Mercurial > repos > iuc > ena_webin_cli

annotate ena_webin_cli.xml @ 0:7f669682f4ac draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
author iuc
date Mon, 06 Oct 2025 12:13:07 +0000
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children 1090ae5e7b29
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7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
iuc
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1 <tool id="ena_webin_cli" name="ENA Webin CLI" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="MIT" profile="24.2">
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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2 <description>Submission of consensus sequences to the European Nucleotide Archive (ENA)</description>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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3 <macros>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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4 <token name="@TOOL_VERSION@">9.0.1</token>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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5 <token name="@VERSION_SUFFIX@">0</token>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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6 </macros>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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7 <requirements>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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8 <requirement type="package" version="@TOOL_VERSION@">ena-webin-cli</requirement>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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9 <requirement type="package" version="5.3">pyyaml</requirement>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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10 </requirements>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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11
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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12 <command detect_errors="exit_code"><![CDATA[
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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13 ## -----------------------------------------------------------------------------
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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14 ## 1) Initialize log and credentials
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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15 ## -----------------------------------------------------------------------------
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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16
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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17 ## Truncate (or create) the Galaxy-captured Webin-CLI log dataset.
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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18 : > "$webin_cli_log";
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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19
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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20 ## Default path where the <configfile name="credentials"> content will be written.
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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21 ## In dry-run we override this with a fake file so tests don’t require real creds.
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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22 #set $credentials = 'credentials'
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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23 #if $dry_run == "true":
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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24 #set $credentials = './test_fake_path'
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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25 touch $credentials;
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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26 echo "username:test_user" >> "$credentials";
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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27 echo "password:test_password" >> "$credentials";
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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28 #end if
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29
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30 ## Extract username/password from the credentials file.
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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31 ## NOTE: $webin_id appears in bash, so we escape it as \$webin_id.
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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32 webin_id=`grep 'username' $credentials | cut -d':' -f2,2`;
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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33 if [ -z "\$webin_id" ]; then
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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34 ## Fail early with guidance if no username is present.
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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35 echo "No ENA credentials defined. Set your credentials via: User -> Preferences -> Manage Information" >&2;
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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36 exit 1;
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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37 else
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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38 ## Pull the password similarly.
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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39 password=`grep 'password' $credentials | cut -d':' -f2,2`;
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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40 fi;
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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41
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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42 ## -----------------------------------------------------------------------------
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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43 ## 2) Create a base manifest (fields common to all submissions)
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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44 ## -----------------------------------------------------------------------------
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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45
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46 ## Name of the base manifest template (we append more fields later).
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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47 #set $manifest_base = 'manifest_base.tab'
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48
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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49 ## Working dirs: per-sample manifests and input sequences.
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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50 mkdir -p manifests;
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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51 mkdir -p fasta;
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52
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53 ## Write assembly-level fields to the base manifest.
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54 echo -e 'ASSEMBLY_TYPE\t$assembly_type' > $manifest_base;
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55 echo -e 'COVERAGE\t$coverage' >> $manifest_base;
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56 echo -e 'PROGRAM\t$assembly_program' >> $manifest_base;
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57 #if $min_gap_length:
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58 echo -e 'MINGAPLENGTH\t$min_gap_length' >> $manifest_base;
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59 #end if
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60 echo -e 'MOLECULETYPE\t$molecule_type' >> $manifest_base;
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61
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62 ## -----------------------------------------------------------------------------
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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63 ## 3) Build per-sample manifests depending on metadata workflow
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64 ## -----------------------------------------------------------------------------
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65
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66 #if $metadata_file_or_form.metadata_format == "file":
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67 ## --------------------------- FILE-DRIVEN WORKFLOW ------------------------
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68 ## For each selected FASTA:
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69 ## - if uncompressed (.fasta), gzip it into ./fasta/<name>.fasta.gz
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70 ## - if already .fasta.gz, symlink it into ./fasta
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71 #import re
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72 #for $file in $metadata_file_or_form.genome_fasta:
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73 #if $file.is_of_type('fasta'):
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74 #set $full_name = $file.element_identifier + '.gz'
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75 gzip -c '$file' > './fasta/$full_name';
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76 #else:
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77 ln -s '$file' './fasta/$file.element_identifier';
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78 #end if
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79 #end for
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80
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81 ## Optionally link AGP and chromosome list files if provided (one per sample).
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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82 #if $metadata_file_or_form.agp_file:
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83 #for $file in $metadata_file_or_form.agp_file:
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84 ln -s '$file' './fasta/$file.element_identifier';
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85 #end for
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86 #end if
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87 #if $metadata_file_or_form.chr_list_file:
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88 #for $file in $metadata_file_or_form.chr_list_file:
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89 #set $chr_name = $file.element_identifier + '.gz'
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90 gzip -c '$file' > './fasta/$chr_name';
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91 #end for
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92 #end if
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93
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94 ## Helper script:
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95 ## - parses ENA receipt (study/sample accessions, platform),
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96 ## - writes per-sample manifests into ./manifests using $manifest_base,
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97 ## - emits "submit_list.tab" (one manifest path per line).
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98 python3 '$__tool_directory__/process_input.py' $metadata_file_or_form.ena_receipt $genome_fasta_files './manifests' $manifest_base >> "$webin_cli_log" 2>&1;
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99
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100 ## Extract center name from the receipt (used as -centerName).
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101 center_name=`grep 'center_name' $metadata_file_or_form.ena_receipt | cut -f2,2 | tr -d '\n'`;
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102
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103 ## Log if submit_list.tab exists, and dump its content for debugging.
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104 if [ -s submit_list.tab ]; then
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105 echo "submit_list.tab present:" >> "$webin_cli_log" 2>&1;
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106 cat submit_list.tab >> "$webin_cli_log" 2>&1;
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107 else
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108 echo "submit_list.tab is missing or empty" >> "$webin_cli_log" 2>&1;
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109 fi;
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110
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111 #else:
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112 ## --------------------------- FORM-DRIVEN WORKFLOW ------------------------
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113 ## Single-manifest flow: copy base, then append form fields.
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114 #set $generated_manifest='./manifests/generated_manifest.txt'
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115 cp $manifest_base $generated_manifest;
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116
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117 ## Use local Cheetah vars for readability.
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118 #set $study_id = $metadata_file_or_form.study_accession
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119 #set $sample_id = $metadata_file_or_form.sample_accession
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120
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121 ## Required accessions.
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122 echo -e 'STUDY\t$study_id' >> $generated_manifest;
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123 echo -e 'SAMPLE\t$sample_id' >> $generated_manifest;
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124
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125 ## center_name is given by the user in this path.
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126 center_name='$metadata_file_or_form.center_name';
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127
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128 ## Assembly name and platform.
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129 echo -e 'NAME\t$metadata_file_or_form.assembly_name' >> $generated_manifest;
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130 echo -e 'PLATFORM\t$metadata_file_or_form.sequencing_platform' >> $generated_manifest;
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131
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132 ## Normalize FASTA name referenced by the manifest.
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133 #if $metadata_file_or_form.genome_fasta.is_of_type('fasta'):
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134 #set $fasta_file_name = $metadata_file_or_form.genome_fasta.element_identifier + '.gz'
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135 gzip -c '$metadata_file_or_form.genome_fasta' > $fasta_file_name;
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136 #else:
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137 #set $fasta_file_name = $metadata_file_or_form.genome_fasta.element_identifier
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138 #end if
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139 echo -e 'FASTA\t$fasta_file_name' >> $generated_manifest;
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140
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141 ## Optional extras for chromosome-scale assemblies.
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142 #if $metadata_file_or_form.agp_file:
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143 echo -e 'AGP\t$metadata_file_or_form.agp_file.element_identifier' >> $generated_manifest;
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144 #end if
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145 #if $metadata_file_or_form.chr_list_file:
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146 ## If the name ends with .tsv, gzip it and reference the .gz; else use as-is.
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147 #set $chr_file_name = $metadata_file_or_form.chr_list_file.element_identifier + '.gz'
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148 gzip -c '$metadata_file_or_form.chr_list_file' > $chr_file_name;
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149 echo -e 'CHROMOSOME_LIST\t$chr_file_name' >> $generated_manifest;
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150 #end if
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151 #end if
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152
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153 ## -----------------------------------------------------------------------------
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154 ## 4) Prepare output directory and build CLI flags safely with Cheetah
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155 ## -----------------------------------------------------------------------------
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156
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157 ## Webin-CLI will write receipts/logs under this directory (we later tar it).
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158 #set $outputs_dir = 'outputs'
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159 mkdir -p "$outputs_dir";
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160
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161 ## Build flags using #set (safer than inline #if within a single shell line).
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162 #set $test_flag = ''
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163 #if $submit_test == "true":
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164 #set $test_flag = ' -test'
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165 #end if
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166
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167 ## By default we submit; in dry_run we validate instead.
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168 #set $action_flag = ' -submit'
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169 #if $dry_run == "true":
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170 #set $action_flag = ' -validate'
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171 #end if
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172
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173 ## -----------------------------------------------------------------------------
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174 ## 5) Execute Webin-CLI
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175 ## -----------------------------------------------------------------------------
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176
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177 #if $metadata_file_or_form.metadata_format == "file":
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178 ## Loop over each manifest written by process_input.py (submit_list.tab).
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179 while IFS= read -r line; do
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180 ## Extract the manifest path (first whitespace-delimited field).
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181 manifest=`echo "\$line" | cut -d' ' -f1`;
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182
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183 ## Log which manifest we are submitting.
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184 echo "Submitting manifest \$manifest" >> "$webin_cli_log" 2>&1;
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185
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186 ## Invoke Webin-CLI with computed flags.
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187 ena-webin-cli -context genome -manifest "\$manifest" -userName "'\$webin_id'" -password "'\$password'" -centerName "'\$center_name'" -inputDir './fasta' $test_flag $action_flag -outputDir $outputs_dir >> '$webin_cli_log' 2>&1 || true;
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188 done < submit_list.tab;
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189
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190 #else:
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191 ## Single run in "form" mode with the one generated manifest.
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192 ena-webin-cli -context genome -manifest $generated_manifest -userName "'\$webin_id'" -password "'\$password'" -centerName "'\$center_name'" -inputDir ./ $test_flag $action_flag -outputDir $outputs_dir >> "$webin_cli_log" 2>&1 || true;
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193 #end if
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194
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195 ## -----------------------------------------------------------------------------
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196 ## 6) Package outputs for Galaxy
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197 ## -----------------------------------------------------------------------------
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198
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199 ## Tar up the Webin-CLI output directory so Galaxy can collect a single dataset.
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200 tar -cf $webin_cli_outputs $outputs_dir ;
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201 ]]></command>
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202
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203 <!--
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204 Config files rendered by Galaxy *before* the command runs.
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205 They are plain text files placed in the job working directory and referenced above.
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206 -->
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207 <configfiles>
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208 <!-- Credentials file:
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209 Pulls stored ENA Webin details (if set) from the Galaxy user preferences and writes
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210 simple "username:..." and "password:..." lines. The command reads from this file. -->
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211 <configfile name="credentials"><![CDATA[
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212 #set $webin_id = $__user__.extra_preferences.get('ena_webin_account|webin_id', "").strip()
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213 #set $password = $__user__.extra_preferences.get('ena_webin_account|password', "").strip()
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214 #if $webin_id != "":
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215 username:$webin_id
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216 password:$password
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217 #end if
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218 ]]></configfile>
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219
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220 <!-- genome_fasta_files:
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221 In "file" mode, build a JSON array containing the *element_identifier* (dataset name)
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222 for each selected FASTA. process_input.py uses these names to derive sample aliases. -->
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223 <configfile name="genome_fasta_files">
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224 #import json
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225 #import re
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226 #if $metadata_file_or_form.metadata_format == "file":
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227 #set $fasta_files_list = list()
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228 #for $file in $metadata_file_or_form.genome_fasta:
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229 $fasta_files_list.append(str($file.element_identifier))
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230 #end for
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231 #echo json.dumps($fasta_files_list)
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232 #end if
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233 </configfile>
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234 </configfiles>
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235
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236 <!--
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237 User-facing inputs:
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238 - Assembly-level parameters
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239 - Choice of metadata workflow (file vs form) with corresponding fields
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240 - Submission toggles for ENA test server and validation-only
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241 -->
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242 <inputs>
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243 <param name="assembly_type" type="select" label="Assembly type">
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244 <option value="clone">Clone</option>
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245 <option value="isolate">Isolate</option>
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246 <option value="COVID-19 outbreak">COVID-19 outbreak</option>
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247 </param>
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248 <param name="assembly_program" type="text" optional="False" label="Assembly program"/>
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249 <param name="molecule_type" type="select" label="Molecule type">
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250 <option value="genomic RNA" selected="True">genomic RNA</option>
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251 <option value="viral cRNA">viral cRNA</option>
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252 <option value="genomic DNA">genomic DNA</option>
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253 </param>
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254 <param name="coverage" type="float" optional="False" value="10000" label="Coverage"/>
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255 <param name="min_gap_length" type="text" optional="True" label="Minimum gap length (optional)"/>
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256
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257 <conditional name="metadata_file_or_form">
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258 <param name="metadata_format" type="select" label="Select the method to load study and sample metadata">
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259 <option value="form" selected="True">Fill in required submission metadata</option>
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260 <option value="file">I used the Galaxy ENA upload tool to submit the raw data: parse the received submission receipt</option>
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261 </param>
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262
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263 <!-- FILE workflow: receipt + multiple FASTA (+ optional AGP/TSV) -->
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264 <when value="file">
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265 <param type="data" format="txt" name="ena_receipt" optional="False" label="Submission receipt obtained from ENA upload tool"/>
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266 <param name="genome_fasta" type="data" optional="False" label="Select the consensus sequence assembly files or a collection of them. Use following syntax: sample_alias.fasta or sample_alias.fasta.gz" format="fasta,fasta.gz" multiple="true"/>
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267 <param name="agp_file" type="data" optional="True" label="Sequences in AGP format. Use following syntax: sample_alias.agp" format="agp" multiple="true"/>
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268 <param name="chr_list_file" type="data" optional="True" label="Chromosome List File, must be provided when the submission contains assembled chromosomes. Use following syntax: sample_alias.tsv" format="tsv" multiple="true"/>
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269 </when>
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270
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271 <!-- FORM workflow: single, user-specified submission -->
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272 <when value="form">
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273 <param name="assembly_name" type="text" optional="False" label="Assembly name"/>
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274 <param name="study_accession" type="text" optional="False" label="Study accession"/>
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275 <param name="sample_accession" type="text" optional="False" label="Sample accession"/>
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276 <param name="sequencing_platform" type="text" optional="False" label="Sequencing platform"/>
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277 <param name="description" type="text" optional="True" value="" label="Description" help="Free text description of the genome assembly (optional)"/>
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278 <param name="center_name" type="text" optional="False" label="Center name"/>
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279 <param name="genome_fasta" type="data" optional="False" label="Select the consensus sequence assembly file" format="fasta,fasta.gz"/>
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280 <param name="agp_file" type="data" optional="True" label="Sequences in AGP format." format="agp"/>
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281 <param name="chr_list_file" type="data" optional="True" label="Chromosome List File, must be provided when the submission contains assembled chromosomes." format="tsv"/>
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282 </when>
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283 </conditional>
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284
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285 <!-- Submission controls -->
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286 <param name="submit_test" type="boolean" truevalue="true" falsevalue="false" label="Submit to ENA test server" help="Uploads to the test server of ENA will not be made public and will be removed automatically in 24 hours. Performing a preliminary test upload is advised to check for errors with metadata structure. You can find these uploads at https://wwwdev.ebi.ac.uk/ena/." />
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287 <param name="dry_run" type="boolean" truevalue="true" falsevalue="false" label="Validate files and metadata but do not submit" help="Generate input files and run Webin-CLI with -validate option. If 'No' is selected then it will validate and submit (-submit flag)"/>
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288 </inputs>
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289
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290 <!--
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291 Outputs:
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292 - generated_manifests: discovered in manifests/ (via regex) for transparency
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293 - webin_cli_log: combined stdout/stderr + helper echo statements
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294 - webin_cli_outputs: tar archive of the Webin-CLI output directory
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295 -->
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296 <outputs>
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297 <collection name="generated_manifests" type="list" label="Generated manifests">
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298 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.txt" ext="txt" directory="manifests/"/>
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299 </collection>
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300 <data name="webin_cli_log" label="ENA submission log" format="txt"/>
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301 <data name="webin_cli_outputs" label="Webin cli outputs" format="tar"/>
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302
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303 </outputs>
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304
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305 <tests>
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306 <!-- Test 1: FORM workflow, no chr/AGP -->
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307 <test>
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308 <param name="submit_test" value="true" />
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309 <param name="dry_run" value="true" />
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310 <param name="assembly_type" value="isolate"/>
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311 <param name="assembly_program" value="Test assembly program"/>
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312 <param name="molecule_type" value="viral cRNA"/>
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313 <param name="coverage" value="10000"/>
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314 <conditional name="metadata_file_or_form">
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315 <param name="metadata_format" value="form"/>
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316 <param name="assembly_name" value="Test assembly name"/>
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317 <param name="study_accession" value="PRJEB49173"/>
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318 <param name="sample_accession" value="SAMEA11953908"/>
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319 <param name="sequencing_platform" value="Nanopore 0011"/>
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320 <param name="description" value="Test Description"/>
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321 <param name="center_name" value="Test center name"/>
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322 <param name="genome_fasta" value="phiX2.fasta"/>
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323 </conditional>
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324 <param name="min_gap_length" value="30"/>
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325 <output name="webin_cli_log">
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326 <assert_contents>
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327 <has_text_matching expression="ERROR: Invalid submission account user name or password\."/>
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328 </assert_contents>
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329 </output>
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330 <output_collection name="generated_manifests">
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331 <element name="generated_manifest">
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332 <assert_contents>
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333 <has_text_matching expression="(?m)^FASTA\tphiX2\.fasta\.gz$"/>
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334 <has_text_matching expression="(?m)^CHROMOSOME_LIST\t" negate="true"/>
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335 <has_text_matching expression="(?m)^AGP\t" negate="true"/>
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336 </assert_contents>
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337 </element>
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338 </output_collection>
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339 </test>
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340
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341 <!-- Test 2: FORM workflow, chr list present -->
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342 <test>
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343 <param name="submit_test" value="true" />
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344 <param name="dry_run" value="true" />
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345 <param name="assembly_type" value="isolate"/>
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346 <param name="assembly_program" value="Test assembly program"/>
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347 <param name="molecule_type" value="genomic DNA"/>
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348 <param name="coverage" value="10000"/>
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349 <conditional name="metadata_file_or_form">
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350 <param name="metadata_format" value="form"/>
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351 <param name="assembly_name" value="Test assembly name"/>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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352 <param name="study_accession" value="PRJEB49173"/>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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353 <param name="sample_accession" value="SAMEA11953908"/>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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354 <param name="sequencing_platform" value="Nanopore 0011"/>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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355 <param name="description" value="Test Description"/>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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356 <param name="center_name" value="Test center name"/>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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357 <param name="genome_fasta" value="phiX3.fasta"/>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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358 <param name="chr_list_file" value="phiX3.tsv"/>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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359 </conditional>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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360 <param name="min_gap_length" value="30"/>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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361 <output name="webin_cli_log">
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362 <assert_contents>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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363 <has_text_matching expression="ERROR: Invalid submission account user name or password\."/>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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364 </assert_contents>
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365 </output>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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366 <output_collection name="generated_manifests">
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367 <element name="generated_manifest">
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368 <assert_contents>
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369 <has_text_matching expression="(?m)^FASTA\tphiX3\.fasta\.gz$"/>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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370 <has_text_matching expression="(?m)^CHROMOSOME_LIST\tphiX3\.tsv\.gz$"/>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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371 <has_text_matching expression="(?m)^AGP\t" negate="true"/>
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372 </assert_contents>
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373 </element>
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374 </output_collection>
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375 </test>
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376
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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377 <!-- Test 3: FILE workflow, two FASTAs; one missing metadata -->
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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378 <test>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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379 <param name="submit_test" value="true" />
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380 <param name="dry_run" value="true" />
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381 <param name="assembly_type" value="isolate"/>
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382 <param name="assembly_program" value="Test assembly program"/>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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383 <param name="molecule_type" value="viral cRNA"/>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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384 <param name="coverage" value="10000"/>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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385 <conditional name="metadata_file_or_form">
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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386 <param name="metadata_format" value="file"/>
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387 <param name="ena_receipt" value="receipt_sample_nophiX2.txt"/>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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388 <param name="genome_fasta" value="phiX2.fasta.gz,sample_alias_001.fasta.gz"/>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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389 </conditional>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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390 <param name="min_gap_length" value="30"/>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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391 <output name="webin_cli_log">
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392 <assert_contents>
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393 <has_text_matching expression="Processing phiX2"/>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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394 <has_text_matching expression="No metadata found for sample phiX2"/>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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395 <has_text_matching expression="Processing sample_alias_001"/>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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396 <has_text_matching expression="Submitting manifest .*manifests/sample_alias_001\.manifest\.txt"/>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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397 <has_text_matching expression="ERROR: Invalid submission account user name or password\. Please try enclosing your password in single quotes\."/>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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398 </assert_contents>
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399 </output>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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400 <output_collection name="generated_manifests">
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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401 <element name="sample_alias_001.manifest">
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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402 <assert_contents>
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403 <has_text_matching expression="(?m)^FASTA\tsample_alias_001\.fasta\.gz$"/>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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404 <has_text_matching expression="(?m)^CHROMOSOME_LIST\t" negate="true"/>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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405 <has_text_matching expression="(?m)^AGP\t" negate="true"/>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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406 </assert_contents>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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407 </element>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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408 </output_collection>
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409 </test>
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410
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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411 <!-- Test 4: FILE workflow, single FASTA with metadata -->
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412 <test>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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413 <param name="submit_test" value="true" />
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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414 <param name="dry_run" value="true" />
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415 <param name="assembly_type" value="isolate"/>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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416 <param name="assembly_program" value="Test assembly program"/>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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417 <param name="molecule_type" value="viral cRNA"/>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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418 <param name="coverage" value="10000"/>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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419 <conditional name="metadata_file_or_form">
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420 <param name="metadata_format" value="file"/>
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421 <param name="ena_receipt" value="receipt_sample.txt"/>
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422 <param name="genome_fasta" value="sample_alias_001.fasta.gz"/>
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423 </conditional>
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424 <param name="min_gap_length" value="30"/>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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425 <output name="webin_cli_log">
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426 <assert_contents>
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427 <has_text_matching expression="Processing sample_alias_001"/>
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428 <has_text_matching expression="ERROR: Invalid submission account user name or password\. Please try enclosing your password in single quotes\."/>
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429 </assert_contents>
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430 </output>
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431 </test>
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parents:
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432
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433 <!-- Test 5: FILE workflow, AGP for phiX2 -->
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diff changeset
434 <test>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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435 <param name="submit_test" value="true" />
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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436 <param name="dry_run" value="true" />
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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437 <param name="assembly_type" value="isolate"/>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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438 <param name="assembly_program" value="Test assembly program"/>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
iuc
parents:
diff changeset
439 <param name="molecule_type" value="genomic DNA"/>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
iuc
parents:
diff changeset
440 <param name="coverage" value="10000"/>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
iuc
parents:
diff changeset
441 <conditional name="metadata_file_or_form">
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
iuc
parents:
diff changeset
442 <param name="metadata_format" value="file"/>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
iuc
parents:
diff changeset
443 <param name="ena_receipt" value="receipt_sample.txt"/>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
iuc
parents:
diff changeset
444 <param name="genome_fasta" value="phiX2.fasta"/>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
iuc
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diff changeset
445 <param name="agp_file" value="phiX2.agp"/>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
iuc
parents:
diff changeset
446 </conditional>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
iuc
parents:
diff changeset
447 <param name="min_gap_length" value="30"/>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
iuc
parents:
diff changeset
448 <output name="webin_cli_log">
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
iuc
parents:
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449 <assert_contents>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
iuc
parents:
diff changeset
450 <has_text_matching expression="Processing phiX2"/>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
iuc
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451 <has_text_matching expression="ERROR: Invalid submission account user name or password\. Please try enclosing your password in single quotes\."/>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
iuc
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452 </assert_contents>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
iuc
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diff changeset
453 </output>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
iuc
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diff changeset
454 <output_collection name="generated_manifests">
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
iuc
parents:
diff changeset
455 <element name="phiX2.manifest">
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
iuc
parents:
diff changeset
456 <assert_contents>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
iuc
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diff changeset
457 <has_text_matching expression="(?m)^FASTA\tphiX2\.fasta\.gz$"/>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
iuc
parents:
diff changeset
458 <has_text_matching expression="(?m)^AGP\tphiX2\.agp$"/>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
iuc
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diff changeset
459 <has_text_matching expression="(?m)^CHROMOSOME_LIST\t" negate="true"/>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
iuc
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diff changeset
460 </assert_contents>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
iuc
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diff changeset
461 </element>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
iuc
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diff changeset
462 </output_collection>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
iuc
parents:
diff changeset
463 </test>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
iuc
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464
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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465 <!-- Test 6: FILE workflow, chr list for phiX3 + extra fasta -->
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
iuc
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466 <test>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
iuc
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467 <param name="submit_test" value="true" />
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
iuc
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diff changeset
468 <param name="dry_run" value="true" />
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
iuc
parents:
diff changeset
469 <param name="assembly_type" value="isolate"/>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
iuc
parents:
diff changeset
470 <param name="assembly_program" value="Test assembly program"/>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
iuc
parents:
diff changeset
471 <param name="molecule_type" value="genomic DNA"/>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
iuc
parents:
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472 <param name="coverage" value="10000"/>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
iuc
parents:
diff changeset
473 <conditional name="metadata_file_or_form">
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
iuc
parents:
diff changeset
474 <param name="metadata_format" value="file"/>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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475 <param name="ena_receipt" value="receipt_sample_phiX3.txt"/>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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476 <param name="genome_fasta" value="phiX3.fasta,phiX2.fasta.gz"/>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
iuc
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477 <param name="chr_list_file" value="phiX3.tsv"/>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
iuc
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478 </conditional>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
iuc
parents:
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479 <param name="min_gap_length" value="30"/>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
iuc
parents:
diff changeset
480 <output name="webin_cli_log">
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
iuc
parents:
diff changeset
481 <assert_contents>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
iuc
parents:
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482 <has_text_matching expression="Processing phiX3"/>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
iuc
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483 <has_text_matching expression="ERROR: Invalid submission account user name or password\. Please try enclosing your password in single quotes\."/>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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484 </assert_contents>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
iuc
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485 </output>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
iuc
parents:
diff changeset
486 <output_collection name="generated_manifests">
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
iuc
parents:
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487 <element name="phiX2.manifest">
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
iuc
parents:
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488 <assert_contents>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
iuc
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diff changeset
489 <has_text_matching expression="(?m)^FASTA\tphiX2\.fasta\.gz$"/>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
iuc
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490 <has_text_matching expression="(?m)^CHROMOSOME_LIST\t" negate="true"/>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
iuc
parents:
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491 <has_text_matching expression="(?m)^AGP\t" negate="true"/>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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492 </assert_contents>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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parents:
diff changeset
493 </element>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
iuc
parents:
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494 <element name="phiX3.manifest">
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
iuc
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495 <assert_contents>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
iuc
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496 <has_text_matching expression="(?m)^FASTA\tphiX3\.fasta\.gz$"/>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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497 <has_text_matching expression="(?m)^CHROMOSOME_LIST\tphiX3\.tsv\.gz$"/>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
iuc
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498 <has_text_matching expression="(?m)^AGP\t" negate="true"/>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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499 </assert_contents>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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500 </element>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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501 </output_collection>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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502 </test>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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503 </tests>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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504
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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505
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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506
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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507 <!-- Help text + citation -->
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
iuc
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508 <help><![CDATA[
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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509 This tool is a wrapper for the ENA Webin CLI submission tool (https://ena-docs.readthedocs.io/en/latest/submit/general-guide/webin-cli.html).
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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diff changeset
510
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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511 .. class:: warningmark
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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parents:
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512
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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513 The ENA upload tool won't work unless you have provided an ENA Webin ID in User > Preferences > Manage Information > ENA Webin account details.]]></help>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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514
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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515 <citations>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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parents:
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516 <citation type="doi">10.1093/nar/gkac1051</citation>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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517 </citations>
7f669682f4ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
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518 </tool>