| Previous changeset 1:025b0113ee97 (2021-05-17) Next changeset 3:4212f20315e5 (2021-09-24) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" |
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modified:
customize_metaphlan_database.xml formatoutput.py macros.xml |
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added:
test-data/no_taxon_input.fasta |
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| diff -r 025b0113ee97 -r 487da152fb43 customize_metaphlan_database.xml --- 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 |
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| @@ -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> |
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| diff -r 025b0113ee97 -r 487da152fb43 formatoutput.py --- a/formatoutput.py Mon May 17 20:09:28 2021 +0000 +++ b/formatoutput.py Mon Jun 14 12:48:54 2021 +0000 |
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| @@ -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('|') |
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| diff -r 025b0113ee97 -r 487da152fb43 macros.xml --- a/macros.xml Mon May 17 20:09:28 2021 +0000 +++ b/macros.xml Mon Jun 14 12:48:54 2021 +0000 |
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| @@ -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> |
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| diff -r 025b0113ee97 -r 487da152fb43 test-data/no_taxon_input.fasta --- /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 |
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| @@ -0,0 +1,4 @@ +> seq1 +ATTAGGGATTTTAGGGGGGGAGATTTAGAGAGAGAGAGAGAGAAGAAGAGAAGAAGAAGAAGAAAAAGGGGGAAGAGAGA +> seq2 +ATTAGGGATTTTAGGGGGGGAGATTTAGAGAGAGAGAGAGAGAAGAAGAGAAGAAGAAGAAGAAAAAGGGGGAAGAGAGA |