Mercurial > repos > iuc > gatk4_mutect2

comparison macros.xml @ 3:287c4af133e6 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
author iuc
date Sun, 10 May 2020 17:58:00 -0400
parents 3be27a9a7313
children 1cea23583655
comparison
equal deleted inserted replaced
2:3be27a9a7313 3:287c4af133e6
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <macros> 2 <macros>
3 <token name="@VERSION@">4.1.4.0</token> 3 <token name="@VERSION@">4.1.7.0</token>
4 <token name="@WRAPPER_VERSION@">@VERSION@+galaxy</token> 4 <token name="@WRAPPER_VERSION@">@VERSION@+galaxy0</token>
5 5
6 <xml name="requirements"> 6 <xml name="requirements">
7 <requirements> 7 <requirements>
8 <requirement type="package" version="@VERSION@">gatk4</requirement> 8 <requirement type="package" version="@VERSION@">gatk4</requirement>
9 <requirement type="package" version="0.2.5">tabix</requirement> 9 <requirement type="package" version="0.2.5">tabix</requirement>
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--> 292 <!--BAM input-->
293 <template name="picard_bam_input"> 293 <template name="picard_tumor_bam_input">
294 --INPUT input.bam 294 --INPUT tumor.bam
295 </template> 295 </template>
296 296
297 <template name="gatk_bam_input"> 297 <template name="gatk_tumor_bam_input">
298 --input input.bam 298 --input tumor.bam
299 </template> 299 </template>
300 300
301 <template name="bam_index_pre_chth"><![CDATA[ 301 <template name="tumor_bam_index_pre_chth"><![CDATA[
302 #for $sect in $sections 302 #for $sect in $sections
303 #if $varExists($sect + "input") 303 #if $varExists($sect + "tumor")
304 #if $getVar($sect + "input").is_of_type("bam") 304 ln -s $getVar($sect + "tumor") tumor.bam &&
305 ln -s $getVar($sect + "input") input.bam && 305 ln -s '${tumor.metadata.bam_index}' tumor.bam.bai &&
306 samtools index input.bam && 306 #end if
307 #else 307 #end for
308 ln -s $getVar($sect + "input") input.sam && 308 ]]></template>
309 samtools view -bS input.sam -o input.bam && 309
310 samtools index input.bam && 310 <xml name="gatk_tumor_bam_req_params">
311 #end if 311 <param name="tumor" argument="--tumor" type="data" format="bam" label="Input Tumor BAM file" />
312 #end if 312 </xml>
313 #end for 313
314 ]]></template> 314 <template name="picard_tumor_bam_index"><![CDATA[
315 315 ln -s $INPUT tumor.bam &&
316 <xml name="gatk_bam_req_params"> 316 ln -s $INPUT tumor.bam.bai &&
317 <param argument="--input" type="data" format="bam,sam" label="Input BAM/SAM/CRAM file" /> 317 ]]></template>
318 </xml> 318
319 319 <template name="picard_normal_bam_input">
320 <template name="picard_bam_index"><![CDATA[ 320 --INPUT normal.bam
321 #if $input.is_of_type("bam") 321 </template>
322 ln -s $INPUT input.bam && 322
323 samtools index input.bam && 323 <template name="gatk_normal_bam_input">
324 #else 324 --input normal.bam
325 ln -s $INPUT input.sam && 325 </template>
326 samtools view -bS input.sam -o input.bam && 326
327 samtools index input.bam && 327 <template name="normal_bam_index_pre_chth"><![CDATA[
328 #end if 328 #for $sect in $sections
329 ]]></template> 329 #if $varExists($sect + "normal")
330 330 ln -s $getVar($sect + "normal") normal.bam &&
331 331 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
332 <!--Output goes to stdout, no output parameter exists.--> 345 <!--Output goes to stdout, no output parameter exists.-->
333 <template name="stdout_to_output"> 346 <template name="stdout_to_output">
334 > output.txt 347 > output.txt
335 </template> 348 </template>
336 349