Mercurial > repos > bgruening > pharmcat

comparison pharmcat.xml @ 1:891283e0ee89 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit dddf99b20ed9b07334505917f362785e3dace3b9"
author bgruening
date Thu, 05 May 2022 20:27:17 +0000
parents d67642a21a1d
children
comparison
equal deleted inserted replaced
0:d67642a21a1d 1:891283e0ee89
1 <tool id="pharmcat" name="pharmCAT" version="@WRAPPER_VERSION@+@VERSION_SUFFIX@" profile="20.01"> 1 <tool id="pharmcat" name="pharmCAT" version="@WRAPPER_VERSION@+@VERSION_SUFFIX@" profile="20.01">
2 <description> 2 <description>
3 Pharmacogenomics Clinical Annotation Tool 3 Pharmacogenomics Clinical Annotation Tool
4 </description> 4 </description>
5 <macros> 5 <macros>
6 <token name="@WRAPPER_VERSION@">1.3.1</token> 6 <token name="@WRAPPER_VERSION@">1.7.0</token>
7 <token name="@VERSION_SUFFIX@">galaxy0</token> 7 <token name="@VERSION_SUFFIX@">galaxy0</token>
8 </macros> 8 </macros>
9 <requirements> 9 <requirements>
10 <container type="docker">pgkb/pharmcat:1.3.1</container> 10 <container type="docker">pgkb/pharmcat:1.7.0</container>
11 </requirements> 11 </requirements>
12 <command detect_errors="exit_code"><![CDATA[ 12 <command detect_errors="exit_code"><![CDATA[
13 ## NAMECALLER FUNCTION 13 ## NAMECALLER FUNCTION
14 #if $function_select.function == 'name': 14 #if $function_select.function == 'name':
15 ln -s '$function_select.input' ./input.vcf && 15 ln -s '$function_select.input' ./input.vcf &&
70 <option value="name">Only named allele matcher</option> 70 <option value="name">Only named allele matcher</option>
71 <option value="pheno">Only phenotyper</option> 71 <option value="pheno">Only phenotyper</option>
72 <option value="report">Only reporter</option> 72 <option value="report">Only reporter</option>
73 </param> 73 </param>
74 <when value="all"> 74 <when value="all">
75 <param name="input" argument="-vcf" type="data" format="vcf" label="Input vcf file" help="Must be formatted in modified official VCF format as detailed here: https://github.com/PharmGKB/PharmCAT/wiki/VCF-Requirements"/> 75 <param name="input" argument="-vcf" type="data" format="vcf" label="Input vcf file"
76 help="Must be formatted in modified official VCF format as detailed here: https://github.com/PharmGKB/PharmCAT/wiki/VCF-Requirements"/>
76 <param name="outside_call" argument="-a" type="data" format="tsv,tabular" label="Gene call TSV file from an outside tool" optional="true"/> 77 <param name="outside_call" argument="-a" type="data" format="tsv,tabular" label="Gene call TSV file from an outside tool" optional="true"/>
77 <param name="json" argument="-j" type="boolean" truevalue="-j" falsevalue="" label="Output reporter JSON report"/> 78 <param name="json" argument="-j" type="boolean" truevalue="-j" falsevalue="" label="Output reporter JSON report"/>
78 <param name="phenojson" argument="-pj" type="boolean" truevalue="-pj" falsevalue="" label="Output phenotyper JSON report"/> 79 <param name="phenojson" argument="-pj" type="boolean" truevalue="-pj" falsevalue="" label="Output phenotyper JSON report"/>
79 <!-- <param name="definitions" argument="-na" type="data" format="list" label="Alternative allele definitions" help="a directory containing allele definitions to use instead of the default packaged allele definitions"/> --> 80 <!-- <param name="definitions" argument="-na" type="data" format="list" label="Alternative allele definitions" help="a directory containing allele definitions to use instead of the default packaged allele definitions"/> -->
80 </when> 81 </when>
81 <when value="name"> 82 <when value="name">
82 <param name="input" argument="-vcf" type="data" format="vcf" label="Input vcf file" help="Must be formatted in modified official VCF format as detailed here: https://github.com/PharmGKB/PharmCAT/wiki/VCF-Requirements"/> 83 <param name="input" argument="-vcf" type="data" format="vcf" label="Input vcf file"
84 help="Must be formatted in modified official VCF format as detailed here: https://github.com/PharmGKB/PharmCAT/wiki/VCF-Requirements"/>
83 <!-- <param name="definitions" argument="-d" type="data" format="list" label="Alternative allele definitions" help="a directory containing allele definitions to use instead of the default packaged allele definitions"/> --> 85 <!-- <param name="definitions" argument="-d" type="data" format="list" label="Alternative allele definitions" help="a directory containing allele definitions to use instead of the default packaged allele definitions"/> -->
84 </when> 86 </when>
85 <when value="pheno"> 87 <when value="pheno">
86 <conditional name="method"> 88 <conditional name="method">
87 <param name="pheno_function" type="select" label="Which function of PharmCAT should be run?"> 89 <param name="pheno_function" type="select" label="Which function of PharmCAT should be run?">
88 <option value="vcf">Run directly from vcf samples</option> 90 <option value="vcf">Run directly from vcf samples</option>
89 <option value="named">Run from the output of the NamedAlleleMatcher</option> 91 <option value="named">Run from the output of the NamedAlleleMatcher</option>
90 </param> 92 </param>
91 <when value="vcf"> 93 <when value="vcf">
92 <param name="input" argument="-vcf" type="data" format="vcf" label="Input vcf file" help="Must be formatted in modified official VCF format as detailed here: https://github.com/PharmGKB/PharmCAT/wiki/VCF-Requirements"/> 94 <param name="input" argument="-vcf" type="data" format="vcf" label="Input vcf file"
95 help="Must be formatted in modified official VCF format as detailed here: https://github.com/PharmGKB/PharmCAT/wiki/VCF-Requirements"/>
93 </when> 96 </when>
94 <when value="named"> 97 <when value="named">
95 <param name="input" argument="-c" type="data" format="json" label="Input json file" help="JSON output of the NamedAlleleCaller pharmcat function"/> 98 <param name="input" argument="-c" type="data" format="json" label="Input json file" help="JSON output of the NamedAlleleCaller pharmcat function"/>
96 </when> 99 </when>
97 </conditional> 100 </conditional>
131 </outputs> 134 </outputs>
132 <tests> 135 <tests>
133 <!-- ALL FUNCTION --> 136 <!-- ALL FUNCTION -->
134 <test expect_num_outputs="3"> 137 <test expect_num_outputs="3">
135 <conditional name="function_select"> 138 <conditional name="function_select">
136 <param name="input" ftype="vcf" value="test.vcf"/> 139 <param name="input" value="test.vcf" ftype="vcf" />
137 <param name="outside_call" ftype="tabular" value="test.tsv"/> 140 <param name="outside_call" value="test.tsv" ftype="tabular"/>
138 <param name="json" value="-j"/> 141 <param name="json" value="-j"/>
139 <param name="phenojson" value="-pj"/> 142 <param name="phenojson" value="-pj"/>
140 </conditional> 143 </conditional>
141 <output name="all_out"> 144 <output name="all_out">
142 <assert_contents> 145 <assert_contents>
156 </test> 159 </test>
157 <!-- NAMECALLER --> 160 <!-- NAMECALLER -->
158 <test expect_num_outputs="2"> 161 <test expect_num_outputs="2">
159 <conditional name="function_select"> 162 <conditional name="function_select">
160 <param name="function" value="name"/> 163 <param name="function" value="name"/>
161 <param name="input" ftype="vcf" value="test.vcf"/> 164 <param name="input" value="test.vcf" ftype="vcf"/>
162 </conditional> 165 </conditional>
163 <output name="namer_html" file="test_2.html" lines_diff="2"/> 166 <output name="namer_html" file="test_2.html" lines_diff="4" ftype="html" />
164 <output name="namer_json" file="test_2.json" lines_diff="2"/> 167 <output name="namer_json" file="test_2.json" lines_diff="2" ftype="json" />
165 </test> 168 </test>
166 <!-- PHENOTYPER FROM VCF WITH OUTSIDE CALLER--> 169 <!-- PHENOTYPER FROM VCF WITH OUTSIDE CALLER-->
167 <test expect_num_outputs="1"> 170 <test expect_num_outputs="1">
168 <conditional name="function_select"> 171 <conditional name="function_select">
169 <param name="function" value="pheno"/> 172 <param name="function" value="pheno"/>
178 <!-- PHENOTYPER FROM NAMECALLER AND NO OUTSIDE CALLER--> 181 <!-- PHENOTYPER FROM NAMECALLER AND NO OUTSIDE CALLER-->
179 <test expect_num_outputs="1"> 182 <test expect_num_outputs="1">
180 <conditional name="function_select"> 183 <conditional name="function_select">
181 <param name="function" value="pheno"/> 184 <param name="function" value="pheno"/>
182 <conditional name="method"> 185 <conditional name="method">
183 <param name="pheno_function" value="named"/> 186 <param name="pheno_function" value="named" />
184 <param name="input" value="test_2.json"/> 187 <param name="input" value="test_2.json" ftype="json" />
185 </conditional> 188 </conditional>
186 </conditional> 189 </conditional>
187 <output name="pheno_json" file="test_4.json" lines_diff="1"/> 190 <output name="pheno_json" file="test_4.json" lines_diff="34"/>
188 </test> 191 </test>
189 <!-- REPORTER --> 192 <!-- REPORTER -->
190 <test expect_num_outputs="2"> 193 <test expect_num_outputs="2">
191 <conditional name="function_select"> 194 <conditional name="function_select">
195 <param name="input" value="test_3.json" ftype="json"/>
192 <param name="function" value="report"/> 196 <param name="function" value="report"/>
193 <param name="input" value="test_3.json"/> 197 <param name="text" value="test text"/>
194 <param name="text" value="test text"/>
195 </conditional> 198 </conditional>
196 <output name="report_json"> 199 <output name="report_json">
197 <assert_contents> 200 <assert_contents>
198 <has_text text="Implication for CYP2C19"/> 201 <has_text text="Implication for CYP2C19"/>
199 <has_text text="Lower dose-adjusted trough concentrations of tacrolimus and decreased chance of achieving target tacrolimus concentrations."/> 202 <has_text text="Lower dose-adjusted trough concentrations of tacrolimus and decreased chance of achieving target tacrolimus concentrations."/>