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1 <?xml version="1.0"?>
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2
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3 <tool id="hgvs_assoc_phenos" name="Associate phenotypes to an HGVS table">
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4 <description>based on the medical literature</description>
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5 <version_string>echo 1.0.0</version_string>
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6 <command interpreter="perl">associate_variant_phenotypes $__tool_data_path__ pheno $input_hgvs_table
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7 ## Handle preselected gene list of interest
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8 #if $preselectedGenesSource.source == "file":
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9 $preselectedGenesSource.file_of_genenames
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10 #else:
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11 #set $glist = str($preselectedGenesSource.genename_list).replace("__cr____cn__", " or ")
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12 "$glist"
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13 #end if
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14
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15 ## Handle human literature terms
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16 #if $litQuerySource.source == "file":
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17 $litQuerySource.file_of_phenotypes
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18 #else:
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19 #set $qlist = str($litQuerySource.phenotype_list).replace("__cr____cn__", " or ")
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20 "$qlist"
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21 #end if
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22
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23 ## Handle human phenotype ontology query
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24 ##if $hpQuerySource.source == "file":
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25 ##$hpQuerySource.file_of_mpterms
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26 ##else:
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27 ##set $hplist = str($hpQuerySource.autocomplete_OLS_HP).replace(";", " or ")
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28 ##"$hplist"
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29 ##end if
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30
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31 ## Handle mouse knockout query (Mammalian Phenotype Ontology)
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32 #if $mpQuerySource.source == "file":
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33 $mpQuerySource.file_of_mpterms
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34 #else:
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35 #set $mplist = str($mpQuerySource.autocomplete_OLS_MP).replace(";", " or ")
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36 "$mplist"
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37 #end if
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38
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39 ## Handle gene ontology terms
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40 #if $goQuerySource.source == "file":
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41 $goQuerySource.file_of_goterms
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42 #else:
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43 #set $golist = str($goQuerySource.autocomplete_OLS_GO).replace(";", " or ")
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44 "$golist"
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45 #end if
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46 </command>
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47
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48 <inputs>
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49 <param name="outfiles_prefix" type="text" label="Prefix for output file names"/>
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50 <param format="achri_annotated_snp_table" name="input_hgvs_table" type="data" label="Basic or functionally annotated HGVS variant table"/>
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51 <conditional name="litQuerySource">
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52 <param name="source" type="select" label="How would you like to specify the phenotypes of interest?">
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53 <option value="list">A list</option>
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54 <option value="file">A file</option>
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55 </param>
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56 <when value="file">
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57 <param format="text" name="file_of_phenotypes" type="data" label="Text file with one phenotype per line, from most to least important" help="Phenotypes can have boolean operators to allow word order swaps. e.g. 'Develop and delay' will match both 'delayed development' and 'developmental delay'."/>
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58 </when>
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59 <when value="list">
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60 <param name="phenotype_list" type="text" area="True" label="One phenotype per line, from most to least important" help="Phenotypes can have boolean operators to allow word order swaps. e.g. 'Develop AND delay' will match both 'delayed development' and 'developmental delay'."/>
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61 </when>
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62 </conditional>
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63
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64 <conditional name="preselectedGenesSource">
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65 <param name="source" type="select" label="How would you like to specify preselected genes of interest?">
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66 <option value="list">A list</option>
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67 <option value="file">A file</option>
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68 </param>
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69 <when value="file">
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70 <param format="text" name="file_of_genenames" type="data" label="Text file with one upper case gene name per line" help="It is recommended to include gene name synonyms to maximize the chance of reference recovery"/>
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71 </when>
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72 <when value="list">
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73 <param name="genename_list" type="text" area="True" label="One upper case gene name per line, e.g. ADH1" help="It is recommended to include gene name synonyms to maximize the chance of reference recovery"/>
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74 </when>
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75 </conditional>
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76
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77 <!--<conditional name="hpQuerySource">
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78 <param name="source" type="select" label="How would you like to specify Human Phenotype Ontology terms of interest?">
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79 <option value="list">A list</option>
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80 <option value="file">A file</option>
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81 </param>
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82 <when value="file">
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83 <param format="text" name="file_of_hpterms" type="data" label="Text file with one Human Phenotype term (text) per line"/>
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84 </when>
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85 <when value="list">
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86 <param name="autocomplete_OLS_HP" type="text" label="Semi-colon separated list of HP terms (with autocomplete)" help="For better search results, do not type punctuation or symbols. For example, if you are looking for 4'-(L-tryptophan), try typing 4 L tryp"/>
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87 </when>
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88 </conditional>-->
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89
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90 <conditional name="mpQuerySource">
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91 <param name="source" type="select" label="How would you like to specify Mammalian Phenotype terms of interest?">
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92 <option value="list">A list</option>
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93 <option value="file">A file</option>
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94 </param>
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95 <when value="file">
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96 <param format="text" name="file_of_mpterms" type="data" label="Text file with one Mammalian Phenotype term (text) per line"/>
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97 </when>
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98 <when value="list">
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99 <param name="autocomplete_OLS_MP" type="text" label="Semi-colon separated list of MP terms (with autocomplete)" help="For better search results, do not type punctuation or symbols. For example, if you are looking for 4'-(L-tryptophan), try typing 4 L tryp"/>
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100 </when>
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101 </conditional>
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102
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103 <conditional name="goQuerySource">
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104 <param name="source" type="select" label="How would you like to specify Gene Ontology terms of interest?">
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105 <option value="list">A list</option>
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106 <option value="file">A file</option>
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107 </param>
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108 <when value="file">
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109 <param format="text" name="file_of_goterms" type="data" label="Text file with one gene ontology term (text) per line"/>
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110 </when>
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111 <when value="list">
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112 <param name="autocomplete_OLS_GO" type="text" label="Semi-colon separated list of GO terms (with autocomplete)" help="For better search results, do not type punctuation or symbols. For example, if you are looking for 4'-(L-tryptophan), try typing 4 L tryp"/>
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113 </when>
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114 </conditional>
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115 </inputs>
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116 <outputs>
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117 <data format="achri_annotated_snp_table" name="out_hgvs_table" type="data" label="${outfiles_prefix} HGVS all variants table with geno-pheno correlates" from_work_dir="pheno.common.hgvs.txt"/>
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118 </outputs>
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119
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120 <tests>
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121 </tests>
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122
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123 <help>
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124 This tools adds columns to an HGVS table that include all of the literature references from OMIM, PubMed, ClinVar, the Human Phenotype
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125 Ontology, the Mouse Knockout Phenotypes, and Gene Ontology that match a given set of clinical phenotype query terms. A combined
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126 probability of gene-phenotype association is calculated to help the user rank potentially causative genes for presumed genetic disorders.
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127 </help>
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128 </tool>
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