| Previous changeset 1:f24eb2f2cb0c (2021-05-18) Next changeset 3:7d751b5943b0 (2022-02-22) |
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Commit message:
Uploaded |
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modified:
ena_consensus_submit.xml |
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added:
test-data/phiX2.fasta |
| b |
| diff -r f24eb2f2cb0c -r 1ecd8ce07db4 ena_consensus_submit.xml --- a/ena_consensus_submit.xml Tue May 18 21:00:09 2021 +0000 +++ b/ena_consensus_submit.xml Fri Feb 04 15:52:45 2022 +0000 |
| [ |
| b'@@ -1,6 +1,6 @@\n-<tool id="ena_consensus_submit" name="Submit consensus sequence to ENA" version="0.1.0" python_template_version="3.5">\n+<tool id="ena_consensus_submit" name="Submit consensus sequence to ENA" version="@VERSION@" python_template_version="3.5">\n <macros>\n- <token name="@VERSION@">3.7.0</token>\n+ <token name="@VERSION@">4.3.0</token>\n </macros>\n <requirements>\n <requirement type="package" version="@VERSION@">ena-webin-cli</requirement>\n@@ -8,16 +8,22 @@\n <requirement type="package" version="5.3">pyyaml</requirement>\n </requirements>\n <command detect_errors="exit_code"><![CDATA[\n+#if $test_submit == "True":\n+ #set $credentials=\'./test_fake_path\';\n+ touch $credentials;\n+ echo "username:test_user" >> $credentials;\n+ echo "password:test_password" >> $credentials;\n+#end if\n \n-webin_id=`grep \'username\' $credentials | cut -f2,2`;\n+webin_id=`grep \'username\' $credentials | cut -d\':\' -f2,2`;\n if [ "\\$webin_id" = "" ]; then\n ## No credentials in user defined preferences \n ## Fallback to global defined credentials (if exist) \n #import os\n #if os.path.isfile(os.environ.get(\'GALAXY_ENA_SECRETS\', \'\')):\n credentials_path=\\${GALAXY_ENA_SECRETS}; \n- webin_id=`grep \'username\' \\$GALAXY_ENA_SECRETS | cut -d\' \' -f2,2`;\n- password=`grep \'password\' \\$GALAXY_ENA_SECRETS | cut -d\' \' -f2,2`;\n+ webin_id=`grep \'username\' \\$GALAXY_ENA_SECRETS | cut -d\':\' -f2,2` | sed -e \'s/^[[:space:]]*//\'`;\n+ password=`grep \'password\' \\$GALAXY_ENA_SECRETS | cut -d\':\' -f2,2` | sed -e \'s/^[[:space:]]*//\'`;\n if [ "\\$webin_id" = "" ]; then\n echo "No global credentials defined. Check your GALAXY_ENA_SECRETS file or set your credentials via: User -> Preferences -> Manage Information";\n exit 1;\n@@ -27,23 +33,22 @@\n exit 1;\n #end if\n else\n- password=`grep \'password\' $credentials | cut -f2,2`;\n+ password=`grep \'password\' $credentials | cut -d\':\' -f2,2`;\n fi;\n \n-## if it is still running at this point then the webin_id and password are set\n \n-## create a manifaste base file with the parameters that are identical for all sequences that will be submited (if submitting a multifasta)\n+## create a manifest base file with the parameters that are identical for all sequences that will be submited (if submitting a multifasta)\n #set $manifest_base = \'manifest_base.tab\'\n mkdir manifests;\n mkdir fasta;\n \n-echo -e "ASSEMBLY_TYPE\\t$assembly_type" >> $manifest_base;\n-echo -e "COVERAGE\\t$coverage" >> $manifest_base;\n-echo -e "PROGRAM\\t$assembly_program" >> $manifest_base;\n+echo -e \'ASSEMBLY_TYPE\\t$assembly_type\' > $manifest_base;\n+echo -e \'COVERAGE\\t$coverage\' >> $manifest_base;\n+echo -e \'PROGRAM\\t$assembly_program\' >> $manifest_base;\n #if $min_gap_length:\n- echo -e "MINGAPLENGTH\\t$min_gap_length" >> $manifest_base;\n+ echo -e \'MINGAPLENGTH\\t$min_gap_length\' >> $manifest_base;\n #end if\n-echo -e "MOLECULETYPE\\t$molecule_type" >> $manifest_base;\n+echo -e \'MOLECULETYPE\\t$molecule_type\' >> $manifest_base;\n \n #if $metadata_file_or_form.metadata_format == "file":\n ## process the input tables, this creates an intermediate file with information\n@@ -51,17 +56,18 @@\n center_name=`grep \'center_name\' $metadata_file_or_form.ena_receipt | cut -f2,2 | tr -d \'\\n\'`;\n #else:\n #set $generated_manifest=\'./manifests/generated_manifest.txt\'\n- cp $manifest_base $generated_manifest\n- $study_id = $metadata_file_or_form.study_accession\n- $sample_id = $metadata_file_or_form.sample_accession\n- echo "STUDY\\t$study_id" > $generated_manifest;\n- echo "SAMPLE\\t$sample_id" >> $generated_manifest;\n- center_name=$metadata_file_or_form.center_name;\n- echo "ASSEMBLY_NAME\\t$metadata_file_or_form.assembly_name" >> $generated_manifest;\n- echo "PLATFORM\\t$platform_name" >> $generated_manifest;\n+ cp $manifest_base $generated_manifest;\n+ #set $study_id = $metadata_file_or_form.study_accession\n+ #set $sample_id = $metadata_file_or_'..b'true" falsevalue="false" label="Validate files and metadata but do not submit" help="Generate input files and run Webin-CLI with -validate option. If \'No\' is selected then it will validate and submit (-submit flag)"/>\n <param name="genome_fasta" type="data" label="Select the consensus sequence assembly file" format="fasta"/>\n <param name="assembly_type" type="select" label="Assembly type">\n <option value="clone">Clone</option>\n@@ -127,8 +140,8 @@\n <param name="coverage" type="float" optional="False" value="10000" label="Coverage"/>\n <conditional name="metadata_file_or_form">\n <param name="metadata_format" type="select" label="Select the method to load study and sample metadata">\n- <option value="file" selected="True">I used Galaxy ENA upload tool for raw data submission, parse my submission receipt</option>\n- <option value="form">Fill in required metadata for linking</option>\n+ <option value="form" selected="True">Fill in required submission metadata</option>\n+ <option value="file">(Beta) I used the Galaxy ENA upload tool to submit the raw data: parse the received submission receipt</option>\n </param>\n <when value="file">\n <param type="data" format="txt" name="ena_receipt" label="Submission receipt obtained from ENA upload tool"/>\n@@ -146,15 +159,40 @@\n </inputs>\n <outputs>\n <collection name="generated_manifests" type="list" label="Generated manifests">\n- <!--<discover_datasets pattern="__name_and_ext__" directory="manifests" />-->\n- <discover_datasets pattern="(?P<designation>.+)\\.manifest\\.txt$" ext="txt" directory="manifests" />\n+ <discover_datasets pattern="(?P<designation>.+)\\.txt" ext="txt" directory="manifests/"/>\n </collection>\n- <collection name="manifests_reports" type="list" label="Manifests reports">\n- <!--[><discover_datasets pattern="__name_and_ext__" directory="manifests" /><]-->\n- <discover_datasets pattern="(?P<designation>.+)\\.manifest\\.txt\\.report$" ext="txt" directory="manifests" />\n- </collection>\n- <data name="webin_cli_report" label="ENA submission receipt" format="txt" from_work_dir="manifests/webin-cli.report"/>\n+ <data name="webin_cli_log" label="ENA submission log" format="txt"/>\n+ <data name="webin_cli_outputs" label="Webin cli outputs" format="tar"/>\n+ \n </outputs>\n+ <tests>\n+ <test>\n+ <param name="submit_test" value="true" />\n+ <param name="dry_run" value="true" />\n+ <param name="test_submit" value="True" />\n+ <param name="genome_fasta" value="phiX2.fasta"/>\n+ <param name="assembly_type" value="isolate"/>\n+ <param name="assembly_program" value="Test assembly program"/>\n+ <param name="molecule_type" value="viral cRNA"/>\n+ <param name="coverage" value="10000"/>\n+ <conditional name="metadata_file_or_form">\n+ <param name="metadata_format" value="form"/>\n+ <param name="assembly_name" value="Test assembly name"/>\n+ <param name="study_accession" value="PRJEB49173"/>\n+ <param name="sample_accession" value="SAMEA11953908"/>\n+ <param name="sequencing_platform" value="Nanopore 0011"/>\n+ <param name="description" value="Test Description"/>\n+ <param name="center_name" value="Test center name"/>\n+ </conditional>\n+ <param name="min_gap_length" value="30"/>\n+ <output name="webin_cli_log">\n+ <assert_contents>\n+ <has_n_lines n="4"/>\n+ <has_text_matching expression="ERROR: Invalid submission account user name or password."/>\n+ </assert_contents>\n+ </output>\n+ </test>\n+ </tests>\n <help><![CDATA[\n TODO: Fill in help.\n ]]></help>\n' |
| b |
| diff -r f24eb2f2cb0c -r 1ecd8ce07db4 test-data/phiX2.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/phiX2.fasta Fri Feb 04 15:52:45 2022 +0000 |
| b |
| @@ -0,0 +1,90 @@ +>phiX174 +GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAAAAATTATCTT +GATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAA +ATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTG +TCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTA +GATATGAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATC +TGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTT +TCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTT +CGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCT +TGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCG +TCATTGCTTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTAC +GGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTA +CGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGTGCAGAAGGAG +TGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACT +AAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGC +CCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCA +TCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGAC +TCCTTCGAGATGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTA +CTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAA +GGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATATTGACCATGCCGCTTTTCTT +GGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACA +ACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGC +TCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTT +TCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGC +ATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCGTGATGTTATTTCTTCATTTGGAGGTAAAAC +CTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTT +GATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGC +CGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGAC +TAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTG +TATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGT +TTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGA +AGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGAT +TATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTT +ATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAAC +GCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCGAAGCGCGGTAGGTTTTCTGC +TTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTCGCCATAATTCAAACTTTTTTTCTGATAAGCTGGT +TCTCACTTCTGTTACTCCAGCTTCTTCGGCACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTA +TATTTTGATAGTTTGACGGTTAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTG +TCAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGC +CTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGTTTATCCTTTG +AATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTATTGACGTCCTTCCCCGTACGC +CGGGCAATAATGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCTACTAAATGCCGCGGATTGGT +TTCGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTG +CTATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAA +AGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCT +GGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTG +GTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGA +TAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTAT +CTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGG +TTGACGCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGA +GATGCAAAATGAGACTCAAAAAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGAC +CAGGTATATGCACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTA +TGGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAAGCTCA +AACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGAC +TTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCATATTGGCGCTACTGCAAAGGATATTT +CTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGA +TACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCG +TCAGGATTGACACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTT +CTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTAT +TGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGC +ATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATG +TTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGA +ATTGGCACAATGCTACAATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGG +GACGAAAAATGGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCC +CTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCAAGATT +GCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTACTATTCAGCGTTTGATGAATGCAATGCGACAG +GCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCACGTTGGCTGACGACCGATTAGAGGCGTTTT +ATGATAATCCCAATGCTTTGCGTGACTATTTTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCG +CAAGGCTAATGATTCACACGCCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTACAGCTAATGGC +CGTCTTCATTTCCATGCGGTGCATTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTC +GTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATGCCCAT +CGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAG +CCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTAAATACGTTAACAAAAAGTCAGATA +TGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACT +TCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAATGACAAATCTG +TCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGATATTGAAGC +AGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTTTGGCGGCGCAACC +TGTGACGACAAATCTGCTCAAATTTATGCGCGCTTCGATAAAAATGATTGGCGTATCCAACCTGCA +>phi2174 +GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAAAAATTATCTT +GATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAA +ATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTG +TCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTA +GATATGAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATC +TGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTT +TCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTT +CGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCT +TGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCG +TCATTGCTTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTAC +GGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTA |