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comparison samtools_stats.xml @ 13:e221fe58c2f5 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit c508c3af0f4121dcc38e0be63db00a604e997b8a
author iuc
date Thu, 19 Jun 2025 13:01:32 +0000
parents fed4aa48ba09
children 1ed8ed887035
comparison
equal deleted inserted replaced
12:541082d03bef 13:e221fe58c2f5
1 <tool id="samtools_stats" name="Samtools stats" version="2.0.5" profile="@PROFILE@"> 1 <tool id="samtools_stats" name="Samtools stats" version="2.0.6" 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"/>
273 </conditional> 273 </conditional>
274 <conditional name="cond_region"> 274 <conditional name="cond_region">
275 <param name="select_region" value="tab"/> 275 <param name="select_region" value="tab"/>
276 <param name="targetregions" value="12_3reads.bed" ftype="tabular" /> 276 <param name="targetregions" value="12_3reads.bed" ftype="tabular" />
277 </conditional> 277 </conditional>
278 <param name="remove_overlaps" value="-p"/> 278 <param name="remove_overlaps" value="true"/>
279 <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" />
280 </test> 280 </test>
281 <!-- test_cmd($opts,out=>'stat/12.3reads.nooverlap.expected',cmd=>"$$opts{bin}/samtools stats $$opts{path}/stat/12_overlaps.bam -p -t $$opts{path}/stat/12_3reads.bed | tail -n+4", exp_fix=>$efix);--> 281 <!-- test_cmd($opts,out=>'stat/12.3reads.nooverlap.expected',cmd=>"$$opts{bin}/samtools stats $$opts{path}/stat/12_overlaps.bam -p -t $$opts{path}/stat/12_3reads.bed | tail -n+4", exp_fix=>$efix);-->
282 <test expect_num_outputs="1"> 282 <test expect_num_outputs="1">
283 <param name="input" value="12_overlaps.bam" ftype="bam" /> 283 <param name="input" value="12_overlaps.bam" ftype="bam" />
298 </conditional> 298 </conditional>
299 <conditional name="cond_region"> 299 <conditional name="cond_region">
300 <param name="select_region" value="tab"/> 300 <param name="select_region" value="tab"/>
301 <param name="targetregions" value="12_2reads.bed" ftype="tabular" /> 301 <param name="targetregions" value="12_2reads.bed" ftype="tabular" />
302 </conditional> 302 </conditional>
303 <param name="remove_overlaps" value="-p"/> 303 <param name="remove_overlaps" value="true"/>
304 <output name="output" file="12.2reads.nooverlap.expected" ftype="tabular" lines_diff="4" /> 304 <output name="output" file="12.2reads.nooverlap.expected" ftype="tabular" lines_diff="4" />
305 </test> 305 </test>
306 <!-- test_cmd($opts,out=>'stat/12.2reads.nooverlap.expected',cmd=>"$$opts{bin}/samtools stats $$opts{path}/stat/12_overlaps.bam -p -t $$opts{path}/stat/12_2reads.bed | tail -n+4", exp_fix=>$efix);--> 306 <!-- test_cmd($opts,out=>'stat/12.2reads.nooverlap.expected',cmd=>"$$opts{bin}/samtools stats $$opts{path}/stat/12_overlaps.bam -p -t $$opts{path}/stat/12_2reads.bed | tail -n+4", exp_fix=>$efix);-->
307 <test expect_num_outputs="1"> 307 <test expect_num_outputs="1">
308 <param name="input" value="samtools_stats_input.bam" ftype="bam" /> 308 <param name="input" value="samtools_stats_input.bam" ftype="bam" />