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comparison tb_profiler_profile.xml @ 14:ba82db72030a draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 7598f8402d6adaab0e7c9a3cd426914f700be336"
author iuc
date Wed, 16 Mar 2022 09:15:13 +0000
parents 59578411e567
children 459895e6c814
comparison
equal deleted inserted replaced
13:59578411e567 14:ba82db72030a
1 <tool id="tb_profiler_profile" name="TB-Profiler Profile" version="@TOOL_VERSION@+galaxy0" profile="20.09"> 1 <tool id="tb_profiler_profile" name="TB-Profiler Profile" version="@TOOL_VERSION@+galaxy0" profile="20.09">
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 <token name="@TOOL_VERSION@">3.0.8</token> 4 <token name="@TOOL_VERSION@">4.1.1</token>
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
7 <requirement type="package" version="@TOOL_VERSION@">tb-profiler</requirement> 7 <requirement type="package" version="@TOOL_VERSION@">tb-profiler</requirement>
8 </requirements> 8 </requirements>
9 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
25 #else if str($fastq_or_bam.input_select.value) == "bam" 25 #else if str($fastq_or_bam.input_select.value) == "bam"
26 ln -s '$fastq_or_bam.bam_input' input.bam && 26 ln -s '$fastq_or_bam.bam_input' input.bam &&
27 #end if 27 #end if
28 28
29 tb-profiler profile 29 tb-profiler profile
30
31 --platform '${platform.value}' 30 --platform '${platform.value}'
32
33 #if str($fastq_or_bam.input_select.value) in ("paired_fastq", "paired_collection_fastq", "single_fastq") 31 #if str($fastq_or_bam.input_select.value) in ("paired_fastq", "paired_collection_fastq", "single_fastq")
34 -1 fastq_r1.'$r1_ext' 32 -1 fastq_r1.'$r1_ext'
35 #end if 33 #end if
36 #if str($fastq_or_bam.input_select.value) in ("paired_fastq", "paired_collection_fastq") 34 #if str($fastq_or_bam.input_select.value) in ("paired_fastq", "paired_collection_fastq")
37 -2 fastq_r2.'$r1_ext' 35 -2 fastq_r2.'$r1_ext'
40 #end if 38 #end if
41 39
42 --threads "\${GALAXY_SLOTS:-1}" 40 --threads "\${GALAXY_SLOTS:-1}"
43 #if $advanced.options == 'yes' 41 #if $advanced.options == 'yes'
44 --mapper '${advanced.mapper}' 42 --mapper '${advanced.mapper}'
43 --caller '${advanced.caller}'
45 --min_depth '${advanced.min_depth}' 44 --min_depth '${advanced.min_depth}'
46 --af '${advanced.min_allele_freq}' 45 --af '${advanced.min_allele_freq}'
47 --reporting_af '${advanced.min_allele_freq_reporting}' 46 --reporting_af '${advanced.min_allele_freq_reporting}'
48 #end if 47 #end if
49 48
100 <option value="no" selected="true">No</option> 99 <option value="no" selected="true">No</option>
101 </param> 100 </param>
102 <when value="no"> 101 <when value="no">
103 </when> 102 </when>
104 <when value="yes"> 103 <when value="yes">
105 <param name="mapper" label="Mapper" type="select" help="Mapping tools to use (default: bwa)"> 104 <param argument="mapper" label="Mapper" type="select" help="Mapping tools to use (default: bwa)">
106 <option value="bwa" selected="true">bwa</option> 105 <option value="bwa" selected="true">bwa</option>
107 <option value="minimap2">minimap2</option> 106 <option value="minimap2">minimap2</option>
108 <option value="bowtie2">bowtie2</option> 107 <option value="bowtie2">bowtie2</option>
108 <option value="bwa-mem2">bwa-mem2</option>
109 </param>
110 <param argument="caller" label="Variant caller" help="Variant calling tool to use" type="select">
111 <option value="freebayes" selected="true">freebayes</option>
112 <option value="bcftools">bcftools</option>
113 <option value="gatk">gatk</option>
114 <option value="pilon">pilon</option>
115 <option value="lofreq">lofreq</option>
109 </param> 116 </param>
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)"/> 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)"/>
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)" /> 118 <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)" />
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)"/> 119 <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)"/>
113 </when> 120 </when>
134 <param name="output_format" value="txt" /> 141 <param name="output_format" value="txt" />
135 <param name="platform" value="illumina" /> 142 <param name="platform" value="illumina" />
136 <param name="options" value="no" /> 143 <param name="options" value="no" />
137 <output name="output_txt"> 144 <output name="output_txt">
138 <assert_contents> 145 <assert_contents>
139 <has_line line="Drug-resistance: Pre-MDR" /> 146 <has_line line="Drug-resistance: RR-TB" />
140 <has_line line="lineage2.2.2&#009;1.000&#009;East-Asian (Beijing)&#009;Beijing-RD105/RD207&#009;RD105;RD207" /> 147 <has_line line="lineage2.2.2&#009;1.000&#009;East-Asian (Beijing)&#009;Beijing-RD105/RD207&#009;RD105;RD207" />
141 <has_line line="Rifampicin&#009;R&#009;rpoB p.Asp435Val (1.00)" /> 148 <has_line line="Rifampicin&#009;R&#009;rpoB p.Asp435Val (1.00)" />
142 <has_line line="763031&#009;Rv0667&#009;rpoB&#009;c.3225T>C&#009;1.000" /> 149 <has_line line="761110&#009;Rv0667&#009;rpoB&#009;p.Asp435Val&#009;1.000&#009;rifampicin" />
143 </assert_contents> 150 </assert_contents>
144 </output> 151 </output>
145 </test> 152 </test>
146 <test expect_num_outputs="3"> 153 <test expect_num_outputs="3">
147 <param name="input_select" value="bam"/> 154 <param name="input_select" value="bam"/>
149 <param name="output_format" value="txt" /> 156 <param name="output_format" value="txt" />
150 <param name="platform" value="illumina" /> 157 <param name="platform" value="illumina" />
151 <param name="options" value="no" /> 158 <param name="options" value="no" />
152 <output name="output_txt"> 159 <output name="output_txt">
153 <assert_contents> 160 <assert_contents>
154 <has_line line="Drug-resistance: Pre-MDR" /> 161 <has_line line="Drug-resistance: RR-TB" />
155 <has_line line="lineage2.2.2&#009;1.000&#009;East-Asian (Beijing)&#009;Beijing-RD105/RD207&#009;RD105;RD207" /> 162 <has_line line="lineage2.2.2&#009;1.000&#009;East-Asian (Beijing)&#009;Beijing-RD105/RD207&#009;RD105;RD207" />
156 <has_line line="Rifampicin&#009;R&#009;rpoB p.Asp435Val (1.00)" /> 163 <has_line line="Rifampicin&#009;R&#009;rpoB p.Asp435Val (1.00)" />
157 <has_line line="763031&#009;Rv0667&#009;rpoB&#009;c.3225T>C&#009;1.000" /> 164 <has_line line="761110&#009;Rv0667&#009;rpoB&#009;p.Asp435Val&#009;1.000&#009;rifampicin" />
158 </assert_contents> 165 </assert_contents>
159 </output> 166 </output>
160 </test> 167 </test>
161 <test expect_num_outputs="4"> 168 <test expect_num_outputs="4">
162 <param name="input_select" value="single_fastq"/> 169 <param name="input_select" value="single_fastq"/>
167 <param name="call_whole_genome" value="true" /> 174 <param name="call_whole_genome" value="true" />
168 <param name="min_allele_freq" value="0.25" /> 175 <param name="min_allele_freq" value="0.25" />
169 <param name="min_allele_freq_reporting" value="0.33" /> 176 <param name="min_allele_freq_reporting" value="0.33" />
170 <output name="output_txt"> 177 <output name="output_txt">
171 <assert_contents> 178 <assert_contents>
172 <has_line line="Drug-resistance: Pre-MDR" /> 179 <has_line line="Drug-resistance: RR-TB" />
173 <has_line line="lineage2.2.2&#009;1.000&#009;East-Asian (Beijing)&#009;Beijing-RD105/RD207&#009;RD105;RD207" /> 180 <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)" /> 181 <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" /> 182 <has_line line="761110&#009;Rv0667&#009;rpoB&#009;p.Asp435Val&#009;1.000&#009;rifampicin" />
176 </assert_contents> 183 </assert_contents>
177 </output> 184 </output>
178 </test> 185 </test>
179 </tests> 186 </tests>
180 <help><![CDATA[ 187 <help><![CDATA[