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annotate pharmcat.xml @ 1:8005ce1418ac draft default tip

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit dddf99b20ed9b07334505917f362785e3dace3b9"
author bgruening
date Thu, 05 May 2022 20:26:42 +0000
parents 28aa54c800c0
children
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1 <tool id="pharmcat" name="pharmCAT" version="@WRAPPER_VERSION@+@VERSION_SUFFIX@" profile="20.01">
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2 <description>
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3 Pharmacogenomics Clinical Annotation Tool
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4 </description>
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5 <macros>
1
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6 <token name="@WRAPPER_VERSION@">1.7.0</token>
0
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7 <token name="@VERSION_SUFFIX@">galaxy0</token>
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8 </macros>
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9 <requirements>
1
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10 <container type="docker">pgkb/pharmcat:1.7.0</container>
0
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11 </requirements>
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12 <command detect_errors="exit_code"><![CDATA[
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13 ## NAMECALLER FUNCTION
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14 #if $function_select.function == 'name':
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15 ln -s '$function_select.input' ./input.vcf &&
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16 java -cp /pharmcat/pharmcat.jar
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17 org.pharmgkb.pharmcat.haplotype.NamedAlleleMatcher
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18 -vcf input.vcf
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19 -json output.json
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20 -html output.html
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21
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22 ## PHENOTYPE CALLER FUNCTION
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23 #else if $function_select.function == 'pheno':
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24 #if $function_select.method.pheno_function == 'vcf':
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25 ln -s '$function_select.method.input' ./input.vcf &&
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26 java -cp /pharmcat/pharmcat.jar
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27 org.pharmgkb.pharmcat.phenotype.Phenotyper
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28 -vcf input.vcf
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29 #else:
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30 ln -s '$function_select.method.input' ./input.json &&
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31 java -cp /pharmcat/pharmcat.jar
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32 org.pharmgkb.pharmcat.phenotype.Phenotyper
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33 -c input.json
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34 #end if
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35 #if $function_select.outside_call:
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36 -o $function_select.outside_call
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37 #end if
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38 -f output.json
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39
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40 ## REPORTER FUNCTION
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41 #else if $function_select.function == 'report':
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42 ln -s '$function_select.input' ./input.json &&
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43 java -cp /pharmcat/pharmcat.jar
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44 org.pharmgkb.pharmcat.reporter.Reporter
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45 -p input.json
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46 #if $function_select.title:
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47 -t '$function_select.title'
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48 #end if
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49 -j output.json
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50 -o output.html
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51
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52 ## ALL FUNCTIONS
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53 #else:
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54 ln -s '$function_select.input' ./input.vcf &&
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55 java -jar /pharmcat/pharmcat.jar
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56 -vcf input.vcf
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57 -o output
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58 -f pharmCAT_report_Galaxy
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59 #if $function_select.outside_call:
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60 -a $function_select.outside_call
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61 #end if
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62 $function_select.json
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63 $function_select.phenojson
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64 #end if
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65 ]]></command>
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66 <inputs>
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67 <conditional name="function_select">
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68 <param name="function" type="select" label="Which function of PharmCAT should be run?">
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69 <option value="all">Full PharmCAT pipeline</option>
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70 <option value="name">Only named allele matcher</option>
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71 <option value="pheno">Only phenotyper</option>
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72 <option value="report">Only reporter</option>
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73 </param>
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74 <when value="all">
1
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75 <param name="input" argument="-vcf" type="data" format="vcf" label="Input vcf file"
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76 help="Must be formatted in modified official VCF format as detailed here: https://github.com/PharmGKB/PharmCAT/wiki/VCF-Requirements"/>
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77 <param name="outside_call" argument="-a" type="data" format="tsv,tabular" label="Gene call TSV file from an outside tool" optional="true"/>
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78 <param name="json" argument="-j" type="boolean" truevalue="-j" falsevalue="" label="Output reporter JSON report"/>
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79 <param name="phenojson" argument="-pj" type="boolean" truevalue="-pj" falsevalue="" label="Output phenotyper JSON report"/>
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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"/> -->
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81 </when>
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82 <when value="name">
1
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83 <param name="input" argument="-vcf" type="data" format="vcf" label="Input vcf file"
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84 help="Must be formatted in modified official VCF format as detailed here: https://github.com/PharmGKB/PharmCAT/wiki/VCF-Requirements"/>
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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"/> -->
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86 </when>
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87 <when value="pheno">
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88 <conditional name="method">
28aa54c800c0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
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89 <param name="pheno_function" type="select" label="Which function of PharmCAT should be run?">
28aa54c800c0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
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90 <option value="vcf">Run directly from vcf samples</option>
28aa54c800c0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
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91 <option value="named">Run from the output of the NamedAlleleMatcher</option>
28aa54c800c0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
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92 </param>
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93 <when value="vcf">
1
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94 <param name="input" argument="-vcf" type="data" format="vcf" label="Input vcf file"
8005ce1418ac "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit dddf99b20ed9b07334505917f362785e3dace3b9"
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95 help="Must be formatted in modified official VCF format as detailed here: https://github.com/PharmGKB/PharmCAT/wiki/VCF-Requirements"/>
0
28aa54c800c0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
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96 </when>
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97 <when value="named">
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98 <param name="input" argument="-c" type="data" format="json" label="Input json file" help="JSON output of the NamedAlleleCaller pharmcat function"/>
28aa54c800c0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
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99 </when>
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100 </conditional>
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101 <param name="outside_call" argument="-o" type="data" format="tabular,tsv" label="Optional TSV of outside caller information" optional="true"/>
28aa54c800c0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
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102 </when>
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103 <when value="report">
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104 <param name="input" argument="-p" type="data" format="json" label="JSON call data output from Phenotyper pharmCAT function"/>
28aa54c800c0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
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105 <param name="title" argument="-t" type="text" label="text to add to the report title" optional="true"/>
28aa54c800c0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
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106 </when>
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107 </conditional>
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108 </inputs>
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109 <outputs>
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110 <data name="all_out" from_work_dir="output/pharmCAT_report_Galaxy.report.html" format="html" label="Full pharmCAT report on ${on_string}">
28aa54c800c0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
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111 <filter>function_select['function'] == "all"</filter>
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112 </data>
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113 <data name="all_pheno" from_work_dir="output/pharmCAT_report_Galaxy.phenotyper.json" format="json" label="pharmCAT Phenotyper report on ${on_string}">
28aa54c800c0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
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114 <filter>function_select['function'] == "all" and function_select["phenojson"]</filter>
28aa54c800c0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
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115 </data>
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116 <data name="all_out_json" from_work_dir="output/pharmCAT_report_Galaxy.report.json" format="json" label="pharmCAT Reporter JSON on ${on_string}">
28aa54c800c0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
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117 <filter>function_select['function'] == "all" and function_select["json"]</filter>
28aa54c800c0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
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118 </data>
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119 <data name="namer_html" from_work_dir="output.html" format="html" label="pharmCAT NamedAlleleMatcher html report on ${on_string}">
28aa54c800c0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
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120 <filter>function_select['function'] == "name"</filter>
28aa54c800c0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
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121 </data>
28aa54c800c0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
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122 <data name="namer_json" from_work_dir="output.json" format="json" label="pharmCAT NamedAlleleMatcher json report on ${on_string}">
28aa54c800c0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
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123 <filter>function_select['function'] == "name"</filter>
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124 </data>
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125 <data name="pheno_json" from_work_dir="output.json" format="json" label="pharmCAT Phenotyper report on ${on_string}">
28aa54c800c0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
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126 <filter>function_select['function'] == "pheno"</filter>
28aa54c800c0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
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127 </data>
28aa54c800c0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
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128 <data name="report_html" from_work_dir="output.html" format="html" label="pharmCAT Reporter html report on ${on_string}">
28aa54c800c0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
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129 <filter>function_select['function'] == "report"</filter>
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130 </data>
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131 <data name="report_json" from_work_dir="output.json" format="json" label="pharmCAT Reporter json report on ${on_string}">
28aa54c800c0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
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132 <filter>function_select['function'] == "report"</filter>
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133 </data>
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134 </outputs>
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135 <tests>
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136 <!-- ALL FUNCTION -->
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137 <test expect_num_outputs="3">
28aa54c800c0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
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138 <conditional name="function_select">
1
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139 <param name="input" value="test.vcf" ftype="vcf" />
8005ce1418ac "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit dddf99b20ed9b07334505917f362785e3dace3b9"
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140 <param name="outside_call" value="test.tsv" ftype="tabular"/>
0
28aa54c800c0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
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141 <param name="json" value="-j"/>
28aa54c800c0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
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142 <param name="phenojson" value="-pj"/>
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143 </conditional>
28aa54c800c0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
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144 <output name="all_out">
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145 <assert_contents>
28aa54c800c0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
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146 <has_text text="rs9923231 reference"/>
28aa54c800c0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
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147 <has_text text="Very high risk of developing hearing loss if administered an aminoglycoside antibiotic."/>
28aa54c800c0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
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148 <has_text text="CPIC Allele Function, Phenotype and Recommendation"/>
28aa54c800c0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
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149 </assert_contents>
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150 </output>
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151 <output name="all_pheno" file="test_1.pheno.json" lines_diff="1"/>
28aa54c800c0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
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152 <output name="all_out_json">
28aa54c800c0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
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153 <assert_contents>
28aa54c800c0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
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154 <has_text text="Therapeutic range of 200 to 1000 ng/mL has been proposed (PMID 29493375)."/>
28aa54c800c0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
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155 <has_text text="Activity Score for CYP2D6"/>
28aa54c800c0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
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156 <has_text text="Implementation Consortium (CPIC) Guideline for CYP2D6 Genotype and Use of Ondansetron and Tropisetron"/>
28aa54c800c0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
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157 </assert_contents>
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158 </output>
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159 </test>
28aa54c800c0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
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160 <!-- NAMECALLER -->
28aa54c800c0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
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161 <test expect_num_outputs="2">
28aa54c800c0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
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162 <conditional name="function_select">
28aa54c800c0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
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163 <param name="function" value="name"/>
1
8005ce1418ac "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit dddf99b20ed9b07334505917f362785e3dace3b9"
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parents: 0
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164 <param name="input" value="test.vcf" ftype="vcf"/>
0
28aa54c800c0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
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165 </conditional>
1
8005ce1418ac "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit dddf99b20ed9b07334505917f362785e3dace3b9"
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diff changeset
166 <output name="namer_html" file="test_2.html" lines_diff="4" ftype="html" />
8005ce1418ac "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit dddf99b20ed9b07334505917f362785e3dace3b9"
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167 <output name="namer_json" file="test_2.json" lines_diff="2" ftype="json" />
0
28aa54c800c0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
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168 </test>
28aa54c800c0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
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169 <!-- PHENOTYPER FROM VCF WITH OUTSIDE CALLER-->
28aa54c800c0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
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170 <test expect_num_outputs="1">
28aa54c800c0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
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171 <conditional name="function_select">
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172 <param name="function" value="pheno"/>
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173 <conditional name="method">
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174 <param name="pheno_function" value="vcf"/>
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175 <param name="input" ftype="vcf" value="test.vcf"/>
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176 </conditional>
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177 <param name="outside_call" value="test.tsv"/>
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178 </conditional>
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179 <output name="pheno_json" file="test_3.json" lines_diff="1"/>
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180 </test>
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181 <!-- PHENOTYPER FROM NAMECALLER AND NO OUTSIDE CALLER-->
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182 <test expect_num_outputs="1">
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183 <conditional name="function_select">
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184 <param name="function" value="pheno"/>
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185 <conditional name="method">
1
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186 <param name="pheno_function" value="named" />
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187 <param name="input" value="test_2.json" ftype="json" />
0
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188 </conditional>
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189 </conditional>
1
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190 <output name="pheno_json" file="test_4.json" lines_diff="34"/>
0
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191 </test>
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192 <!-- REPORTER -->
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193 <test expect_num_outputs="2">
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194 <conditional name="function_select">
1
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195 <param name="input" value="test_3.json" ftype="json"/>
0
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196 <param name="function" value="report"/>
1
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197 <param name="text" value="test text"/>
0
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198 </conditional>
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199 <output name="report_json">
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200 <assert_contents>
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201 <has_text text="Implication for CYP2C19"/>
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202 <has_text text="Lower dose-adjusted trough concentrations of tacrolimus and decreased chance of achieving target tacrolimus concentrations."/>
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203 <has_text text="c.1840C\u003eT"/>
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204 </assert_contents>
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205 </output>
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206 <output name="report_html">
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207 <assert_contents>
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208 <has_text text="Two ivacaftor non-responsive alleles"/>
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209 <has_text text="rs12979860 reference (C)/rs12979860 reference (C)"/>
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210 <has_text text="MT-RNR1: 1555A"/>
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211 </assert_contents>
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212 </output>
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213 </test>
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214 </tests>
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215 <help><![CDATA[
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216 PharmCAT is a tool to extract all CPIC guideline gene variants from a genetic dataset (represented as a VCF file), interpret the variant alleles, and generate a report.
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217 ]]></help>
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218 <citations>
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219 <citation type="doi" >10.1002/cpt.928</citation>
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220 </citations>
1
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221 </tool>