Mercurial > repos > iuc > bcftools_mpileup

comparison bcftools_mpileup.xml @ 10:6d7dc9a1bef3 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit af43d9cf6824f88726900857116f333ff4cdd336"
author iuc
date Sat, 15 Jan 2022 13:30:22 +0000
parents ce9396ddcb2b
children 31ea13dfe5e6
comparison
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9:ce9396ddcb2b 10:6d7dc9a1bef3
1 <?xml version='1.0' encoding='utf-8'?> 1 <?xml version='1.0' encoding='utf-8'?>
2 <tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@"> 2 <tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy1">
3 <description>Generate VCF or BCF containing genotype likelihoods for one or multiple alignment (BAM or CRAM) files</description> 3 <description>Generate VCF or BCF containing genotype likelihoods for one or multiple alignment (BAM or CRAM) files</description>
4 <expand macro="bio_tools" />
5 <macros> 4 <macros>
6 <token name="@EXECUTABLE@">mpileup</token> 5 <token name="@EXECUTABLE@">mpileup</token>
7 <import>macros.xml</import> 6 <import>macros.xml</import>
8 <xml name="bam_flag_options"> 7 <xml name="bam_flag_options">
9 <option value="1">Read is paired</option> 8 <option value="1">Read is paired</option>
17 <option value="256">The alignment or this read is not primary</option> 16 <option value="256">The alignment or this read is not primary</option>
18 <option value="512">The read fails platform/vendor quality checks</option> 17 <option value="512">The read fails platform/vendor quality checks</option>
19 <option value="1024">The read is a PCR or optical duplicate</option> 18 <option value="1024">The read is a PCR or optical duplicate</option>
20 </xml> 19 </xml>
21 </macros> 20 </macros>
21 <expand macro="bio_tools" />
22 <expand macro="requirements"> 22 <expand macro="requirements">
23 <expand macro="samtools_requirement"/> 23 <expand macro="samtools_requirement"/>
24 </expand> 24 </expand>
25 <expand macro="version_command" /> 25 <expand macro="version_command" />
26 <command detect_errors="aggressive"><![CDATA[ 26 <command detect_errors="aggressive"><![CDATA[
221 <when value="do_not_perform_indel_calling" /> 221 <when value="do_not_perform_indel_calling" />
222 </conditional> 222 </conditional>
223 </section> 223 </section>
224 224
225 <section name="sec_filtering" expanded="false" title="Input Filtering Options"> 225 <section name="sec_filtering" expanded="false" title="Input Filtering Options">
226 <param name="max_reads_per_bam" type="integer" value="250" max="1024" min="1" label="Max reads per BAM" help="--max-depth; default=250"/> 226 <param name="max_reads_per_bam" type="integer" value="250" min="1" label="Max reads per BAM" help="--max-depth; default=250"/>
227 <param name="ignore_overlaps" type="boolean" truevalue="-x" falsevalue="" checked="False" label="Disable read-pair overlap detection" help="--ignore-overlaps"/> 227 <param name="ignore_overlaps" type="boolean" truevalue="-x" falsevalue="" checked="False" label="Disable read-pair overlap detection" help="--ignore-overlaps"/>
228 <param name="skip_anomalous_read_pairs" type="boolean" truevalue="-A" falsevalue="" checked="False" label="Do not skip anomalous read pairs in variant calling" help="--count-orphans"/> 228 <param name="skip_anomalous_read_pairs" type="boolean" truevalue="-A" falsevalue="" checked="False" label="Do not skip anomalous read pairs in variant calling" help="--count-orphans"/>
229 <conditional name="filter_by_flags"> 229 <conditional name="filter_by_flags">
230 <param name="filter_flags" type="select" label="Set filter by flags"> 230 <param name="filter_flags" type="select" label="Set filter by flags">
231 <option selected="True" value="nofilter">Do not filter</option> 231 <option selected="True" value="nofilter">Do not filter</option>