Mercurial > repos > iuc > ena_webin_cli

annotate ena_webin_cli.xml @ 0:c9f87770ba8f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
author iuc
date Tue, 05 Aug 2025 11:53:57 +0000
parents
children 93fac0ae859f
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c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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">
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
iuc
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2 <description>Submission of consensus sequences to the European Nucleotide Archive (ENA)</description>
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
iuc
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3 <macros>
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
iuc
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4 <token name="@TOOL_VERSION@">8.1.1</token>
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
iuc
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5 <token name="@VERSION_SUFFIX@">0</token>
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
iuc
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6 </macros>
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
iuc
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7 <requirements>
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
iuc
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8 <requirement type="package" version="@TOOL_VERSION@">ena-webin-cli</requirement>
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
iuc
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9 <requirement type="package" version="1.76">biopython</requirement>
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
iuc
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10 <requirement type="package" version="5.3">pyyaml</requirement>
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
iuc
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11 </requirements>
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
iuc
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12 <command detect_errors="exit_code"><![CDATA[
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
iuc
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13 #if $dry_run == "True":
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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14 #set $credentials='./test_fake_path';
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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15 touch $credentials;
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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16 echo "username:test_user" >> $credentials;
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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17 echo "password:test_password" >> $credentials;
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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18 #end if
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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19
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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20 webin_id=`grep 'username' $credentials | cut -d':' -f2,2`;
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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21 if [ "\$webin_id" = "" ]; then
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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22 ## No credentials in user defined preferences
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
iuc
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23 ## Fallback to global defined credentials (if exist)
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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24 #import os
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
iuc
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25 #if os.path.isfile(os.environ.get('GALAXY_ENA_SECRETS', '')):
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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26 credentials_path=\${GALAXY_ENA_SECRETS};
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
iuc
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27 webin_id=`grep 'username' \$GALAXY_ENA_SECRETS | cut -d':' -f2,2` | sed -e 's/^[[:space:]]*//'`;
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
iuc
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28 password=`grep 'password' \$GALAXY_ENA_SECRETS | cut -d':' -f2,2` | sed -e 's/^[[:space:]]*//'`;
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
iuc
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29 if [ "\$webin_id" = "" ]; then
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
iuc
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30 echo "No global credentials defined. Check your GALAXY_ENA_SECRETS file or set your credentials via: User -> Preferences -> Manage Information";
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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31 exit 1;
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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32 fi;
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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33 #else:
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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34 echo "No ENA credentials defined. Set your credentials via: User -> Preferences -> Manage Information";
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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35 exit 1;
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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36 #end if
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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37 else
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
iuc
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38 password=`grep 'password' $credentials | cut -d':' -f2,2`;
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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39 fi;
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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40
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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41
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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42 ## create a manifest base file with the parameters that are identical for all sequences that will be submited (if submitting a multifasta)
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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43 #set $manifest_base = 'manifest_base.tab'
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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44 mkdir manifests;
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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45 mkdir fasta;
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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46
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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47 echo -e 'ASSEMBLY_TYPE\t$assembly_type' > $manifest_base;
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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48 echo -e 'COVERAGE\t$coverage' >> $manifest_base;
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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49 echo -e 'PROGRAM\t$assembly_program' >> $manifest_base;
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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50 #if $min_gap_length:
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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51 echo -e 'MINGAPLENGTH\t$min_gap_length' >> $manifest_base;
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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52 #end if
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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53 echo -e 'MOLECULETYPE\t$molecule_type' >> $manifest_base;
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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54
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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55 #if $metadata_file_or_form.metadata_format == "file":
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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56 #import re
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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57 #for $file in $metadata_file_or_form.genome_fasta:
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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58 #if $file.is_of_type('fasta'):
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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59 #set $full_name = $file.element_identifier + '.gz'
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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60 gzip -c '$file' > './fasta/$full_name';
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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61 #else:
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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62 ln -s '$file' './fasta/$file.element_identifier';
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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63 #end if
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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64
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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65 #end for
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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66 ## process the input tables, this creates an intermediate file with information
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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67 python3 '$__tool_directory__/process_input.py' $metadata_file_or_form.ena_receipt $genome_fasta_files './manifests' $manifest_base >> $webin_cli_log;
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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68 center_name=`grep 'center_name' $metadata_file_or_form.ena_receipt | cut -f2,2 | tr -d '\n'`;
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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69 #else:
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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70 #set $generated_manifest='./manifests/generated_manifest.txt'
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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71 cp $manifest_base $generated_manifest;
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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72 #set $study_id = $metadata_file_or_form.study_accession
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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73 #set $sample_id = $metadata_file_or_form.sample_accession
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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74 echo -e 'STUDY\t$study_id' >> $generated_manifest;
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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75 echo -e 'SAMPLE\t$sample_id' >> $generated_manifest;
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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76 center_name='$metadata_file_or_form.center_name';
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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77 echo -e 'NAME\t$metadata_file_or_form.assembly_name' >> $generated_manifest;
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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78 echo -e 'PLATFORM\t$metadata_file_or_form.sequencing_platform' >> $generated_manifest;
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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79 #if $metadata_file_or_form.genome_fasta.is_of_type('fasta'):
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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80 gzip -c $metadata_file_or_form.genome_fasta > consensus.fasta.gz;
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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81 #else:
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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82 ln -s $metadata_file_or_form.genome_fasta consensus.fasta.gz;
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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83 #end if
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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84 echo -e 'FASTA\tconsensus.fasta.gz' >> $generated_manifest;
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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85 #end if
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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86
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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87 #set $outputs_dir = 'outputs'
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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88 mkdir $outputs_dir;
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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89 #if $metadata_file_or_form.metadata_format == "file":
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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90 ## iterate over the list of manifest - fasta generated by the process_input
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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91 ## in case of errors, this list is empty
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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92 while read line; do
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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93 manifest=`echo \$line | cut -d' ' -f1,1`;
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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94 echo "Submitting manifest \$manifest" >> $webin_cli_log;
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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95 ena-webin-cli
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96 -context genome
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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97 -userName "'\$webin_id'"
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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98 -password "'\$password'"
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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99 -centerName "'\$center_name'"
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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100 -manifest \$manifest
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101 -inputDir './fasta'
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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102 #if $submit_test == "true":
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103 -test
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104 #end if
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105 #if $dry_run == "true":
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106 -validate
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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107 #else:
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108 -submit
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109 #end if
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110 -outputDir $outputs_dir
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111 >> $webin_cli_log;
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112 done < submit_list.tab;
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113
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114 #else:
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115 ena-webin-cli
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116 #if $submit_test == "true":
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117 -test
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118 #end if
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119 #if $dry_run == "true":
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120 -validate
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121 #else:
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122 -submit
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123 #end if
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124 -context genome
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125 -manifest $generated_manifest
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126 -password "'\$password'"
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127 -userName "'\$webin_id'"
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128 -inputDir "./"
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129 -centerName "'\$center_name'"
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130 -outputDir $outputs_dir
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131 >> $webin_cli_log ;
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132 #end if
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133 tar -cf $webin_cli_outputs $outputs_dir ;
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134 ]]></command>
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135 <configfiles>
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136 <configfile name="credentials"><![CDATA[
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137 #set $webin_id = $__user__.extra_preferences.get('ena_webin_account|webin_id', "").strip()
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138 #set $password = $__user__.extra_preferences.get('ena_webin_account|password', "").strip()
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139 #if $webin_id != "":
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140 username:$webin_id
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141 password:$password
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142 #end if
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143
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144 ]]></configfile>
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145 <configfile name="genome_fasta_files">
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146 #import json
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147 #import re
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148 #if $metadata_file_or_form.metadata_format == "file":
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149 #set $fasta_files_list = list()
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150 #for $file in $metadata_file_or_form.genome_fasta:
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151 $fasta_files_list.append(str($file.element_identifier))
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152 #end for
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153 #echo json.dumps($fasta_files_list)
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154 #end if
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155 </configfile>
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156 </configfiles>
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157 <inputs>
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158 <param name="assembly_type" type="select" label="Assembly type">
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159 <option value="clone">Clone</option>
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160 <option value="isolate">Isolate</option>
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161 <option value="COVID-19 outbreak">COVID-19 outbreak</option>
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162 </param>
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163 <param name="assembly_program" type="text" optional="False" label="Assembly program"/>
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164 <param name="molecule_type" type="select" label="Molecule type">
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165 <option value="genomic RNA" selected="True">genomic RNA</option>
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166 <option value="viral cRNA">viral cRNA</option>
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167 <option value="genomic DNA">genomic DNA</option>
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168 </param>
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169 <param name="coverage" type="float" optional="False" value="10000" label="Coverage"/>
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170 <param name="min_gap_length" type="text" optional="True" label="Minimum gap length (optional)"/>
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171 <conditional name="metadata_file_or_form">
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172 <param name="metadata_format" type="select" label="Select the method to load study and sample metadata">
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173 <option value="form" selected="True">Fill in required submission metadata</option>
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174 <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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175 </param>
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176 <when value="file">
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177 <param type="data" format="txt" name="ena_receipt" label="Submission receipt obtained from ENA upload tool"/>
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178 <param name="genome_fasta" type="data" label="Select the consensus sequence assembly files or a collection of them" format="fasta,fasta.gz" multiple="true"/>
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179 </when>
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180 <when value="form">
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181 <param name="assembly_name" type="text" optional="False" label="Assembly name"/>
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182 <param name="study_accession" type="text" optional="False" label="Study accession"/>
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183 <param name="sample_accession" type="text" optional="False" label="Sample accession"/>
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184 <param name="sequencing_platform" type="text" optional="False" label="Sequencing platform"/>
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185 <param name="description" type="text" optional="True" value="" label="Description" help="Free text description of the genome assembly (optional)"/>
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186 <param name="center_name" type="text" optional="False" label="Center name"/>
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187 <param name="genome_fasta" type="data" label="Select the consensus sequence assembly file" format="fasta,fasta.gz"/>
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188 </when>
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189 </conditional>
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190 <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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191 <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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192 </inputs>
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193 <outputs>
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194 <collection name="generated_manifests" type="list" label="Generated manifests">
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195 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.txt" ext="txt" directory="manifests/"/>
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196 </collection>
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197 <data name="webin_cli_log" label="ENA submission log" format="txt"/>
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198 <data name="webin_cli_outputs" label="Webin cli outputs" format="tar"/>
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199
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200 </outputs>
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201 <tests>
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202 <test>
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203 <param name="submit_test" value="true" />
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204 <param name="dry_run" value="true" />
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205 <param name="assembly_type" value="isolate"/>
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206 <param name="assembly_program" value="Test assembly program"/>
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207 <param name="molecule_type" value="viral cRNA"/>
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208 <param name="coverage" value="10000"/>
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209 <conditional name="metadata_file_or_form">
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210 <param name="metadata_format" value="form"/>
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211 <param name="assembly_name" value="Test assembly name"/>
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212 <param name="study_accession" value="PRJEB49173"/>
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213 <param name="sample_accession" value="SAMEA11953908"/>
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214 <param name="sequencing_platform" value="Nanopore 0011"/>
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215 <param name="description" value="Test Description"/>
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216 <param name="center_name" value="Test center name"/>
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217 <param name="genome_fasta" value="phiX2.fasta"/>
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218 </conditional>
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219 <param name="min_gap_length" value="30"/>
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220 <output name="webin_cli_log">
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221 <assert_contents>
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222 <has_n_lines n="4"/>
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223 <has_text_matching expression="ERROR: Invalid submission account user name or password."/>
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224 </assert_contents>
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225 </output>
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226 </test>
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227 <test>
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228 <param name="submit_test" value="true" />
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229 <param name="dry_run" value="true" />
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230 <param name="assembly_type" value="isolate"/>
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231 <param name="assembly_program" value="Test assembly program"/>
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232 <param name="molecule_type" value="viral cRNA"/>
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233 <param name="coverage" value="10000"/>
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234 <conditional name="metadata_file_or_form">
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235 <param name="metadata_format" value="file"/>
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236 <param name="ena_receipt" value="receipt_sample_noPhiX.txt"/>
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237 <param name="genome_fasta" value="phiX2.fasta.gz,sample_alias_001.fasta.gz"/>
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238 </conditional>
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239 <param name="min_gap_length" value="30"/>
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240 <output name="webin_cli_log">
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241 <assert_contents>
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242 <has_text_matching expression="Processing phiX2"/>
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243 <has_text_matching expression="No metadata found for sample phiX2"/>
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244 <has_text_matching expression="Processing sample_alias_001"/>
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245 <has_text_matching expression="Submitting manifest ./manifests/sample_alias_001.manifest.txt"/>
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246 <has_text_matching expression="ERROR: Invalid submission account user name or password. Please try enclosing your password in single quotes."/>
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247 </assert_contents>
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248 </output>
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249 </test>
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250 <test>
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251 <param name="submit_test" value="true" />
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252 <param name="dry_run" value="true" />
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253 <param name="assembly_type" value="isolate"/>
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254 <param name="assembly_program" value="Test assembly program"/>
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255 <param name="molecule_type" value="viral cRNA"/>
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256 <param name="coverage" value="10000"/>
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257 <conditional name="metadata_file_or_form">
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258 <param name="metadata_format" value="file"/>
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259 <param name="ena_receipt" value="receipt_sample.txt"/>
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260 <param name="genome_fasta" value="sample_alias_001.fasta.gz"/>
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261 </conditional>
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262 <param name="min_gap_length" value="30"/>
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263 <output name="webin_cli_log">
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264 <assert_contents>
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265 <has_text_matching expression="ERROR: Invalid submission account user name or password. Please try enclosing your password in single quotes."/>
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266 </assert_contents>
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267 </output>
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268 </test>
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269 </tests>
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270 <help><![CDATA[
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271 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).
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272
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273 .. class:: warningmark
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274
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275 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>
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276 <citations>
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277 <citation type="doi">10.1093/nar/gkac1051</citation>
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278 </citations>
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279 </tool>