Mercurial > repos > iuc > bbtools_callvariants

comparison callvariants.xml @ 6:51b4b41b7034 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit cd59ba2c349865259b92302a1d70e103b8a5e3cb
author iuc
date Tue, 27 Aug 2024 10:13:01 +0000
parents 4eef1fff762e
children 0df19a0b6eb9
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5:94d49b9331cd 6:51b4b41b7034
1 <tool id="bbtools_callvariants" name="BBTools: call variants" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> 1 <tool id="bbtools_callvariants" name="BBTools: call variants" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>in aligned Bam files</description> 2 <description>in aligned Bam files</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="bio.tools"/>
6 <expand macro="requirements"/> 7 <expand macro="requirements"/>
7 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
8 #import os 9 #import os
9 10
10 #if str($ref_source_cond.ref_source) == 'cached' 11 #if str($ref_source_cond.ref_source) == 'cached'
36 #end if 37 #end if
37 ]]></command> 38 ]]></command>
38 <inputs> 39 <inputs>
39 <param name="input" type="data" format="bam" label="Bam file" help="Bam files produced by BBMap are recommended"/> 40 <param name="input" type="data" format="bam" label="Bam file" help="Bam files produced by BBMap are recommended"/>
40 <expand macro="reference_source_cond"/> 41 <expand macro="reference_source_cond"/>
41 <param name="ploidy" type="integer" value="1" min="1" label="Ploidy" help="See help section below"/> 42 <param name="ploidy" type="integer" min="1" value="1" label="Ploidy" help="See help section below"/>
42 <param name="output_format" type="select" label="Select output format"> 43 <param name="output_format" type="select" label="Select output format">
43 <option value="vcf" selected="true">vcf</option> 44 <option value="vcf" selected="true">vcf</option>
44 <option value="gff">gff</option> 45 <option value="gff">gff</option>
45 <option value="txt">txt</option> 46 <option value="txt">txt</option>
46 </param> 47 </param>
70 <param name="input" value="cv_input.bam" ftype="bam"/> 71 <param name="input" value="cv_input.bam" ftype="bam"/>
71 <param name="ploidy" value="2"/> 72 <param name="ploidy" value="2"/>
72 <param name="output_variant_score_hist" value="yes"/> 73 <param name="output_variant_score_hist" value="yes"/>
73 <param name="output_zygosity_hist" value="yes"/> 74 <param name="output_zygosity_hist" value="yes"/>
74 <param name="output_quality_hist" value="yes"/> 75 <param name="output_quality_hist" value="yes"/>
75 <output name="output" file="cv_output.vcf" ftype="vcf" compare="contains"/> 76 <output name="output" file="cv_output.vcf" ftype="vcf" compare="diff" lines_diff="4"/>
76 <output name="output_scorehist" file="cv_scorehist_output.tabular" ftype="tabular" compare="contains"/> 77 <output name="output_scorehist" file="cv_scorehist_output.tabular" ftype="tabular" compare="contains"/>
77 <output name="output_zygosityhist" file="cv_zygosityhist_output.tabular" ftype="tabular" compare="contains"/> 78 <output name="output_zygosityhist" file="cv_zygosityhist_output.tabular" ftype="tabular" compare="contains"/>
78 <output name="output_qualityhist" file="cv_qualityhist_output.tabular" ftype="tabular" compare="contains"/> 79 <output name="output_qualityhist" file="cv_qualityhist_output.tabular" ftype="tabular" compare="contains"/>
79 </test> 80 </test>
80 <test expect_num_outputs="1"> 81 <test expect_num_outputs="1">
81 <param name="input" value="cv_input.bam" ftype="bam"/> 82 <param name="input" value="cv_input.bam" ftype="bam"/>
82 <param name="ploidy" value="2"/> 83 <param name="ploidy" value="2"/>
83 <param name="output_format" value="gff"/> 84 <param name="output_format" value="gff"/>
84 <output name="output" file="cv_output.gff" ftype="gff" compare="contains"/> 85 <output name="output" file="cv_output.gff" ftype="gff" compare="contains" lines_diff="2"/>
85 </test> 86 </test>
86 <test expect_num_outputs="1"> 87 <test expect_num_outputs="1">
87 <param name="input" value="cv_input.bam" ftype="bam"/> 88 <param name="input" value="cv_input.bam" ftype="bam"/>
88 <param name="ploidy" value="2"/> 89 <param name="ploidy" value="2"/>
89 <param name="output_format" value="txt"/> 90 <param name="output_format" value="txt"/>
90 <output name="output" file="cv_output.txt" ftype="txt" compare="contains"/> 91 <output name="output" file="cv_output.txt" ftype="txt" compare="contains" lines_diff="2"/>
91 </test> 92 </test>
92 </tests> 93 </tests>
93 <help> 94 <help>
94 **What it does** 95 **What it does**
95 96
105 * **Ploidy** - Arbitrary ploidy is supported - the default is 1 which works for haploid organisms. Allele fractions lower than those expected for the ploidy (for example, anything below 0.5 for a diploid, or 0.25 for a tetraploid) will incur a score penalty. When calling variants on non-haploid organisms, it is crucial to set the ploidy. 106 * **Ploidy** - Arbitrary ploidy is supported - the default is 1 which works for haploid organisms. Allele fractions lower than those expected for the ploidy (for example, anything below 0.5 for a diploid, or 0.25 for a tetraploid) will incur a score penalty. When calling variants on non-haploid organisms, it is crucial to set the ploidy.
106 107
107 </help> 108 </help>
108 <expand macro="citations"/> 109 <expand macro="citations"/>
109 </tool> 110 </tool>
110