Mercurial > repos > earlhaminst > ete
changeset 11:2db72467da51 draft
"planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 67e136d433c0d925db362342919305b46fdffecd"
| author | earlhaminst |
|---|---|
| date | Thu, 10 Mar 2022 14:01:44 +0000 |
| parents | 541a2ffc01ff |
| children | dc32007a6b36 |
| files | ete_homology_classifier.xml ete_lineage_generator.py ete_lineage_generator.xml test-data/species_ids.txt |
| diffstat | 4 files changed, 28 insertions(+), 3 deletions(-) [+] |
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--- a/ete_homology_classifier.xml Fri Nov 20 16:56:22 2020 +0000 +++ b/ete_homology_classifier.xml Thu Mar 10 14:01:44 2022 +0000 @@ -3,7 +3,7 @@ <macros> <import>ete_macros.xml</import> <xml name="homologies_macro" token_label="" token_help=""> - <param name="homologies" type="select" multiple="true" optional="false" display="checkboxes" label="@LABEL@" help="@HELP@"> + <param name="homologies" type="select" multiple="true" optional="false" label="@LABEL@" help="@HELP@"> <option value="one-to-one" selected="true">one-to-one</option> <option value="one-to-many" selected="true">one-to-many</option> <option value="many-to-one" selected="true">many-to-one</option>
--- a/ete_lineage_generator.py Fri Nov 20 16:56:22 2020 +0000 +++ b/ete_lineage_generator.py Thu Mar 10 14:01:44 2022 +0000 @@ -41,7 +41,14 @@ RANK_IDX: mapping from rank names to indices (distance to root/leaf?) lower: use lower taxa for filling "NA"s """ - lineage_taxids = ncbi.get_lineage(taxid) + try: + lineage_taxids = ncbi.get_lineage(taxid) + except ValueError: + sys.stderr.write("[%s] could not determine lineage!\n" % taxid) + return + if lineage_taxids is None: + sys.stderr.write("[%s] could not determine lineage!\n" % taxid) + return lineage_ranks = ncbi.get_rank(lineage_taxids) lineage_names = ncbi.get_taxid_translator(lineage_taxids, try_synonyms=True) if lower: @@ -121,6 +128,8 @@ with open(options.input_species_filename) as f: for line in f.readlines(): line = line.strip().replace('_', ' ') + if line == "": + continue try: taxid = int(line) except ValueError:
--- a/ete_lineage_generator.xml Fri Nov 20 16:56:22 2020 +0000 +++ b/ete_lineage_generator.xml Thu Mar 10 14:01:44 2022 +0000 @@ -1,4 +1,4 @@ -<tool id="ete_lineage_generator" name="ETE lineage generator" version="@VERSION@"> +<tool id="ete_lineage_generator" name="ETE lineage generator" version="@VERSION@+galaxy1"> <description>from a list of species/taxids using the ETE Toolkit</description> <macros> <import>ete_macros.xml</import> @@ -120,6 +120,19 @@ <param name="includeid" value="--includeid" /> <output name="outputFile" file="lineage-wid.txt" /> </test> + <test> + <param name="speciesFile" ftype="txt" value="species_ids.txt" /> + <param name="database" ftype="sqlite" value="taxdump.sqlite" /> + <output name="outputFile"> + <assert_contents> + <has_line line="9606	Eukaryota	Chordata	Mammalia	Euarchontoglires	Hominoidea	Homo	Homo sapiens"/> + <has_line line="0	NA	NA	NA	NA	NA	NA	NA"/> + </assert_contents> + </output> + <assert_stderr> + <has_line line="[0] could not determine lineage!"/> + </assert_stderr> + </test> </tests> <help><![CDATA[ Generates a table with lineage information for a list of species (also taxids and arbitrary taxons are accepted) using the `ETE Toolkit`_.