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comparison samtools_view.xml @ 3:097c44aaf6d4 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 640b53919bfc0ae4b895451218e919a52ac14b9d
author iuc
date Tue, 20 Nov 2018 06:19:49 -0500
parents 80d8ca44f8da
children f2b321f691e4
comparison
equal deleted inserted replaced
2:80d8ca44f8da 3:097c44aaf6d4
39 #end if 39 #end if
40 40
41 ## filter options (regions filter is the last parameter) 41 ## filter options (regions filter is the last parameter)
42 #if $cond_filter.select_filter == 'yes': 42 #if $cond_filter.select_filter == 'yes':
43 #if $cond_filter.cond_region.select_region == 'bed' and str( $cond_filter.cond_region.bedfile ) != 'None' 43 #if $cond_filter.cond_region.select_region == 'bed' and str( $cond_filter.cond_region.bedfile ) != 'None'
44 -L '$cond_filter.bedfile' 44 -L '$cond_filter.cond_region.bedfile'
45 #end if 45 #end if
46 #if $cond_filter.cond_rg.select_rg == 'text': 46 #if $cond_filter.cond_rg.select_rg == 'text':
47 -r '$cond_filter.cond_rg.readgr' 47 -r '$cond_filter.cond_rg.readgr'
48 #else if $cond_filter.cond_rg.select_rg == 'file': 48 #else if $cond_filter.cond_rg.select_rg == 'file':
49 -R '$cond_filter.cond_rg.rgfile' 49 -R '$cond_filter.cond_rg.rgfile'
261 <when input="outtype" value="sam" format="sam" /> 261 <when input="outtype" value="sam" format="sam" />
262 <when input="outtype" value="bam" format="bam" /> 262 <when input="outtype" value="bam" format="bam" />
263 <when input="outtype" value="cram" format="cram" /> 263 <when input="outtype" value="cram" format="cram" />
264 </change_format> 264 </change_format>
265 </data> 265 </data>
266 <data name="outputcnt" format="txt" from_work_dir="sam" label="${tool.name} on ${on_string}: Counts"> 266 <data name="outputcnt" format="txt" from_work_dir="outfile" label="${tool.name} on ${on_string}: Counts">
267 <filter>outtype == 'count'</filter> 267 <filter>outtype == 'count'</filter>
268 </data> 268 </data>
269 </outputs> 269 </outputs>
270 <tests> 270 <tests>
271 <!-- sam to bam (copied from the sam_to_bam tool) --> 271 <!-- sam to bam (copied from the sam_to_bam tool) -->
309 <conditional name="cond_region"> 309 <conditional name="cond_region">
310 <param name="select_region" value="no"/> 310 <param name="select_region" value="no"/>
311 </conditional> 311 </conditional>
312 </conditional> 312 </conditional>
313 <output name="outputsam" file="test.cram" ftype="cram" compare="sim_size" delta="250" /> 313 <output name="outputsam" file="test.cram" ftype="cram" compare="sim_size" delta="250" />
314 </test>
315 <!-- count alignments -->
316 <test>
317 <param name="input" value="test.bam" ftype="bam" />
318 <param name="outtype" value="count" />
319 <output name="outputcnt" file="test_counts.tab" ftype="txt" />
314 </test> 320 </test>
315 <test> 321 <test>
316 <param name="input" value="test.sam" ftype="sam" /> 322 <param name="input" value="test.sam" ftype="sam" />
317 <param name="outtype" value="cram" /> 323 <param name="outtype" value="cram" />
318 <conditional name="addref_cond"> 324 <conditional name="addref_cond">
423 <conditional name="cond_subsample"> 429 <conditional name="cond_subsample">
424 <param name="select_subsample" value="target" /> 430 <param name="select_subsample" value="target" />
425 <param name="seed" value="7" /> 431 <param name="seed" value="7" />
426 <param name="target" value="2" /> 432 <param name="target" value="2" />
427 </conditional> 433 </conditional>
428 <output name="outputsam" file="test_ds.sam" ftype="sam" compare="diff" lines_diff="4" /> 434 <output name="outputsam" file="test_ds.sam" ftype="sam" compare="diff" lines_diff="6" />
429 </test> 435 </test>
430 <test> 436 <test>
431 <param name="input" value="test.bam" ftype="bam" /> 437 <param name="input" value="test.bam" ftype="bam" />
432 <param name="outtype" value="bam" /> 438 <param name="outtype" value="bam" />
433 <conditional name="cond_subsample"> 439 <conditional name="cond_subsample">