Mercurial > repos > artbio > rsem
changeset 6:39b8e13b1fc9 draft
planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f01c120abce1894ac9c6b298d301d4a2c740fc67
| author | artbio |
|---|---|
| date | Sat, 31 Mar 2018 12:18:07 -0400 |
| parents | 78a1909aca3e |
| children | 20e2c68f776a |
| files | datatypes_conf.xml extract_transcript_to_gene_map_from_trinity.xml rsem-bwt2.xml rsem.py rsem.xml |
| diffstat | 5 files changed, 194 insertions(+), 1 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/datatypes_conf.xml Sat Mar 31 12:18:07 2018 -0400 @@ -0,0 +1,14 @@ +<?xml version="1.0"?> +<datatypes> + <datatype_files> + <datatype_file name="rsem.py"/> + </datatype_files> + <registration> + <datatype extension="rsem_ref" type="galaxy.datatypes.rsem:RsemReference" display_in_upload="true"/> + <datatype extension="rsem.genes.results" type="galaxy.datatypes.rsem:RsemGenesResults" display_in_upload="true"/> + <datatype extension="rsem.isoforms.results" type="galaxy.datatypes.rsem:RsemIsoformsResults" display_in_upload="true"/> + <datatype extension="rsem.ngvec" type="galaxy.datatypes.tabular:Tabular" subclass="True" display_in_upload="true"/> + <datatype extension="rsem.genemat" type="galaxy.datatypes.tabular:Tabular" subclass="True" display_in_upload="true"/> + <datatype extension="rsem.isomat" type="galaxy.datatypes.tabular:Tabular" subclass="True" display_in_upload="true"/> + </registration> +</datatypes>
--- a/extract_transcript_to_gene_map_from_trinity.xml Sat Mar 31 10:17:42 2018 -0400 +++ b/extract_transcript_to_gene_map_from_trinity.xml Sat Mar 31 12:18:07 2018 -0400 @@ -1,4 +1,4 @@ -<tool id="extract_transcript_to_gene_map_from_trinity" name="RSEM trinity fasta to gene map" version="0.1.0"> +<tool id="extract_transcript_to_gene_map_from_trinity" name="RSEM trinity fasta to gene map" version="0.4.0"> <description>extract transcript to gene map from trinity</description> <requirements> <requirement type="package" version="1.3.0">rsem</requirement> @@ -38,4 +38,7 @@ </help> + <citations> + <citation type="doi">10.1038/nbt.1883</citation> + </citations> </tool>
--- a/rsem-bwt2.xml Sat Mar 31 10:17:42 2018 -0400 +++ b/rsem-bwt2.xml Sat Mar 31 12:18:07 2018 -0400 @@ -423,6 +423,7 @@ </tests> <help> +.. class:: infomark RSEM HOME PAGE - http://deweylab.biostat.wisc.edu/rsem/
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rsem.py Sat Mar 31 12:18:07 2018 -0400 @@ -0,0 +1,174 @@ +""" +RSEM datatypes +""" +import logging +import os +import os.path + +from galaxy.datatypes.images import Html +from galaxy.datatypes.metadata import MetadataElement +from galaxy.datatypes.sniff import get_headers +from galaxy.datatypes.tabular import Tabular + + +log = logging.getLogger(__name__) + + +class RsemIsoformsResults(Tabular): + file_ext = "rsem.isoforms.results" + """ + required columns: + transcript_id gene_id length effective_length expected_count TPM + FPKM IsoPct + optional columns: + pme_expected_count pme_TPM pme_FPKM IsoPct_from_pme_TPM TPM_ci_lower_bound + TPM_ci_upper_bound FPKM_ci_lower_bound FPKM_ci_upper_bound + """ + + def __init__(self, **kwd): + Tabular.__init__(self, **kwd) + """Initialize RsemResults datatype""" + self.comment_lines = 1 + + def sniff(self, filename): + headers = get_headers(filename, '\n', count=1) + return (len(headers) > 0 and len(headers[0]) >= 8 and + headers[0][0] == "transcript_id" and + headers[0][1] == "gene_id" and headers[0][6] == "FPKM") + + def set_meta(self, dataset, **kwd): + Tabular.set_meta(self, dataset, skip=None, **kwd) + + +class RsemGenesResults(Tabular): + file_ext = "rsem.genes.results" + """ + required columns: + gene_id transcript_id(s) length effective_length expected_count TPM FPKM + optional columns: + pme_expected_count pme_TPM pme_FPKM TPM_ci_lower_bound TPM_ci_upper_bound + FPKM_ci_lower_bound FPKM_ci_upper_bound + """ + + def __init__(self, **kwd): + Tabular.__init__(self, **kwd) + """Initialize RsemResults datatype""" + self.comment_lines = 1 + + def sniff(self, filename): + headers = get_headers(filename, '\n', count=1) + return (len(headers) > 0 and len(headers[0]) >= 7 and + headers[0][0] == "gene_id" and + headers[0][1].startswith("transcript_id") and + headers[0][6] == "FPKM") + + def set_meta(self, dataset, **kwd): + Tabular.set_meta(self, dataset, skip=None, **kwd) + + +class RsemReference(Html): + """Class describing an RSEM reference""" + MetadataElement(name='reference_name', default='rsem_ref', + desc='RSEM Reference Name', readonly=True, visible=True, + set_in_upload=True, no_value='rsem_ref') + file_ext = 'rsem_ref' + allow_datatype_change = False + composite_type = 'auto_primary_file' + + def __init__(self, **kwd): + Html.__init__(self, **kwd) + """ + Expecting files: + extra_files_path/<reference_name>.grp + extra_files_path/<reference_name>.ti + extra_files_path/<reference_name>.seq + extra_files_path/<reference_name>.transcripts.fa + Optionally includes files: + extra_files_path/<reference_name>.chrlist + extra_files_path/<reference_name>.idx.fa + extra_files_path/<reference_name>.1.ebwt + extra_files_path/<reference_name>.2.ebwt + extra_files_path/<reference_name>.3.ebwt + extra_files_path/<reference_name>.4.ebwt + extra_files_path/<reference_name>.rev.1.ebwt + extra_files_path/<reference_name>.rev.2.ebwt + """ + self.add_composite_file('%s.grp', description='Group File', + substitute_name_with_metadata='reference_name', + is_binary=False) + self.add_composite_file('%s.ti', description='', + substitute_name_with_metadata='reference_name', + is_binary=False) + self.add_composite_file('%s.seq', description='', + substitute_name_with_metadata='reference_name', + is_binary=False) + self.add_composite_file('%s.transcripts.fa', description='', + substitute_name_with_metadata='reference_name', + is_binary=False) + self.add_composite_file('%s.chrlist', description='', + substitute_name_with_metadata='reference_name', + is_binary=False, optional=True) + self.add_composite_file('%s.idx.fa', description='', + substitute_name_with_metadata='reference_name', + is_binary=False, optional=True) + self.add_composite_file('%s.1.ebwt', description='', + substitute_name_with_metadata='reference_name', + is_binary=True, optional=True) + self.add_composite_file('%s.2.ebwt', description='', + substitute_name_with_metadata='reference_name', + is_binary=True, optional=True) + self.add_composite_file('%s.3.ebwt', description='', + substitute_name_with_metadata='reference_name', + is_binary=True, optional=True) + self.add_composite_file('%s.4.ebwt', description='', + substitute_name_with_metadata='reference_name', + is_binary=True, optional=True) + self.add_composite_file('%s.rev.1.ebwt', description='', + substitute_name_with_metadata='reference_name', + is_binary=True, optional=True) + self.add_composite_file('%s.rev.2.ebwt', description='', + substitute_name_with_metadata='reference_name', + is_binary=True, optional=True) + + def generate_primary_file(self, dataset=None): + """ + This is called only at upload to write the file + cannot rename the datasets here - they come with + the default unfortunately + """ + + def regenerate_primary_file(self, dataset): + """ + cannot do this until we are setting metadata + """ + link_to_exts = ['.grp', '.ti', '.seq', '.fa', '.chrlist', '.log'] + ref_name = dataset.metadata.reference_name + efp = dataset.extra_files_path + flist = os.listdir(efp) + rval = ['<html><head><title>%s</title></head><body><p/>RSEM \ + Reference %s files:<p/><ul>' % (dataset.name, ref_name)] + rvalb = [] + for i, fname in enumerate(flist): + sfname = os.path.split(fname)[-1] + f, e = os.path.splitext(fname) + if e in link_to_exts: + rval.append('<li><a href="%s">%s</a></li>' % (sfname, sfname)) + else: + rvalb.append('<li>%s</li>' % (sfname)) + if len(rvalb) > 0: + rval += rvalb + rval.append('</ul></body></html>') + fh = file(dataset.file_name, 'w') + fh.write("\n".join(rval)) + fh.write('\n') + fh.close() + + def set_meta(self, dataset, **kwd): + Html.set_meta(self, dataset, **kwd) + efp = dataset.extra_files_path + flist = os.listdir(efp) + for i, fname in enumerate(flist): + if fname.endswith('.grp'): + dataset.metadata.reference_name = fname[:-4] + break + self.regenerate_primary_file(dataset)