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18
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1 <macros>
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2 <xml name="viral_samples">
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3 <repeat name="rep_study" title="Study" min="1">
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4 <param name="study_title" type="text" optional="False" label="Please provide a short descriptive title for the study"/>
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5 <param name="study_abstract" type="text" optional="True" label="Please provide an abstract to describe the study in detail"/>
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6 <param name="study_type" type="select" label="Please select the type of study">
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7 <options from_data_table="study_type">
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8 <column name="value" index="0"/>
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9 </options>
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10 </param>
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11 <param name="study_pubmed_id" type="text" optional="True" value="" label="Please provide the PubMed id if exists (or leave it blank)"/>
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12 <repeat name="rep_sample" title="Samples associated with this study" min="1" >
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13 <param name="sample_title" type="text" label="Sample title"/>
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14 <param name="sample_description" type="text" help="e.g: liver cells" label="Describe the type of sample"/>
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15 <param name="scientific_name" type="text" label="Enter the species of the sample" help="e.g Severe acute respiratory syndrome coronavirus 2"/>
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16 <param name="tax_id" type="text" label="Enter the taxonomic ID corresponding to the sample species" />
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17 <param name="collection_date" type="text" label="Collection date" optional="True" help="options are: YYYY, YYYY/MM, YYYY/MM/DD, not collected, restricted access or leave blank">
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18 <validator type="regex" message="Data format is not valid">(^[0-9]{4}(-[0-9]{2}(-[0-9]{2}(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?(/[0-9]{4}(-[0-9]{2}(-[0-9]{2}(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?)?$)|(^not colected$)|(^not provided$)|(^restricted access$)</validator>
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19 </param>
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20 <param name="geo_location_country" type="select" label="Select the country where the sample was obtained">
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21 <options from_data_table="geographic_location_1">
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22 <column name="value" index="0"/>
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23 </options>
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24 </param>
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25 <param name="host_common_name" type="text" label="Host common name" help="e.g human"/>
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26 <param name="host_subject_id" type="text" label="Host subject id"/>
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27 <param name="host_health_state" type="select" label="Host health state">
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28 <options from_data_table="host_health_state_1">
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29 <column name="value" index="0"/>
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30 </options>
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31 </param>
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32 <param name="host_sex" type="select" label="Host sex">
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33 <options from_data_table="host_sex_1">
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34 <column name="value" index="0"/>
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35 </options>
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36 </param>
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37 <param name="host_scientific_name" type="text" label="Host scientific name" help="e.g Homo sapiens"/>
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38 <param name="collector_name" type="text" label="Collector name" help="Leave blank if unknown"/>
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39 <param name="collecting_institution" type="text" label="Collecting institution"/>
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40 <param name="isolate" type="text" label="Isolate"/>
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41 <repeat name="rep_experiment" title="Sequencing experiments performed with this sample" min="1" >
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42 <param name="experiment_title" type="text" label="Specify an experiment title" />
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43 <param name="experiment_design" type="text" label="Describe the experiment design" />
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44 <param name="library_strategy" type="select" label="Library strategy" help="The library strategy specifies the sequencing technique intended for this library">
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45 <options from_data_table="library_strategy">
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46 <column name="value" index="0"/>
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47 </options>
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48 </param>
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49 <param name="library_source" type="select" label="Select library source" help="The library source specifies the type of source material that is being sequenced">
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50 <options from_data_table="library_source">
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51 <column name="value" index="0"/>
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52 </options>
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53 </param>
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54 <param name="library_selection" type="select" label="Library selection" help="The library selection specifies whether any method was used to select for or against, enrich, or screen the material being sequenced">
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55 <options from_data_table="library_selection">
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56 <column name="value" index="0"/>
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57 </options>
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58 </param>
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59 <param name="library_layout" type="select" label="Library layout">
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60 <options from_data_table="library_layout">
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61 <column name="value" index="0"/>
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62 </options>
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63 </param>
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64 <param name="insert_size" type="integer" value="0" label="Specify the insert size"/>
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65 <param name="library_construction_protocol" type="text" label="Please describe the library construction protocol"/>
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66 <param name="platform" type="select" label="Select the sequencing platform used">
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67 <option value="LS454">LS454</option>
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68 <option value="ILLUMINA">Illumina</option>
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69 <option value="HELICOS">Helicos</option>
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70 <option value="ABI_SOLID">ABI Solid</option>
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71 <option value="COMPLETE_GENOMICS">Complete Genomics</option>
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72 <option value="BGISEQ">BGI Seq</option>
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73 <option value="OXFORD_NANOPORE">Oxford Nanopore</option>
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74 <option value="PACBIO_SMRT">PacBio</option>
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75 <option value="ION_TORRENT">Ion Torrent</option>
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76 <option value="CAPILLARY">Capillary sequencing</option>
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77 </param>
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78 <param name="instrument_model" type="select" label="Instrument model">
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79 <options from_data_table="instrument_model">
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80 <column name="value" index="0"/>
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81 </options>
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82 </param>
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83 <repeat name="rep_runs" title="Runs executed within this experiment" min="1" >
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84 <param name="upload_files" type="data" format="fastqsanger.gz,fastqsanger.bz2,fastq.gz,fastq.bz" multiple="true" label="File(s) associated with this run"/>
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85 </repeat>
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86 </repeat>
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87 </repeat>
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88 </repeat>
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89 </xml>
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90 <xml name="nonviral_samples">
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91 <repeat name="rep_study" title="Study" min="1">
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92 <param name="study_title" type="text" optional="False" label="Please provide a short descriptive title for the study"/>
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93 <param name="study_abstract" type="text" optional="True" label="Please provide an abstract to describe the study in detail"/>
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94 <param name="study_type" type="select" label="Please select the type of study">
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95 <options from_data_table="study_type">
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96 <column name="value" index="0"/>
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97 </options>
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98 </param>
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99 <param name="study_pubmed_id" type="text" optional="True" value="" label="Please provide the PubMed id if exists (or leave it blank)"/>
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100 <repeat name="rep_sample" title="Samples associated with this study" min="1" >
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101 <param name="sample_title" type="text" label="Sample title"/>
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102 <param name="sample_description" type="text" help="e.g: liver cells" label="Describe the type of sample"/>
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103 <param name="scientific_name" type="text" label="Enter the species of the sample" help="e.g Severe acute respiratory syndrome coronavirus 2"/>
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104 <param name="tax_id" type="text" label="Enter the taxonomic ID corresponding to the sample species" />
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105 <repeat name="rep_experiment" title="Sequencing experiments performed with this sample" min="1" >
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106 <param name="experiment_title" type="text" label="Specify an experiment title" />
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107 <param name="experiment_design" type="text" label="Describe the experiment design" />
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108 <param name="library_strategy" type="select" label="Library strategy" help="The library strategy specifies the sequencing technique intended for this library">
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109 <options from_data_table="library_strategy">
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110 <column name="value" index="0"/>
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111 </options>
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112 </param>
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113 <param name="library_source" type="select" label="Select library source" help="The library source specifies the type of source material that is being sequenced">
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114 <options from_data_table="library_source">
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115 <column name="value" index="0"/>
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116 </options>
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117 </param>
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118 <param name="library_selection" type="select" label="Library selection" help="The library selection specifies whether any method was used to select for or against, enrich, or screen the material being sequenced">
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119 <options from_data_table="library_selection">
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120 <column name="value" index="0"/>
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121 </options>
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122 </param>
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123 <param name="library_layout" type="select" label="Library layout">
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124 <options from_data_table="library_layout">
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125 <column name="value" index="0"/>
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126 </options>
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127 </param>
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128 <param name="insert_size" type="integer" value="0" label="Specify the insert size"/>
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129 <param name="library_construction_protocol" type="text" label="Please describe the library construction protocol"/>
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130 <param name="platform" type="select" label="Select the sequencing platform used">
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131 <option value="LS454">LS454</option>
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132 <option value="ILLUMINA">Illumina</option>
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133 <option value="HELICOS">Helicos</option>
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134 <option value="ABI_SOLID">ABI Solid</option>
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135 <option value="COMPLETE_GENOMICS">Complete Genomics</option>
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136 <option value="BGISEQ">BGI Seq</option>
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137 <option value="OXFORD_NANOPORE">Oxford Nanopore</option>
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138 <option value="PACBIO_SMRT">PacBio</option>
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139 <option value="ION_TORRENT">Ion Torrent</option>
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140 <option value="CAPILLARY">Capillary sequencing</option>
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141 </param>
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142 <param name="instrument_model" type="select" label="Instrument model">
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143 <options from_data_table="instrument_model">
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144 <column name="value" index="0"/>
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145 </options>
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146 </param>
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147 <repeat name="rep_runs" title="Runs executed within this experiment" min="1" >
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148 <param name="upload_files" type="data" format="fastqsanger.gz,fastqsanger.bz2,fastq.gz,fastq.bz" multiple="true" label="File(s) associated with this run"/>
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149 </repeat>
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150 </repeat>
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151 </repeat>
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152 </repeat>
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153 </xml>
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154 </macros>
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