Mercurial > repos > iuc > tbprofiler

comparison tb_profiler_profile.xml @ 7:200c378d85f3 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 53f6ccebd38e89bb2e67b2eec3aee30b4e141b5b"
author iuc
date Thu, 23 Jan 2020 03:44:33 -0500
parents 4272bd430a01
children e1a9d6fd258d
comparison
equal deleted inserted replaced
6:f7f32674f751 7:200c378d85f3
1 <tool id="tb_profiler_profile" name="TB-Profiler Profile" version="@TOOL_VERSION@+galaxy0"> 1 <tool id="tb_profiler_profile" name="TB-Profiler Profile" version="@TOOL_VERSION@+galaxy1">
2 <description>Infer strain types and drug resistance markers from sequences</description> 2 <description>Infer strain types and drug resistance markers from sequences</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
39 --bam input.bam 39 --bam input.bam
40 #end if 40 #end if
41 41
42 --threads "\${GALAXY_SLOTS:-1}" 42 --threads "\${GALAXY_SLOTS:-1}"
43 #if $advanced.options == 'yes' 43 #if $advanced.options == 'yes'
44 '${advanced.call_whole_genome}'
45 --call_method '${advanced.call_method}'
46 --min_gene_frac '${advanced.min_gene_frac}'
47 --mapper '${advanced.mapper}' 44 --mapper '${advanced.mapper}'
48 --min_depth '${advanced.min_depth}' 45 --min_depth '${advanced.min_depth}'
49 --af '${min_allel_freq}' 46 --af '${advanced.min_allele_freq}'
50 --reporting_af '${min_allel_freq_reporting}' 47 --reporting_af '${advanced.min_allele_freq_reporting}'
51 #end if 48 #end if
52 49
53 #if $output_format == "pdf" 50 #if $output_format == "pdf"
54 --pdf 51 --pdf
55 #else if $output_format == "txt" 52 #else if $output_format == "txt"
103 <option value="no" selected="true">No</option> 100 <option value="no" selected="true">No</option>
104 </param> 101 </param>
105 <when value="no"> 102 <when value="no">
106 </when> 103 </when>
107 <when value="yes"> 104 <when value="yes">
108 <param label="Quality required for calls to be accepted" type="select" argument="--call_method">
109 <option value="low" selected="true">Low</option>
110 <option value="high">High</option>
111 <option value="optimise">Optimise</option>
112 </param>
113 <param label="Call variants on the whole genome" type="boolean" argument="--call_whole_genome"
114 truevalue="--call_whole_genome" falsevalue="" help="Call variants on whole genome (Useful if you need to use whole genome variants later)" />
115 <param label="Minimum coverage fraction to infer deletion" type="float" help="Used to infer a deletion if the fraction of a gene covered falls below this value." argument="--min_gene_frac" value="0.9" />
116
117 <param name="min_depth" label="Min Depth" type="integer" value="10" help="Minimum depth required to call variant. Bases with depth below this cutoff will be marked as missing (default: 10)"/>
118 <param name="mapper" label="Mapper" type="select" help="Mapping tools to use (default: bwa)"> 105 <param name="mapper" label="Mapper" type="select" help="Mapping tools to use (default: bwa)">
119 <option value="bwa" selected="true">bwa</option> 106 <option value="bwa" selected="true">bwa</option>
120 <option value="minimap2">minimap2</option> 107 <option value="minimap2">minimap2</option>
121 <option value="bowtie2">bowtie2</option> 108 <option value="bowtie2">bowtie2</option>
122 </param> 109 </param>
123 <param name="min_gene_frac" label="Minimum Gene Fraction" type="float" value="0.9" help="Used to infer a deletion if the fraction of a gene covered falls below this value. Also used to see if sample is high quality to continue by checking the fraction for rpoB (where deletion should not occur). (default: 0.9)" /> 110 <param name="min_depth" label="Min Depth" type="integer" value="10" help="Minimum depth required to call variant. Bases with depth below this cutoff will be marked as missing (default: 10)"/>
124 <param name="min_allel_freq" argument="--af" type="float" value="0.1" label="Minimum allele frequency to call variants" help=" Minimum allele frequency to call variants (default: 0.1)" /> 111 <param name="min_allele_freq" argument="--af" type="float" value="0.1" label="Minimum allele frequency to call variants" help=" Minimum allele frequency to call variants (default: 0.1)" />
125 <param name="min_allel_freq_reporting" argument="--reporting_af" value="0.1" label="Reporting Minimum allele frequency to call variants" type="float" help=" Minimum allele frequency to call variants (default: 0.1)"/> 112 <param name="min_allele_freq_reporting" argument="--reporting_af" value="0.1" label="Reporting Minimum allele frequency to call variants" type="float" help=" Minimum allele frequency to call variants (default: 0.1)"/>
126 </when> 113 </when>
127 </conditional> 114 </conditional>
128 </inputs> 115 </inputs>
129 <outputs> 116 <outputs>
130 <data name="results_json" format="json" from_work_dir="results/tbprofiler.results.json" label="${tool.name} on ${on_string}: Results.json"/> 117 <data name="results_json" format="json" from_work_dir="results/tbprofiler.results.json" label="${tool.name} on ${on_string}: Results.json"/>
169 <has_line line="Rifampicin&#009;R&#009;rpoB p.Asp435Val (1.00)" /> 156 <has_line line="Rifampicin&#009;R&#009;rpoB p.Asp435Val (1.00)" />
170 <has_line line="763031&#009;Rv0667&#009;rpoB&#009;c.3225T>C&#009;1.000" /> 157 <has_line line="763031&#009;Rv0667&#009;rpoB&#009;c.3225T>C&#009;1.000" />
171 </assert_contents> 158 </assert_contents>
172 </output> 159 </output>
173 </test> 160 </test>
161 <test>
162 <param name="input_select" value="single_fastq"/>
163 <param name="fastq" ftype="fastq.gz" value="rif_resistant.fastq.gz" />
164 <param name="output_format" value="txt" />
165 <param name="platform" value="illumina" />
166 <param name="options" value="yes" />
167 <param name="call_whole_genome" value="true" />
168 <param name="min_allele_freq" value="0.25" />
169 <param name="min_allele_freq_reporting" value="0.33" />
170 <output name="output_txt">
171 <assert_contents>
172 <has_line line="Drug-resistance: Drug-resistant" />
173 <has_line line="lineage2.2.2&#009;1.000&#009;East-Asian (Beijing)&#009;Beijing-RD105/RD207&#009;RD105;RD207" />
174 <has_line line="Rifampicin&#009;R&#009;rpoB p.Asp435Val (1.00)" />
175 <has_line line="763031&#009;Rv0667&#009;rpoB&#009;c.3225T>C&#009;1.000" />
176 </assert_contents>
177 </output>
178 </test>
174 </tests> 179 </tests>
175 <help><![CDATA[ 180 <help><![CDATA[
176 Summary 181 Summary
177 ======= 182 =======
178 183