Mercurial > repos > iuc > gatk4_mutect2

comparison macros.xml @ 4:1cea23583655 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit ff4bacd218035b7052ceadfadaec81dfd5d07b0e"
author iuc
date Fri, 14 Aug 2020 04:55:49 -0400
parents 287c4af133e6
children 53ce8be43212
comparison
equal deleted inserted replaced
3:287c4af133e6 4:1cea23583655
287 </when> 287 </when>
288 <when value="no_seq_dict" /> 288 <when value="no_seq_dict" />
289 </conditional> 289 </conditional>
290 </xml> 290 </xml>
291 291
292 <!--BAM input-->
293 <template name="picard_tumor_bam_input">
294 --INPUT tumor.bam
295 </template>
296
297 <template name="gatk_tumor_bam_input">
298 --input tumor.bam
299 </template>
300
301 <template name="tumor_bam_index_pre_chth"><![CDATA[
302 #for $sect in $sections
303 #if $varExists($sect + "tumor")
304 ln -s $getVar($sect + "tumor") tumor.bam &&
305 ln -s '${tumor.metadata.bam_index}' tumor.bam.bai &&
306 #end if
307 #end for
308 ]]></template>
309
310 <xml name="gatk_tumor_bam_req_params">
311 <param name="tumor" argument="--tumor" type="data" format="bam" label="Input Tumor BAM file" />
312 </xml>
313
314 <template name="picard_tumor_bam_index"><![CDATA[
315 ln -s $INPUT tumor.bam &&
316 ln -s $INPUT tumor.bam.bai &&
317 ]]></template>
318
319 <template name="picard_normal_bam_input">
320 --INPUT normal.bam
321 </template>
322
323 <template name="gatk_normal_bam_input">
324 --input normal.bam
325 </template>
326
327 <template name="normal_bam_index_pre_chth"><![CDATA[
328 #for $sect in $sections
329 #if $varExists($sect + "normal")
330 ln -s $getVar($sect + "normal") normal.bam &&
331 ln -s '${normal.metadata.bam_index}' normal.bam.bai &&
332 #end if
333 #end for
334 ]]></template>
335
336 <xml name="gatk_normal_bam_req_params">
337 <param name="normal" argument="--normal" type="data" format="bam" label="Input Normal BAM file" />
338 </xml>
339
340 <template name="picard_normal_bam_index"><![CDATA[
341 ln -s $INPUT normal.bam &&
342 ln -s $INPUT normal.bam.bai &&
343 ]]></template>
344
345 <!--Output goes to stdout, no output parameter exists.--> 292 <!--Output goes to stdout, no output parameter exists.-->
346 <template name="stdout_to_output"> 293 <template name="stdout_to_output">
347 > output.txt 294 > output.txt
348 </template> 295 </template>
349 296