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comparison lofreq_call.xml @ 3:54d8209e83f5 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 53bf37f3bf192c4a9d14f2055f106b429cf7b5c1"
author iuc
date Sat, 21 Mar 2020 14:50:10 +0000
parents 7b0c9772af4e
children 6bf3b0f614c5
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2:7b0c9772af4e 3:54d8209e83f5
1 <tool id="lofreq_call" name="Call variants" version="@TOOL_VERSION@+galaxy1"> 1 <tool id="lofreq_call" name="Call variants" version="@TOOL_VERSION@+galaxy2">
2 <description>with LoFreq</description> 2 <description>with LoFreq</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" />
124 label="BED dataset with regions to examine" /> 124 label="BED dataset with regions to examine" />
125 </when> 125 </when>
126 </conditional> 126 </conditional>
127 <param name="variant_types" type="select" 127 <param name="variant_types" type="select"
128 label="Types of variants to call" 128 label="Types of variants to call"
129 help="Note: When including indels in the called variants you should preprocess your input data to include indel alignment qualities"> 129 help="Note: To have indels included in the called variants you HAVE to preprocess your input data using lofreq indelqual to include indel qualities. In addition, it is highly recommended that you calculate and make use of indel alignment qualities. See the detailed tool help below.">
130 <option value="--call-indels">SNVs and indels</option> 130 <option value="--call-indels">SNVs and indels</option>
131 <option value="" selected="True">Only SNVs</option> 131 <option value="" selected="True">Only SNVs</option>
132 <option value="--only-indels">Only indels</option> 132 <option value="--call-indels --only-indels">Only indels</option>
133 </param> 133 </param>
134 <conditional name="call_control"> 134 <conditional name="call_control">
135 <param name="set_call_options" type="select" 135 <param name="set_call_options" type="select"
136 label="Variant calling parameters"> 136 label="Variant calling parameters">
137 <option value="no">Use default settings</option> 137 <option value="no">Use default settings</option>
324 <conditional name="filter_control"> 324 <conditional name="filter_control">
325 <param name="filter_type" value="set_all_off" /> 325 <param name="filter_type" value="set_all_off" />
326 </conditional> 326 </conditional>
327 <output name="variants" file="call-out2.vcf" lines_diff="4" /> 327 <output name="variants" file="call-out2.vcf" lines_diff="4" />
328 </test> 328 </test>
329 <test>
330 <param name="reads" ftype="bam" value="indelqual-out3.bam" />
331 <param name="ref_selector" value="history" />
332 <param name="ref" ftype="fasta" value="pBR322.fa" />
333 <param name="variant_types" value="--call-indels --only-indels" />
334 <conditional name="filter_control">
335 <param name="filter_type" value="set_all_off" />
336 </conditional>
337 <output name="variants" file="indel-call-out.vcf" lines_diff="4" />
338 </test>
329 </tests> 339 </tests>
330 <help><![CDATA[ 340 <help><![CDATA[
331 lofreq call: call variants from BAM file 341 lofreq call: call variants from BAM file
332 342
333 LoFreq is a fast and sensitive variant-caller for inferring SNVs and indels 343 LoFreq is a fast and sensitive variant-caller for inferring SNVs and indels
362 For insertions/deletions this is defined, analogously, as the Phred-scaled 372 For insertions/deletions this is defined, analogously, as the Phred-scaled
363 likelihood that any inserted/deleted base is real, however, you are 373 likelihood that any inserted/deleted base is real, however, you are
364 responsible for adding indel qualitites, which are required for indel 374 responsible for adding indel qualitites, which are required for indel
365 calling with lofreq, to your input. 375 calling with lofreq, to your input.
366 376
367 For doing so, you can use ``lofreq indelqual`` or GATK's BQSR. 377 For doing so, you can use ``lofreq indelqual``.
368 378
369 - Base/indel alignment quality 379 - Base/indel alignment quality
370 380
371 For any read, this is the Phred-scaled likelihood that the read's base or 381 For any read, this is the Phred-scaled likelihood that the read's base or
372 indel mapped to a given reference genome position is mapped to this position 382 indel mapped to a given reference genome position is mapped to this position