318 <param name="addref_select" value="history" />
320 <param name="ref" value="samtools_stats_ref.fa" ftype="fasta" /> 319 <param name="ref" value="samtools_stats_ref.fa" ftype="fasta" />
321 </conditional> 320 </conditional>