[WIP] EBI improvements

[antgonza]

Make sure that these are done:

• Understand/Fix what lib_strategies = {'metagenome': 'POOLCLONE', is doing. // This has been coded in step-3 and now is dynamic
• remove str from error reporting in commands.submit_EBI, note that this full method is gonna change. // Removed in cover-some-joy-list-issues
• Remove the parsing of the XML string in the write_xml_file function. // Modified in cover-some-joy-list-issues
• Add a test in which the prep template includes less samples than the sample template, to check that the EBI submission correctly subsets the sample template and makes the submission of the samples in the prep template. // Removed in cover-some-joy-list-issues
• The modification of the ASPERA_SCP_PASS environment variable should happen when the command is called, not when the command is generated. // fixed in step 4 #1477
• Add tests for submit_EBI in qiita_ware/commands.py // Done in WIP: Next steps #1488 but see Add ascp to travis to test EBI #406
• Modify EBI code to use previous accession numbers if they exist (@josenavas) // done in Ebi: ability to extend a submission #1489
• Fix qiita pet to correctly show the EBI information (@josenavas) // Done in Ebi improvements pet #1490
• Raise an error in case that all samples get filtered in the generate_demultiplexed_fastq step (hit this edge case while I was writing tests for other sections of the code) // Done in WIP: Next steps #1488

Things that are not gonna be done and explanation:

• Revisit the EBISubmission.__init__ as it is getting long and complex. Not really needed. We could split the code in a couple of methods but will not add much clarity + that code is not used anywhere else.
• Use the ParallelWrapper class // this is not needed due to how the ebi flow is.
• Change CCME-COLORADO and confirm with EBI // UPDATE: the new name is going to be "UCSD Microbiome Initiative" and EBI already made the change. // EXPLANATION: we agreed that this is an example and it's fine to leave under Colorado
• Add a test using UTF-8 characters // EXPLANATION: we agreed that this should be expanded to all Qiita and the best will be to do what's in add utf-8 chars to database #1466
• Add UPDATE code (from @adamrp). For updates of metadata where none of the samples have been added or removed, I think it is relatively straightforward just to change the action that is passed.
  For all other updates (where samples are added or removed, or sequence files need to be updated), I believe we cannot actually do the update automatically. However, if we store the proper information in the database (i.e., the EBI aliases for everything that we submit), then we can automatically send an email requesting changes. update EBI study #1487