Mercurial > repos > artbio > rsem
changeset 1:49795544dac7 draft
planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 62e8088d5f73cbb9b2f93e23a74636c77a06b492
| author | artbio |
|---|---|
| date | Sun, 01 Apr 2018 18:28:24 -0400 |
| parents | e5e836936d60 |
| children | 9fa602bc29ec |
| files | datatypes_conf.xml extract_transcript_to_gene_map_from_trinity.xml macros.xml rsem-bwt2.xml rsem.py rsem.xml |
| diffstat | 6 files changed, 122 insertions(+), 5 deletions(-) [+] |
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--- a/datatypes_conf.xml Sat Mar 31 21:30:07 2018 -0400 +++ b/datatypes_conf.xml Sun Apr 01 18:28:24 2018 -0400 @@ -5,6 +5,7 @@ </datatype_files> <registration> <datatype extension="rsem_ref" type="galaxy.datatypes.rsem:RsemReference" display_in_upload="true"/> + <datatype extension="rsem_bt2_ref" type="galaxy.datatypes.rsem:RsemBt2Reference" 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"/>
--- a/extract_transcript_to_gene_map_from_trinity.xml Sat Mar 31 21:30:07 2018 -0400 +++ b/extract_transcript_to_gene_map_from_trinity.xml Sun Apr 01 18:28:24 2018 -0400 @@ -1,5 +1,8 @@ -<tool id="extract_transcript_to_gene_map_from_trinity" name="RSEM trinity fasta to gene map" version="0.4.0"> +<tool id="extract_transcript_to_gene_map_from_trinity" name="RSEM trinity fasta to gene map" version="@WRAPPER_VERSION@"> <description>extract transcript to gene map from trinity</description> + <macros> + <import>macros.xml</import> + </macros> <requirements> <requirement type="package" version="1.3.0">rsem</requirement> </requirements>
--- a/macros.xml Sat Mar 31 21:30:07 2018 -0400 +++ b/macros.xml Sun Apr 01 18:28:24 2018 -0400 @@ -1,5 +1,6 @@ <?xml version="1.0"?> <macros> + <token name="@WRAPPER_VERSION@">0.5.1</token> <xml name="rsem_options"> <param name="seedlength" type="integer" value="25" optional="true" label="Seed length used by the read aligner" help="Providing the correct value for this parameter is important for RSEM's accuracy if the data are single-end reads. RSEM uses this value for Bowtie's seed length parameter. The minimum value is 25. (Default:25)"> </param>
--- a/rsem-bwt2.xml Sat Mar 31 21:30:07 2018 -0400 +++ b/rsem-bwt2.xml Sun Apr 01 18:28:24 2018 -0400 @@ -1,4 +1,4 @@ -<tool id="rsembowtie2" name="RSEM-Bowtie2" version="0.4.0"> +<tool id="rsembowtie2" name="RSEM-Bowtie2" version="@WRAPPER_VERSION@"> <description></description> <macros> <import>macros.xml</import> @@ -241,7 +241,7 @@ <option value="self">Prepare RSEM Reference with this tool</option> </param> <when value="history"> - <param name="rsem_ref" type="data" format="rsem_ref" label="RSEM reference" /> + <param name="rsem_ref" type="data" format="rsem_bt2_ref" label="RSEM reference" /> </when> <when value="self"> </when> @@ -321,7 +321,7 @@ </inputs> <outputs> - <data format="rsem_ref" name="reference_file" label="RSEM ${job.reference_name} reference"> + <data format="rsem_bt2_ref" name="reference_file" label="RSEM ${job.reference_name} reference"> <filter>job['select_job'] == "index"</filter> </data> <data format="tabular" name="gene_abundances" label="${run_rsem.sample}.gene_abundances" from_work_dir="rsem_output.genes.results">
--- a/rsem.py Sat Mar 31 21:30:07 2018 -0400 +++ b/rsem.py Sun Apr 01 18:28:24 2018 -0400 @@ -172,3 +172,115 @@ dataset.metadata.reference_name = fname[:-4] break self.regenerate_primary_file(dataset) + + +class RsemBt2Reference(Html): + """Class describing an RSEM reference""" + MetadataElement(name='reference_name', default='rsem_bt2_ref', + desc='RSEM Bowtie2 Reference Name', readonly=True, + visible=True, set_in_upload=True, no_value='rsem_bt2_ref') + file_ext = 'rsem_bt2_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>.n2g.idx.fa + extra_files_path/<reference_name>.1.bt2 + extra_files_path/<reference_name>.2.bt2 + extra_files_path/<reference_name>.3.bt2 + extra_files_path/<reference_name>.4.bt2 + extra_files_path/<reference_name>.rev.1.bt2 + extra_files_path/<reference_name>.rev.2.bt2 + """ + 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.n2g.idx.fa', description='', + substitute_name_with_metadata='reference_name', + is_binary=False, optional=True) + self.add_composite_file('%s.1.bt2', description='', + substitute_name_with_metadata='reference_name', + is_binary=True, optional=True) + self.add_composite_file('%s.2.bt2', description='', + substitute_name_with_metadata='reference_name', + is_binary=True, optional=True) + self.add_composite_file('%s.3.bt2', description='', + substitute_name_with_metadata='reference_name', + is_binary=True, optional=True) + self.add_composite_file('%s.4.bt2', description='', + substitute_name_with_metadata='reference_name', + is_binary=True, optional=True) + self.add_composite_file('%s.rev.1.bt2', description='', + substitute_name_with_metadata='reference_name', + is_binary=True, optional=True) + self.add_composite_file('%s.rev.2.bt2', 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)
--- a/rsem.xml Sat Mar 31 21:30:07 2018 -0400 +++ b/rsem.xml Sun Apr 01 18:28:24 2018 -0400 @@ -1,4 +1,4 @@ -<tool id="rsembowtie" name="RSEM-Bowtie" version="0.4.0"> +<tool id="rsembowtie" name="RSEM-Bowtie" version="@WRAPPER_VERSION@"> <description></description> <macros> <import>macros.xml</import>