Mercurial > repos > iuc > customize_metaphlan_database
changeset 2:487da152fb43 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
| author | iuc |
|---|---|
| date | Mon, 14 Jun 2021 12:48:54 +0000 |
| parents | 025b0113ee97 |
| children | 4212f20315e5 |
| files | customize_metaphlan_database.xml formatoutput.py macros.xml test-data/no_taxon_input.fasta |
| diffstat | 4 files changed, 21 insertions(+), 3 deletions(-) [+] |
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--- a/customize_metaphlan_database.xml Mon May 17 20:09:28 2021 +0000 +++ b/customize_metaphlan_database.xml Mon Jun 14 12:48:54 2021 +0000 @@ -191,10 +191,14 @@ </repeat> </conditional> <output name="out_fasta" file="test-db.fasta" compare="sim_size"> + <assert_contents> <has_text text="13076__A0A2I1PE66__CYJ72_10760" /> + </assert_contents> </output> <output name="out_json" file="test-db.json" compare="sim_size"> + <assert_contents> <has_text text="13076__A0A2I1PE66__CYJ72_10760" /> + </assert_contents> </output> </test> <test expect_num_outputs="2"> @@ -205,10 +209,14 @@ <param name="markers" value="marker.txt"/> </conditional> <output name="out_fasta" file="test-db-without-one-marker.fasta" compare="sim_size"> + <assert_contents> <not_has_text text="13076__A0A2I1PE66__CYJ72_10760" /> + </assert_contents> </output> <output name="out_json" file="test-db-without-one-marker.json" compare="sim_size"> + <assert_contents> <not_has_text text="13076__A0A2I1PE66__CYJ72_10760" /> + </assert_contents> </output> </test> <test expect_num_outputs="2"> @@ -219,10 +227,14 @@ <param name="markers" value="marker.txt"/> </conditional> <output name="out_fasta" file="test-db-with-one-marker.fasta" compare="sim_size"> + <assert_contents> <has_text text="13076__A0A2I1PE66__CYJ72_10760" /> + </assert_contents> </output> <output name="out_json" file="test-db-with-one-marker.json" compare="sim_size"> + <assert_contents> <has_text text="13076__A0A2I1PE66__CYJ72_10760" /> + </assert_contents> </output> </test> </tests>
--- a/formatoutput.py Mon May 17 20:09:28 2021 +0000 +++ b/formatoutput.py Mon Jun 14 12:48:54 2021 +0000 @@ -57,7 +57,9 @@ # skip headers if line.startswith("#"): continue - + # skip UNKNOWN lines in Predicted taxon relative abundances + if "UNKNOWN" in line: + continue # spit lines split_line = line[:-1].split('\t') taxo_n = split_line[0].split('|')
--- a/macros.xml Mon May 17 20:09:28 2021 +0000 +++ b/macros.xml Mon Jun 14 12:48:54 2021 +0000 @@ -1,6 +1,6 @@ <?xml version="1.0"?> <macros> - <token name="@TOOL_VERSION@">3.0.8</token> + <token name="@TOOL_VERSION@">3.0.9</token> <token name="@VERSION_SUFFIX@">0</token> <token name="@PROFILE@">20.01</token> <xml name="edam_ontology"> @@ -21,7 +21,7 @@ </xml> <xml name="citations"> <citations> - <citation type="doi">1101/2020.11.19.388223</citation> + <citation type="doi">10.7554/eLife.65088</citation> </citations> </xml> </macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/no_taxon_input.fasta Mon Jun 14 12:48:54 2021 +0000 @@ -0,0 +1,4 @@ +> seq1 +ATTAGGGATTTTAGGGGGGGAGATTTAGAGAGAGAGAGAGAGAAGAAGAGAAGAAGAAGAAGAAAAAGGGGGAAGAGAGA +> seq2 +ATTAGGGATTTTAGGGGGGGAGATTTAGAGAGAGAGAGAGAGAAGAAGAGAAGAAGAAGAAGAAAAAGGGGGAAGAGAGA