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comparison ena_upload.xml @ 2:9e2df763086c draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
author iuc
date Thu, 15 Jul 2021 20:12:34 +0000
parents 57251c760cab
children 59bb6d34fca6
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1:57251c760cab 2:9e2df763086c
1 <tool id="ena_upload" name="ENA Upload tool" version="0.3.1" profile="20.01" license="MIT"> 1 <tool id="ena_upload" name="ENA Upload tool" version="0.3.2" profile="20.01" license="MIT">
2 <macros> 2 <macros>
3 <token name="@VERSION@">0.2.7</token> 3 <token name="@VERSION@">0.3.1</token>
4 <import>samples_macros.xml</import> 4 <import>samples_macros.xml</import>
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
7 <requirement type="package" version="@VERSION@">ena-upload-cli</requirement> 7 <requirement type="package" version="@VERSION@">ena-upload-cli</requirement>
8 <requirement type="package" version="1.2.0">xlrd</requirement> 8 <requirement type="package" version="1.2.0">xlrd</requirement>
45 ln -s '$action_options.input_format_conditional.experiments_users_table' $experiments_table_path && 45 ln -s '$action_options.input_format_conditional.experiments_users_table' $experiments_table_path &&
46 ln -s '$action_options.input_format_conditional.studies_users_table' $studies_table_path && 46 ln -s '$action_options.input_format_conditional.studies_users_table' $studies_table_path &&
47 ln -s '$action_options.input_format_conditional.runs_users_table' $runs_table_path && 47 ln -s '$action_options.input_format_conditional.runs_users_table' $runs_table_path &&
48 ln -s '$action_options.input_format_conditional.samples_users_table' $samples_table_path && 48 ln -s '$action_options.input_format_conditional.samples_users_table' $samples_table_path &&
49 #end if 49 #end if
50
51 50
52 #if $action_options.test_submit_parameters.dry_run == "false" and $action_options.test_submit == "False": 51 #if $action_options.test_submit_parameters.dry_run == "false" and $action_options.test_submit == "False":
53 webin_id=`grep 'username' $credentials`; 52 webin_id=`grep 'username' $credentials`;
54 if [ "\$webin_id" = "" ]; then 53 if [ "\$webin_id" = "" ]; then
55 ## No credentials in user defined preferences 54 ## No credentials in user defined preferences
290 </output> 289 </output>
291 <output name="samples_table_out"> 290 <output name="samples_table_out">
292 <assert_contents> 291 <assert_contents>
293 <has_n_lines n="5"/> 292 <has_n_lines n="5"/>
294 <has_n_columns n="18"/> 293 <has_n_columns n="18"/>
295 <has_line_matching expression="alias\tstatus\taccession\ttitle\tscientific_name\ttaxon_id\tsample_description\tcollection_date\tgeographic_location\thost_common_name\thost_subject_id\thost_health_state\thost_sex\thost_scientific_name\tcollector_name\tcollecting_institution\tisolate\tsubmission_date"/> 294 <has_line_matching expression="alias\ttitle\tscientific_name\tsample_description\tstatus\taccession\ttaxon_id\tsubmission_date\tgeographic_location\thost_common_name\thost_subject_id\thost_health_state\thost_sex\thost_scientific_name\tcollector_name\tcollecting_institution\tisolate\tcollection_date"/>
295 </assert_contents>
296 </output>
297 <output name="runs_table_out">
298 <assert_contents>
299 <has_n_lines n="5"/>
300 <has_n_columns n="8"/>
301 <has_line_matching expression="alias\tstatus\taccession\texperiment_alias\tfile_name\tfile_format\tfile_checksum\tsubmission_date"/>
302 <has_line_matching expression="r_(.*)_026\tadd\tena_run_accession\te_(.*)_026\tC026_exp5_clean.fastq.gz\tfastq\tfile_checksum\tsubmission_date_ENA"/>
303 </assert_contents>
304 </output>
305 </test>
306 <!--Test excel input of VIRAL samples with extended columns-->
307 <test>
308 <conditional name="action_options">
309 <param name="action" value="add"/>
310 <section name="test_submit_parameters">
311 <param name="submit_dev" value="false" />
312 <param name="dry_run" value="true" />
313 </section>
314 <conditional name="input_format_conditional">
315 <param name="input_format" value="excel_tables"/>
316 <param name="viral_submission" value="True"/>
317 <param name="xlsx_file" value="metadata_test_viral_optional_columns.xlsx"/>
318 <conditional name="run_input_format_conditional">
319 <param name="run_input_format" value="multiple_selection_list"/>
320 <param name="data" value="sample.fq"/>
321 </conditional>
322 </conditional>
323 </conditional>
324 <param name="center" value="Some research center"/>
325 <output name="experiments_table_out">
326 <assert_contents>
327 <has_n_lines n="5"/>
328 <has_n_columns n="17"/>
329 <has_line_matching expression="alias\tstatus\taccession\ttitle\tstudy_alias\tsample_alias\tdesign_description\tlibrary_name\tlibrary_strategy\tlibrary_source\tlibrary_selection\tlibrary_layout\tinsert_size\tlibrary_construction_protocol\tplatform\tinstrument_model\tsubmission_date" />
330 <has_line_matching expression="e_(.*)_026\tadd\taccession_ena\tNanopore sequencing\tSARS-CoV-2_genomes_01\ts_(.*)"/>
331 </assert_contents>
332 </output>
333 <output name="studies_table_out">
334 <assert_contents>
335 <has_n_lines n="2"/>
336 <has_n_columns n="8"/>
337 <has_line_matching expression="alias\tstatus\taccession\ttitle\tstudy_type\tstudy_abstract\tpubmed_id\tsubmission_date"/>
338 <has_line_matching expression="SARS-CoV-2_genomes_01\tadd\tENA_accession\tWhole-genome sequencing of SARS-CoV-2 from Covid-19 patients\tWhole Genome Sequencing\tWhole-genome sequences of SARS-CoV-2 from oro-pharyngeal swabs obtained from Covid-19 patients(.*)"/>
339 </assert_contents>
340 </output>
341 <output name="samples_table_out">
342 <assert_contents>
343 <has_n_lines n="5"/>
344 <has_n_columns n="42"/>
345 <has_line_matching expression="alias\ttitle\tscientific_name\tsample_description\tstatus\taccession\ttaxon_id\tsubmission_date\tgeographic_location\thost_common_name\thost_subject_id\thost_health_state\thost_sex\thost_scientific_name\tcollector_name\tcollecting_institution\tisolate\tcollection_date\tgeographic_location_latitude\tgeographic_location_longitude\tsample_capture_status\thost_disease_outcome\thost_age\tvirus_identifier\treceipt_date\tdefinition_for_seropositive_sample\tserotype\thost_habitat\tisolation_source_host_associated\thost_behaviour\tisolation_source_non_host_associated\tsubject_exposure\tsubject_exposure_duration\ttype_exposure\tpersonal_protective_equipment\thospitalisation\tillness_duration\tillness_symptoms\tsample_storage_conditions\tstrain\thost_description\tgravidity"/>
296 </assert_contents> 346 </assert_contents>
297 </output> 347 </output>
298 <output name="runs_table_out"> 348 <output name="runs_table_out">
299 <assert_contents> 349 <assert_contents>
300 <has_n_lines n="5"/> 350 <has_n_lines n="5"/>
339 </output> 389 </output>
340 <output name="samples_table_out"> 390 <output name="samples_table_out">
341 <assert_contents> 391 <assert_contents>
342 <has_n_lines n="5"/> 392 <has_n_lines n="5"/>
343 <has_n_columns n="8"/> 393 <has_n_columns n="8"/>
344 <has_line_matching expression="alias\tstatus\taccession\ttitle\tscientific_name\ttaxon_id\tsample_description\tsubmission_date"/> 394 <has_line_matching expression="alias\ttitle\tscientific_name\tsample_description\tstatus\taccession\ttaxon_id\tsubmission_date"/>
345 </assert_contents> 395 </assert_contents>
346 </output> 396 </output>
347 <output name="runs_table_out"> 397 <output name="runs_table_out">
348 <assert_contents> 398 <assert_contents>
349 <has_n_lines n="5"/> 399 <has_n_lines n="5"/>
626 </tests> 676 </tests>
627 <help><![CDATA[ 677 <help><![CDATA[
628 This is a wrapper for the ENA upload tool in https://github.com/usegalaxy-eu/ena-upload-cli 678 This is a wrapper for the ENA upload tool in https://github.com/usegalaxy-eu/ena-upload-cli
629 The input metadata can be submitted following the tabular format of the templates in https://github.com/usegalaxy-eu/ena-upload-cli/tree/master/example_tables 679 The input metadata can be submitted following the tabular format of the templates in https://github.com/usegalaxy-eu/ena-upload-cli/tree/master/example_tables
630 It is also possible to submit an excel file by following the template in https://drive.google.com/file/d/1ncC22--tW2v-EI-te_r86sAZujIPAjlX/view?usp=sharing 680 It is also possible to submit an excel file by following the template in https://drive.google.com/file/d/1ncC22--tW2v-EI-te_r86sAZujIPAjlX/view?usp=sharing
631 For viral submissions a larger set of metadata is required, you can find the template in https://drive.google.com/file/d/1U4VdcczsIecIXxseV8svE1zO_CBUadog/view?usp=sharing 681 For viral submissions a larger set of metadata is required, you can find the template in https://drive.google.com/file/d/1Gx78GKh58PmRjdmJ05DBbpObAL-3oUFX/view?usp=sharing
632 ]]></help> 682 ]]></help>
633 <citations> 683 <citations>
634 </citations> 684 </citations>
635 </tool> 685 </tool>