Mercurial > repos > earlhaminst > ete
changeset 16:e4d5d9a69c9d draft default tip
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/main/tools/ete commit a0d7ab86b86bb764e457767bf8e8bc29868d0cbb
| author | earlhaminst |
|---|---|
| date | Mon, 10 Mar 2025 23:28:17 +0000 |
| parents | 1e85af7a29c4 |
| children | |
| files | ete_gene_cnv.xml ete_genetree_splitter.xml ete_homology_classifier.xml ete_init_taxdb.xml ete_lineage_generator.xml ete_macros.xml ete_mod.xml ete_species_tree_generator.py ete_species_tree_generator.xml |
| diffstat | 9 files changed, 78 insertions(+), 42 deletions(-) [+] |
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--- a/ete_gene_cnv.xml Mon Feb 24 16:34:12 2025 +0000 +++ b/ete_gene_cnv.xml Mon Mar 10 23:28:17 2025 +0000 @@ -1,4 +1,4 @@ -<tool id="ete_gene_csv_finder" name="Gene Copy Number Finder" version="@VERSION@"> +<tool id="ete_gene_csv_finder" name="Gene Copy Number Finder" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> <description>from a genetree using the ETE Toolkit</description> <macros> <import>ete_macros.xml</import>
--- a/ete_genetree_splitter.xml Mon Feb 24 16:34:12 2025 +0000 +++ b/ete_genetree_splitter.xml Mon Mar 10 23:28:17 2025 +0000 @@ -1,4 +1,4 @@ -<tool id="ete_genetree_splitter" name="ETE GeneTree splitter" version="@VERSION@"> +<tool id="ete_genetree_splitter" name="ETE GeneTree splitter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> <description>from a genetree using the ETE Toolkit</description> <macros> <import>ete_macros.xml</import> @@ -91,7 +91,9 @@ <test> <param name="genetreeFile" ftype="nhx" value="genetree.nhx" /> <param name="gene_node" value="0"/> - <param name="splitter" value="dups"/> + <conditional name="splitting_conditional"> + <param name="splitter" value="dups"/> + </conditional> <param name="output_format" value="9" /> <output_collection name="genetrees_lists" type="list" count="4"> <element name="1" file="11_genetree.nhx" ftype="nhx" /> @@ -103,10 +105,14 @@ <test> <param name="genetreeFile" ftype="nhx" value="genetree.nhx" /> <param name="gene_node" value="0"/> - <param name="splitter" value="dups"/> - <param name="gainlose" value="True" /> - <param name="speciesFile" ftype="nhx" value="speciestree.nhx" /> - <param name="species_format" value="8" /> + <conditional name="splitting_conditional"> + <param name="splitter" value="dups"/> + </conditional> + <conditional name="gainlose_conditional"> + <param name="gainlose" value="True" /> + <param name="speciesFile" ftype="nhx" value="speciestree.nhx" /> + <param name="species_format" value="8" /> + </conditional> <param name="output_format" value="9" /> <output_collection name="genetrees_lists" type="list" count="5"> <element name="1" file="21_genetree.nhx" ftype="nhx" /> @@ -119,7 +125,9 @@ <test> <param name="genetreeFile" ftype="nhx" value="genetree.nhx" /> <param name="gene_node" value="0"/> - <param name="splitter" value="treeko"/> + <conditional name="splitting_conditional"> + <param name="splitter" value="treeko"/> + </conditional> <param name="output_format" value="9" /> <output_collection name="genetrees_lists" type="list" count="4"> <element name="1" file="31_genetree.nhx" ftype="nhx" /> @@ -132,9 +140,11 @@ <test> <param name="genetreeFile" ftype="nhx" value="genetree.nhx" /> <param name="gene_node" value="0"/> - <param name="splitter" value="species"/> - <param name="ingroup" value="pantroglodytes,homosapiens,rattusnorvegicus,musmusculus,canisfamiliaris" /> - <param name="outgroup" value="susscrofa" /> + <conditional name="splitting_conditional"> + <param name="splitter" value="species"/> + <param name="ingroup" value="pantroglodytes,homosapiens,rattusnorvegicus,musmusculus,canisfamiliaris" /> + <param name="outgroup" value="susscrofa" /> + </conditional> <param name="output_format" value="9" /> <output_collection name="genetrees_lists" type="list" count="4"> <element name="1" file="41_genetree.nhx" ftype="nhx" />
--- a/ete_homology_classifier.xml Mon Feb 24 16:34:12 2025 +0000 +++ b/ete_homology_classifier.xml Mon Mar 10 23:28:17 2025 +0000 @@ -1,4 +1,4 @@ -<tool id="ete_homology_classifier" name="Homology Classifier and Filter" version="@VERSION@"> +<tool id="ete_homology_classifier" name="Homology Classifier and Filter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> <description>from a genetree using the ETE Toolkit</description> <macros> <import>ete_macros.xml</import> @@ -50,13 +50,17 @@ <tests> <test> <param name="genetreeFile" ftype="nhx" value="genetree.nhx" /> - <param name="out_format" value="tabular"/> - <param name="homologies" value="one-to-one,one-to-many,many-to-one,many-to-many,paralogs" /> + <conditional name="format_type"> + <param name="out_format" value="tabular"/> + <param name="homologies" value="one-to-one,one-to-many,many-to-one,many-to-many,paralogs" /> + </conditional> <output name="homology" file="11_homology.tabular" /> </test> <test> <param name="genetreeFile" ftype="nhx" value="11_genetree.nhx" /> - <param name="out_format" value="csv"/> + <conditional name="format_type"> + <param name="out_format" value="csv"/> + </conditional> <output name="homology" file="11_homology.csv" /> </test> </tests>
--- a/ete_init_taxdb.xml Mon Feb 24 16:34:12 2025 +0000 +++ b/ete_init_taxdb.xml Mon Mar 10 23:28:17 2025 +0000 @@ -1,4 +1,4 @@ -<tool id="ete_init_taxdb" name="ETE taxa DB generator" version="@VERSION@"> +<tool id="ete_init_taxdb" name="ETE taxa DB generator" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> <description>generates the ETE sqlite DB from the NCBI taxdump.tar.gz</description> <macros> <import>ete_macros.xml</import> @@ -29,8 +29,10 @@ </outputs> <tests> <test> - <param name="latest" value="local" /> - <param name="taxdump" ftype="tar" value="taxdump.tar.gz" /> + <conditional name="latestcond"> + <param name="latest" value="local" /> + <param name="taxdump" ftype="tar" value="taxdump.tar.gz" /> + </conditional> <output name="database" file="taxdump.sqlite" compare="sim_size" /> </test> </tests>
--- a/ete_lineage_generator.xml Mon Feb 24 16:34:12 2025 +0000 +++ b/ete_lineage_generator.xml Mon Mar 10 23:28:17 2025 +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="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> <description>from a list of species/taxids using the ETE Toolkit</description> <macros> <import>ete_macros.xml</import> @@ -88,37 +88,53 @@ <test> <param name="speciesFile" ftype="txt" value="species.txt" /> <param name="database" ftype="sqlite" value="taxdump.sqlite" /> - <param name="compress" value="" /> - <param name="levels" value="full" /> + <conditional name="compresscond"> + <param name="compress" value="" /> + </conditional> + <conditional name="ranks"> + <param name="levels" value="full" /> + </conditional> <output name="outputFile" file="lineage.txt" /> </test> <test> <param name="speciesFile" ftype="txt" value="species.txt" /> <param name="database" ftype="sqlite" value="taxdump.sqlite" /> - <param name="compress" value="-c" /> - <param name="levels" value="primary" /> + <conditional name="compresscond"> + <param name="compress" value="-c" /> + </conditional> + <conditional name="ranks"> + <param name="levels" value="primary" /> + </conditional> <output name="outputFile" file="lineage-compress.txt" /> </test> <test> <param name="speciesFile" ftype="txt" value="species.txt" /> <param name="database" ftype="sqlite" value="taxdump.sqlite" /> - <param name="compress" value="-c" /> - <param name="levels" value="primary" /> - <param name="lower" value="-l" /> + <conditional name="compresscond"> + <param name="compress" value="-c" /> + <param name="lower" value="true" /> + </conditional> + <conditional name="ranks"> + <param name="levels" value="primary" /> + </conditional> <output name="outputFile" file="lineage-compress-lower.txt" /> </test> <test> <param name="speciesFile" ftype="txt" value="species.txt" /> <param name="database" ftype="sqlite" value="taxdump.sqlite" /> - <param name="compress" value="" /> - <param name="levels" value="manual" /> - <param name="manualranks" value="kingdom,family" /> + <conditional name="compresscond"> + <param name="compress" value="" /> + </conditional> + <conditional name="ranks"> + <param name="levels" value="manual" /> + <param name="manualranks" value="kingdom,family" /> + </conditional> <output name="outputFile" file="lineage-full.txt" /> </test> <test> <param name="speciesFile" ftype="txt" value="species.txt" /> <param name="database" ftype="sqlite" value="taxdump.sqlite" /> - <param name="includeid" value="--includeid" /> + <param name="includeid" value="true" /> <output name="outputFile" file="lineage-wid.txt" /> </test> <test>
--- a/ete_macros.xml Mon Feb 24 16:34:12 2025 +0000 +++ b/ete_macros.xml Mon Mar 10 23:28:17 2025 +0000 @@ -1,6 +1,7 @@ <?xml version="1.0"?> <macros> - <token name="@VERSION@">3.1.3</token> + <token name="@TOOL_VERSION@">3.1.3</token> + <token name="@VERSION_SUFFIX@">1</token> <xml name="bio_tools"> <xrefs> <xref type="bio.tools">ete</xref> @@ -8,7 +9,9 @@ </xml> <xml name="requirements"> <requirements> - <requirement type="package" version="@VERSION@">ete3</requirement> + <requirement type="package" version="@TOOL_VERSION@">ete3</requirement> + <!-- Workaround for https://github.com/etetoolkit/ete/pull/770 until ete3 >3.1.3 is released --> + <requirement type="package" version="3.40">sqlite</requirement> </requirements> </xml> <xml name="citations">
--- a/ete_mod.xml Mon Feb 24 16:34:12 2025 +0000 +++ b/ete_mod.xml Mon Mar 10 23:28:17 2025 +0000 @@ -1,4 +1,4 @@ -<tool id="ete3_mod" name="ETE mod" version="@VERSION@"> +<tool id="ete3_mod" name="ETE mod" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> <description>manipulates tree topology by rooting, pruning or sorting branches</description> <macros> <import>ete_macros.xml</import> @@ -73,32 +73,32 @@ <test> <param name="input_trees" ftype="nhx" value="tree1.nhx" /> <param name="prune" value="A,C" /> - <param name="prune_preserve_lengths" value="--prune_preserve_lengths" /> + <param name="prune_preserve_lengths" value="true" /> <output name="output_tree" file="tree1_pruneACpreserve.nhx" /> </test> <test> <param name="input_trees" ftype="nhx" value="tree1.nhx" /> - <param name="unroot" value="--unroot" /> + <param name="unroot" value="true" /> <output name="output_tree" file="tree1_unroot.nhx" /> </test> <test> <param name="input_trees" ftype="nhx" value="tree2.nhx" /> - <param name="sort_branches" value="--sort_branches" /> + <param name="sort_branches" value="true" /> <output name="output_tree" file="tree2_sort.nhx" /> </test> <test> <param name="input_trees" ftype="nhx" value="tree1.nhx" /> - <param name="ladderize" value="--ladderize" /> + <param name="ladderize" value="true" /> <output name="output_tree" file="tree1_ladder.nhx" /> </test> <test> <param name="input_trees" ftype="nhx" value="tree1_unroot.nhx" /> - <param name="resolve_polytomies" value="--resolve_polytomies" /> + <param name="resolve_polytomies" value="true" /> <output name="output_tree" file="tree1_unroot_resolve.nhx" /> </test> <test> <param name="input_trees" ftype="nhx" value="tree3.nhx" /> - <param name="standardize" value="--standardize" /> + <param name="standardize" value="true" /> <output name="output_tree" file="tree3_stand.nhx" /> </test> </tests>
--- a/ete_species_tree_generator.py Mon Feb 24 16:34:12 2025 +0000 +++ b/ete_species_tree_generator.py Mon Mar 10 23:28:17 2025 +0000 @@ -22,7 +22,6 @@ with open(options.input_species_filename) as f: species_name = [_.strip().replace('_', ' ') for _ in f.readlines()] -breakpoint() name2taxid = ncbi.get_name_translator(species_name) taxid = [name2taxid[_][0] for _ in species_name]
--- a/ete_species_tree_generator.xml Mon Feb 24 16:34:12 2025 +0000 +++ b/ete_species_tree_generator.xml Mon Mar 10 23:28:17 2025 +0000 @@ -1,4 +1,4 @@ -<tool id="ete_species_tree_generator" name="ETE species tree generator" version="@VERSION@"> +<tool id="ete_species_tree_generator" name="ETE species tree generator" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> <description>from a list of species using the ETE Toolkit</description> <macros> <import>ete_macros.xml</import> @@ -54,7 +54,9 @@ <test> <param name="speciesFile" ftype="txt" value="species.txt" /> <param name="database" ftype="sqlite" value="taxdump.sqlite" /> - <param name="treebest" value="yes" /> + <conditional name="output_format"> + <param name="treebest" value="yes" /> + </conditional> <output name="outputFile"> <assert_contents> <has_text text="(Homosapiens*,Pantroglodytes*,Gorillagorillagorilla*)" />