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