Mercurial > repos > devteam > samtools_stats
comparison samtools_stats.xml @ 10:3a0efe14891f draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 84db51c96845854eb42c1a9949e4b79316b41925
author | iuc |
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date | Wed, 22 Jun 2022 07:48:55 +0000 |
parents | 1cc79f49b8d5 |
children | fed4aa48ba09 |
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9:1cc79f49b8d5 | 10:3a0efe14891f |
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1 <tool id="samtools_stats" name="Samtools stats" version="2.0.3" profile="@PROFILE@"> | 1 <tool id="samtools_stats" name="Samtools stats" version="2.0.4" 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"/> |
168 <param name="input" value="1_map_cigar.sam" ftype="sam" /> | 168 <param name="input" value="1_map_cigar.sam" ftype="sam" /> |
169 <conditional name="addref_cond"> | 169 <conditional name="addref_cond"> |
170 <param name="addref_select" value="history" /> | 170 <param name="addref_select" value="history" /> |
171 <param name="ref" value="test.fa" ftype="fasta" /> | 171 <param name="ref" value="test.fa" ftype="fasta" /> |
172 </conditional> | 172 </conditional> |
173 <output name="output" file="1.stats.expected" ftype="tabular" lines_diff="2" /> | 173 <output name="output" file="1.stats.expected" ftype="tabular" lines_diff="4" /> |
174 </test> | 174 </test> |
175 <!-- test_cmd($opts,out=>'stat/1.stats.expected',cmd=>"$$opts{bin}/samtools stats -r $$opts{path}/stat/test.fa $$opts{path}/stat/1_map_cigar.sam | tail -n+4", exp_fix=>$efix);--> | 175 <!-- test_cmd($opts,out=>'stat/1.stats.expected',cmd=>"$$opts{bin}/samtools stats -r $$opts{path}/stat/test.fa $$opts{path}/stat/1_map_cigar.sam | tail -n+4", exp_fix=>$efix);--> |
176 <test> | 176 <test> |
177 <param name="input" value="2_equal_cigar_full_seq.sam" ftype="sam" /> | 177 <param name="input" value="2_equal_cigar_full_seq.sam" ftype="sam" /> |
178 <conditional name="addref_cond"> | 178 <conditional name="addref_cond"> |
179 <param name="addref_select" value="history" /> | 179 <param name="addref_select" value="history" /> |
180 <param name="ref" value="test.fa" ftype="fasta" /> | 180 <param name="ref" value="test.fa" ftype="fasta" /> |
181 </conditional> | 181 </conditional> |
182 <output name="output" file="2.stats.expected" ftype="tabular" lines_diff="2" /> | 182 <output name="output" file="2.stats.expected" ftype="tabular" lines_diff="4" /> |
183 </test> | 183 </test> |
184 <!-- test_cmd($opts,out=>'stat/2.stats.expected',cmd=>"$$opts{bin}/samtools stats -r $$opts{path}/stat/test.fa $$opts{path}/stat/2_equal_cigar_full_seq.sam | tail -n+4", exp_fix=>$efix);--> | 184 <!-- test_cmd($opts,out=>'stat/2.stats.expected',cmd=>"$$opts{bin}/samtools stats -r $$opts{path}/stat/test.fa $$opts{path}/stat/2_equal_cigar_full_seq.sam | tail -n+4", exp_fix=>$efix);--> |
185 <!-- test_cmd($opts,out=>'stat/3.stats.expected',cmd=>"$$opts{bin}/samtools stats -r $$opts{path}/stat/test.fa $$opts{path}/stat/3_map_cigar_equal_seq.sam | tail -n+4", exp_fix=>$efix);--> | 185 <!-- test_cmd($opts,out=>'stat/3.stats.expected',cmd=>"$$opts{bin}/samtools stats -r $$opts{path}/stat/test.fa $$opts{path}/stat/3_map_cigar_equal_seq.sam | tail -n+4", exp_fix=>$efix);--> |
186 <!-- test_cmd($opts,out=>'stat/4.stats.expected',cmd=>"$$opts{bin}/samtools stats -r $$opts{path}/stat/test.fa $$opts{path}/stat/4_X_cigar_full_seq.sam | tail -n+4", exp_fix=>$efix);--> | 186 <!-- test_cmd($opts,out=>'stat/4.stats.expected',cmd=>"$$opts{bin}/samtools stats -r $$opts{path}/stat/test.fa $$opts{path}/stat/4_X_cigar_full_seq.sam | tail -n+4", exp_fix=>$efix);--> |
187 <!-- test_cmd($opts,out=>'stat/5.stats.expected',cmd=>"$$opts{bin}/samtools stats -r $$opts{path}/stat/test.fa $$opts{path}/stat/5_insert_cigar.sam | tail -n+4", exp_fix=>$efix); --> | 187 <!-- test_cmd($opts,out=>'stat/5.stats.expected',cmd=>"$$opts{bin}/samtools stats -r $$opts{path}/stat/test.fa $$opts{path}/stat/5_insert_cigar.sam | tail -n+4", exp_fix=>$efix); --> |
190 <param name="insert_size" value="0" /> | 190 <param name="insert_size" value="0" /> |
191 <conditional name="addref_cond"> | 191 <conditional name="addref_cond"> |
192 <param name="addref_select" value="history" /> | 192 <param name="addref_select" value="history" /> |
193 <param name="ref" value="test.fa" ftype="fasta" /> | 193 <param name="ref" value="test.fa" ftype="fasta" /> |
194 </conditional> | 194 </conditional> |
195 <output name="output" file="6.stats.expected" ftype="tabular" lines_diff="2" /> | 195 <output name="output" file="6.stats.expected" ftype="tabular" lines_diff="4" /> |
196 </test> | 196 </test> |
197 <!-- test_cmd($opts,out=>'stat/6.stats.expected',cmd=>"$$opts{bin}/samtools stats -r $$opts{path}/stat/test.fa -i 0 $$opts{path}/stat/5_insert_cigar.sam | tail -n+4", exp_fix=>$efix); --> | 197 <!-- test_cmd($opts,out=>'stat/6.stats.expected',cmd=>"$$opts{bin}/samtools stats -r $$opts{path}/stat/test.fa -i 0 $$opts{path}/stat/5_insert_cigar.sam | tail -n+4", exp_fix=>$efix); --> |
198 <!-- test_cmd($opts,out=>'stat/7.stats.expected',cmd=>"$$opts{bin}/samtools stats -r $$opts{path}/stat/test.fa $$opts{path}/stat/7_supp.sam | tail -n+4", exp_fix=>$efix); --> | 198 <!-- test_cmd($opts,out=>'stat/7.stats.expected',cmd=>"$$opts{bin}/samtools stats -r $$opts{path}/stat/test.fa $$opts{path}/stat/7_supp.sam | tail -n+4", exp_fix=>$efix); --> |
199 <!-- test_cmd($opts,out=>'stat/8.stats.expected',cmd=>"$$opts{bin}/samtools stats -r $$opts{path}/stat/test.fa $$opts{path}/stat/8_secondary.sam | tail -n+4", exp_fix=>$efix);--> | 199 <!-- test_cmd($opts,out=>'stat/8.stats.expected',cmd=>"$$opts{bin}/samtools stats -r $$opts{path}/stat/test.fa $$opts{path}/stat/8_secondary.sam | tail -n+4", exp_fix=>$efix);--> |
200 <!-- test_cmd($opts,out=>'stat/9.stats.expected',cmd=>"$$opts{bin}/samtools stats -S RG -r $$opts{path}/stat/test.fa $$opts{path}/stat/1_map_cigar.sam | tail -n+4", exp_fix=>$efix,out_map=>{"stat/1_map_cigar.sam_s1_a_1.bamstat"=>"stat/1_map_cigar.sam_s1_a_1.expected.bamstat"},hskip=>3);--> | 200 <!-- test_cmd($opts,out=>'stat/9.stats.expected',cmd=>"$$opts{bin}/samtools stats -S RG -r $$opts{path}/stat/test.fa $$opts{path}/stat/1_map_cigar.sam | tail -n+4", exp_fix=>$efix,out_map=>{"stat/1_map_cigar.sam_s1_a_1.bamstat"=>"stat/1_map_cigar.sam_s1_a_1.expected.bamstat"},hskip=>3);--> |
221 <param name="select_region" value="text"/> | 221 <param name="select_region" value="text"/> |
222 <param name="regions_repeat_0|region" value="ref1:10-24"/> | 222 <param name="regions_repeat_0|region" value="ref1:10-24"/> |
223 <param name="regions_repeat_1|region" value="ref1:30-46"/> | 223 <param name="regions_repeat_1|region" value="ref1:30-46"/> |
224 <param name="regions_repeat_2|region" value="ref1:39-56"/> | 224 <param name="regions_repeat_2|region" value="ref1:39-56"/> |
225 </conditional> | 225 </conditional> |
226 <output name="output" file="11.stats.expected" ftype="tabular" lines_diff="2" /> | 226 <output name="output" file="11.stats.expected" ftype="tabular" lines_diff="4" /> |
227 </test> | 227 </test> |
228 <!-- test_cmd($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=>$efix); | 228 <!-- test_cmd($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=>$efix); |
229 --> | 229 --> |
230 <test> | 230 <test> |
231 <param name="input" value="11_target.sam" ftype="sam" /> | 231 <param name="input" value="11_target.sam" ftype="sam" /> |
250 <param name="regions_repeat_0|region" value="ref1:10-24"/> | 250 <param name="regions_repeat_0|region" value="ref1:10-24"/> |
251 <param name="regions_repeat_1|region" value="ref1:30-46"/> | 251 <param name="regions_repeat_1|region" value="ref1:30-46"/> |
252 <param name="regions_repeat_2|region" value="ref1:39-56"/> | 252 <param name="regions_repeat_2|region" value="ref1:39-56"/> |
253 </conditional> | 253 </conditional> |
254 <param name="cov_threshold" value="4" /> | 254 <param name="cov_threshold" value="4" /> |
255 <output name="output" file="11.stats.g4.expected" ftype="tabular" lines_diff="2" /> | 255 <output name="output" file="11.stats.g4.expected" ftype="tabular" lines_diff="4" /> |
256 </test> | 256 </test> |
257 <!-- test_cmd($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=>$efix); --> | 257 <!-- test_cmd($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); --> |
258 <test> | 258 <test> |
259 <param name="input" value="12_overlaps.bam" ftype="bam" /> | 259 <param name="input" value="12_overlaps.bam" ftype="bam" /> |
260 <conditional name="addref_cond"> | 260 <conditional name="addref_cond"> |
309 <param name="input" value="samtools_stats_input.bam" ftype="bam" /> | 309 <param name="input" value="samtools_stats_input.bam" ftype="bam" /> |
310 <conditional name="addref_cond"> | 310 <conditional name="addref_cond"> |
311 <param name="addref_select" value="history" /> | 311 <param name="addref_select" value="history" /> |
312 <param name="ref" value="samtools_stats_ref.fa" ftype="fasta" /> | 312 <param name="ref" value="samtools_stats_ref.fa" ftype="fasta" /> |
313 </conditional> | 313 </conditional> |
314 <output name="output" file="samtools_stats_out1.tab" ftype="tabular" lines_diff="2" /> | 314 <output name="output" file="samtools_stats_out1.tab" ftype="tabular" lines_diff="4" /> |
315 </test> | 315 </test> |
316 <test> | 316 <test> |
317 <param name="input" value="samtools_stats_input.bam" ftype="bam" /> | 317 <param name="input" value="samtools_stats_input.bam" ftype="bam" /> |
318 <conditional name="addref_cond"> | 318 <conditional name="addref_cond"> |
319 <param name="addref_select" value="history" /> | 319 <param name="addref_select" value="history" /> |