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1 <tool id="ena_consensus_submit" name="Submit consensus sequence to ENA" version="0.1.0" python_template_version="3.5">
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2 <macros>
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3 <token name="@VERSION@">3.7.0</token>
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4 </macros>
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5 <requirements>
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6 <requirement type="package" version="@VERSION@">ena-webin-cli</requirement>
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7 <requirement type="package" version="1.76">biopython</requirement>
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8 <requirement type="package" version="5.3">pyyaml</requirement>
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9 </requirements>
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10 <command detect_errors="exit_code"><![CDATA[
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11
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12 webin_id=`grep 'username' $credentials | cut -f2,2`;
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13 if [ "\$webin_id" = "" ]; then
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14 ## No credentials in user defined preferences
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15 ## Fallback to global defined credentials (if exist)
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16 #import os
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17 #if os.path.isfile(os.environ.get('GALAXY_ENA_SECRETS', '')):
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18 credentials_path=\${GALAXY_ENA_SECRETS};
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19 webin_id=`grep 'username' \$GALAXY_ENA_SECRETS | cut -d' ' -f2,2`;
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20 password=`grep 'password' \$GALAXY_ENA_SECRETS | cut -d' ' -f2,2`;
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21 if [ "\$webin_id" = "" ]; then
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22 echo "No global credentials defined. Check your GALAXY_ENA_SECRETS file or set your credentials via: User -> Preferences -> Manage Information";
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23 exit 1;
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24 fi;
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25 #else:
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26 echo "No ENA credentials defined. Set your credentials via: User -> Preferences -> Manage Information";
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27 exit 1;
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28 #end if
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29 else
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30 password=`grep 'password' $credentials | cut -f2,2`;
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31 fi;
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32
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33 ## if it is still running at this point then the webin_id and password are set
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34
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35 ## create a manifaste base file with the parameters that are identical for all sequences that will be submited (if submitting a multifasta)
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36 #set $manifest_base = 'manifest_base.tab'
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37 mkdir manifests;
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38 mkdir fasta;
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39
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40 echo -e "ASSEMBLY_TYPE\t$assembly_type" >> $manifest_base;
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41 echo -e "COVERAGE\t$coverage" >> $manifest_base;
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42 echo -e "PROGRAM\t$assembly_program" >> $manifest_base;
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1
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43 #if $min_gap_length:
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44 echo -e "MINGAPLENGTH\t$min_gap_length" >> $manifest_base;
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45 #end if
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0
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46 echo -e "MOLECULETYPE\t$molecule_type" >> $manifest_base;
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47
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48 #if $metadata_file_or_form.metadata_format == "file":
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49 ## process the input tables, this creates an intermediate file with information
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50 python3 '$__tool_directory__/process_input.py' $metadata_file_or_form.ena_receipt $genome_fasta './manifests' './fasta' $manifest_base;
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51 center_name=`grep 'center_name' $metadata_file_or_form.ena_receipt | cut -f2,2 | tr -d '\n'`;
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52 #else:
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53 #set $generated_manifest='./manifests/generated_manifest.txt'
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54 cp $manifest_base $generated_manifest
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55 $study_id = $metadata_file_or_form.study_accession
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56 $sample_id = $metadata_file_or_form.sample_accession
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57 echo "STUDY\t$study_id" > $generated_manifest;
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58 echo "SAMPLE\t$sample_id" >> $generated_manifest;
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59 center_name=$metadata_file_or_form.center_name;
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60 echo "ASSEMBLY_NAME\t$metadata_file_or_form.assembly_name" >> $generated_manifest;
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61 echo "PLATFORM\t$platform_name" >> $generated_manifest;
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62 #end if
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63
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64
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65 #if $metadata_file_or_form.metadata_format == "file":
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66 ## iterate over the list of manifest - fasta generated by the process_input
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67 ## in case of errors, this list is empty
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68 while read line; do
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69 manifest=`echo \$line | cut -d' ' -f1,1`;
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70 ena-webin-cli
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71 -context genome
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72 -userName \$webin_id
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73 -password \$password
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74 -centerName \$center_name
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75 -manifest \$manifest
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76 -inputDir "./fasta"
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77 #if $dry_run == "true":
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78 -validate
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79 #end if
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80 ;
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81 done < submit_list.tab
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82
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83 #else:
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84 gzip -c $genome_fasta > consensus.fasta.gz;
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85 echo -e "FASTA\tconsensus.fasta.gz" >> $generated_manifest;
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86 ena-webin-cli
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87 -context genome
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88 -userName \$webin_id
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89 -password \$password
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90 -centerName '\$center_name'
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91 -manifest $generated_manifest
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92 -inputDir "./"
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93 #if $submit_test == "true":
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94 -test
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95 #end if
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96 #if $dry_run == "true":
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97 -validate
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98 #else:
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99 -submit
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100 #end if
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101 #end if
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102 ]]></command>
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103 <configfiles>
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104 <configfile name="credentials"><![CDATA[
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105 #set $webin_id = $__user__.extra_preferences.get('ena_webin_account|webin_id', "").strip()
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106 #set $password = $__user__.extra_preferences.get('ena_webin_account|password', "").strip()
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107 #if $webin_id != "":
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108 username\t"$webin_id"
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109 password\t"$password"
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110 #end if
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111 ]]></configfile>
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112 </configfiles>
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113 <inputs>
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114 <param name="submit_test" type="boolean" default="False" label="Submit to test server" help="Suggested to test metadata format" />
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115 <param name="dry_run" type="boolean" default="False" label="Validate files and metadata but do not submit" help="Generate input files and run Webin-CLI with -validate option."/>
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116 <param name="genome_fasta" type="data" label="Select the consensus sequence assembly file" format="fasta"/>
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117 <param name="assembly_type" type="select" label="Assembly type">
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118 <option value="clone">Clone</option>
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119 <option value="isolate">Isolate</option>
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120 </param>
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121 <param name="assembly_program" type="text" optional="False" label="Assembly program"/>
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122 <param name="molecule_type" type="select" label="Molecule type">
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123 <option value="genomic RNA" selected="True">genomic RNA</option>
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124 <option value="viral cRNA">viral cRNA</option>
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125 <option value="genomic DNA">genomic DNA</option>
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126 </param>
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127 <param name="coverage" type="float" optional="False" value="10000" label="Coverage"/>
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128 <conditional name="metadata_file_or_form">
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129 <param name="metadata_format" type="select" label="Select the method to load study and sample metadata">
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130 <option value="file" selected="True">I used Galaxy ENA upload tool for raw data submission, parse my submission receipt</option>
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131 <option value="form">Fill in required metadata for linking</option>
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132 </param>
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133 <when value="file">
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134 <param type="data" format="txt" name="ena_receipt" label="Submission receipt obtained from ENA upload tool"/>
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135 </when>
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136 <when value="form">
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137 <param name="assembly_name" type="text" optional="False" label="Assembly name"/>
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138 <param name="study_accession" type="text" optional="False" label="Study accession or unique name (alias)"/>
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139 <param name="sample_accession" type="text" optional="False" label="Sample accession or unique name (alias)"/>
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140 <param name="sequencing_platform" type="text" optional="False" label="Sequencing platform"/>
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141 <param name="description" type="text" optional="True" value="" label="Description" help="Free text description of the genome assembly (optional)"/>
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142 <param name="center_name" type="text" optional="False" label="Center name"/>
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143 </when>
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144 </conditional>
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145 <param name="min_gap_length" type="text" optional="True" label="Minimum gap length (optional)"/>
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146 </inputs>
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147 <outputs>
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148 <collection name="generated_manifests" type="list" label="Generated manifests">
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149 <!--<discover_datasets pattern="__name_and_ext__" directory="manifests" />-->
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150 <discover_datasets pattern="(?P<designation>.+)\.manifest\.txt$" ext="txt" directory="manifests" />
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151 </collection>
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152 <collection name="manifests_reports" type="list" label="Manifests reports">
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153 <!--[><discover_datasets pattern="__name_and_ext__" directory="manifests" /><]-->
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154 <discover_datasets pattern="(?P<designation>.+)\.manifest\.txt\.report$" ext="txt" directory="manifests" />
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155 </collection>
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156 <data name="webin_cli_report" label="ENA submission receipt" format="txt" from_work_dir="manifests/webin-cli.report"/>
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157 </outputs>
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158 <help><![CDATA[
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159 TODO: Fill in help.
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160 ]]></help>
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161 </tool>
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