| Previous changeset 10:289b3807e80c (2024-04-30) Next changeset 12:1a037928504c (2024-08-11) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05 |
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modified:
macros.xml metaphlan.xml tool_data_table_conf.xml.test |
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added:
test-data/SRS014464-Anterior_nares.fastq.gz test-data/test_database_versioned.loc.test |
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removed:
test-data/test_database_versioned.loc |
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| diff -r 289b3807e80c -r b6897977d13e macros.xml --- a/macros.xml Tue Apr 30 09:09:32 2024 +0000 +++ b/macros.xml Mon Jul 29 07:14:21 2024 +0000 |
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| @@ -1,7 +1,7 @@ <?xml version="1.0"?> <macros> - <token name="@TOOL_VERSION@">4.0.6</token> - <token name="@VERSION_SUFFIX@">3</token> + <token name="@TOOL_VERSION@">4.1.1</token> + <token name="@VERSION_SUFFIX@">0</token> <token name="@PROFILE@">22.05</token> <!-- Metaphlan DB compatible with this version of Metaphlan v4 introduced single genome level bins (SGB) and the index syntax differs from previous versions --> @@ -23,4 +23,9 @@ <citation type="doi">10.7554/eLife.65088</citation> </citations> </xml> + + <xml name="subsample_common"> + <param argument="--mapping_subsampling" type="boolean" truevalue="--mapping_subsampling" falsevalue="" label="Subsampling on the mapping results" help="instead of on the reads"/> + <param argument="--subsampling_seed" type="integer" optional="true" label="Subsampling seed" help="No value: random"/> + </xml> </macros> |
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| diff -r 289b3807e80c -r b6897977d13e metaphlan.xml --- a/metaphlan.xml Tue Apr 30 09:09:32 2024 +0000 +++ b/metaphlan.xml Mon Jul 29 07:14:21 2024 +0000 |
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| b'@@ -38,14 +38,12 @@\n #set full_ext=$inputs.in.raw_in.in.datatype.file_ext\n #if $full_ext.endswith("gz")\n #set $file_path="in" \n-zcat \'$inputs.in.raw_in.in\' > \'$file_path\'\n-&&\n+ zcat \'$inputs.in.raw_in.in\' > \'$file_path\' &&\n #else if $full_ext.endswith("bz2")\n #set $file_path="in"\n-bzcat \'$inputs.in.raw_in.in\' > \'$file_path\'\n-&&\n+ bzcat \'$inputs.in.raw_in.in\' > \'$file_path\' &&\n #else\n- #set $file_path=$inputs.in.raw_in.in\n+ #set $file_path="\'%s\'" % $inputs.in.raw_in.in\n #end if\n #else if $inputs.in.raw_in.selector == "multiple"\n #set full_ext=$inputs.in.raw_in.in[0].datatype.file_ext\n@@ -53,45 +51,54 @@\n #set sep=""\n #for $i, $f in enumerate($inputs.in.raw_in.in)\n #if $f.datatype.file_ext != $full_ext\n-echo "Different datatypes for input files"\n-&&\n-exit 1\n+ echo "Different datatypes for input files" &&\n+ exit 1\n #end if \n #if $full_ext.endswith("gz")\n #set fp="input_%s" % ($i)\n-zcat \'$f\' > \'$fp\'\n-&&\n+ zcat \'$f\' > \'$fp\' &&\n #else if $full_ext.endswith("bz2")\n #set fp="input_%s" % ($i)\n-bzcat \'$f\' > \'$fp\'\n-&&\n+ bzcat \'$f\' > \'$fp\' &&\n #else\n #set fp=$f\n #end if\n- #set $file_path+="%s%s" % ($sep, $fp)\n+ #set $file_path+="\'%s%s\'" % ($sep, $fp)\n #set $sep=","\n #end for\n #else if $inputs.in.raw_in.selector == "paired"\n #set full_ext=$inputs.in.raw_in.in_f.datatype.file_ext\n #if $full_ext != $inputs.in.raw_in.in_r.datatype.file_ext\n-echo "Different datatypes for input paired-end files"\n-&&\n-exit 1\n+ echo "Different datatypes for input paired-end files" &&\n+ exit 1\n #end if\n #if $full_ext.endswith("gz")\n-zcat \'$inputs.in.raw_in.in_f\' > \'in_f\'\n-&&\n-zcat \'$inputs.in.raw_in.in_r\' > \'in_r\'\n-&&\n- #set file_path="in_f,in_r"\n+ zcat \'$inputs.in.raw_in.in_f\' > \'in_f\' &&\n+ zcat \'$inputs.in.raw_in.in_r\' > \'in_r\' &&\n+ #set file_path="-1 in_f -2 in_r"\n #else if $full_ext.endswith("bz2")\n-bzcat \'$inputs.in.raw_in.in_f\' > \'in_f\'\n-&&\n-bzcat \'$inputs.in.raw_in.in_r\' > \'in_r\'\n-&&\n- #set file_path="in_f,in_r"\n+ bzcat \'$inputs.in.raw_in.in_f\' > \'in_f\' && \n+ bzcat \'$inputs.in.raw_in.in_r\' > \'in_r\' &&\n+ #set file_path="-1 in_f -2 in_r"\n #else\n- #set file_path="%s,%s" % ($inputs.in.raw_in.in_f,$inputs.in.raw_in.in_r)\n+ #set file_path="-1 \'%s\' -2 \'%s\'" % ($inputs.in.raw_in.in_f,$inputs.in.raw_in.in_r)\n+ #end if\n+ #else if $inputs.in.raw_in.selector == "paired_collection"\n+ #set full_ext=$inputs.in.raw_in.in.forward.ext\n+ #if $full_ext != $inputs.in.raw_in.in.reverse.ext\n+ echo "Different datatypes for input paired-end files" &&\n+ exit 1\n+ #end if\n+ #if $full_ext.endswith("gz")\n+ zcat \'$inputs.in.raw_in.in.forward\' > \'in_f\' &&\n+ zcat \'$inputs.in.raw_in.in.reverse\' > \'in_r\' &&\n+ #set file_path="-1 in_f -2 in_r"\n+ #else if $full_ext.endswith("bz2")\n+ bzcat \'$inputs.in.raw_in.in.forward\' > \'in_f\' && \n+ bzcat \'$inputs.in.raw_in.in.reverse\' > \'in_r\' &&\n+ #set file_path="-1 in_f -2 in_r"\n+ #else\n+ #set file_path="-1 \'%s\' -2 \'%s\'" % ($inputs.in.raw_in.in_f,$inputs.in.raw_in.in_r)\n #end if\n #end if\n \n@@ -105,20 +112,18 @@\n #end if\n \n #if $inputs.db.db_selector == "history"\n-mkdir \'ref_db\'\n-&&\n-bowtie2-build --large-index \'$inputs.db.bowtie2db\' \'ref_db/custom_db\'\n-&&\n-python \'$__tool_directory__/customizemetadata.py\'\n+mkdir \'ref_db\' &&\n+bowtie2-build --large-index \'$inputs.db.bowtie2db\' \'ref_db/custom_db\' &&\n+python\n+ \'$__tool_directory__/customizemetadata.py\'\n tra'..b'="raw_in">\n- <!-- Single FASTA file -->\n <param name="selector" value="single"/>\n <param name="in" value="SRS014464-Anterior_nares.fasta"/>\n </conditional>\n@@ -930,7 +1127,6 @@\n </section>\n </conditional>\n <conditional name="db">\n- <!-- Cached db -->\n <param name="db_selector" value="cached"/>\n <param name="cached_db" value="test-db-20210409"/>\n </conditional>\n@@ -1054,20 +1250,24 @@\n <has_n_columns n="9"/>\n </assert_contents>\n </output>\n+ <assert_stderr>\n+ <has_text text="Downloading" negate="true"/>\n+ </assert_stderr>\n </test>\n- <!-- Check a non-default analysis mode -->\n- <test expect_num_outputs="4">\n+ <!-- Check a non-default analysis mode \n+ and viral analysis -->\n+ <test expect_num_outputs="6">\n <section name="inputs">\n <conditional name="in">\n <param name="selector" value="raw"/>\n <conditional name="raw_in">\n <param name="selector" value="single"/>\n- <param name="in" value="SRS014464-Anterior_nares.fasta"/>\n+ <param name="in" value="SRS014464-Anterior_nares.fastq.gz"/>\n </conditional>\n </conditional>\n <conditional name="db">\n <param name="db_selector" value="cached"/>\n- <param name="cached_db" value="test-db-20210409"/>\n+ <param name="cached_db" value="mpa_vJan21_TOY_CHOCOPhlAnSGB"/>\n </conditional>\n </section>\n <section name="analysis">\n@@ -1075,13 +1275,43 @@\n <param name="t" value="marker_ab_table"/>\n </conditional>\n </section>\n+ <conditional name="viral_analysis">\n+ <param name="profile_vsc" value="--profile_vsc"/>\n+ <param name="vsc_out" value="true"/>\n+ </conditional>\n+ <conditional name="subsample">\n+ <param name="selector" value="single"/>\n+ <param name="subsampling" value="10000"/>\n+ <param name="subsampling_seed" value="42"/>\n+ </conditional>\n+ <param name="test" value="true"/>\n <output name="output_file" ftype="tabular" file="SRS014464-Anterior_nares-legacy-abundances.tabular" compare="sim_size">\n <assert_contents>\n- <has_text text="29394__H3NC06__B8A41_08715"/>\n+ <has_text text="SGB7017__MKDPKOFL_00679"/>\n <has_text text="SampleID"/>\n <has_text text="Metaphlan_Analysis"/>\n </assert_contents>\n </output>\n+ <output name="subsample_single">\n+ <assert_contents>\n+ <has_text text="@" n="10000"/>\n+ </assert_contents>\n+ </output>\n+ <!-- reference data empty -> empty output -->\n+ <output name="vcs_breath_coverage" ftype="tabular">\n+ <assert_contents>\n+ <has_size size="0"/>\n+ </assert_contents>\n+ </output>\n+ <assert_command>\n+ <has_text text="--profile_vsc"/>\n+ <has_text text="--vsc_breadth 0.75"/>\n+ <has_text text="--vsc_out"/>\n+ </assert_command>\n+ <assert_stderr>\n+ <has_text text="Downloading"/> <!-- due to test=true and the absence of the TOY reference DB Metaphlan will download to ~10MB-->\n+ <has_text text="No reads aligning to VSC markers"/>\n+ </assert_stderr>\n </test>\n </tests>\n <help><![CDATA[\n' |
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| diff -r 289b3807e80c -r b6897977d13e test-data/SRS014464-Anterior_nares.fastq.gz |
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| Binary file test-data/SRS014464-Anterior_nares.fastq.gz has changed |
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| diff -r 289b3807e80c -r b6897977d13e test-data/test_database_versioned.loc --- a/test-data/test_database_versioned.loc Tue Apr 30 09:09:32 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,7 +0,0 @@ -# Tab separated with 5 columns: -# - value (Galaxy records this in the Galaxy DB) -# - name (Galaxy shows this in the UI) -# - value (Galaxy records this in the Galaxy DB) -# - path (folder name containing the Kraken DB) -# - db version (whether it is SGB of Metaphlan v4 or not) -test-db-20210409 "Test Database" test-db ${__HERE__}/test-db SGB |
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| diff -r 289b3807e80c -r b6897977d13e test-data/test_database_versioned.loc.test --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_database_versioned.loc.test Mon Jul 29 07:14:21 2024 +0000 |
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| @@ -0,0 +1,11 @@ +# Tab separated with 5 columns: +# - value (Galaxy records this in the Galaxy DB) +# - name (Galaxy shows this in the UI) +# - dbkey +# - path (folder name containing the Kraken DB) +# - db version (whether it is SGB of Metaphlan v4 or not) +test-db-20210409 "Test Database" test-db ${__HERE__}/test-db SGB +# the TOY DB should be called in tests with the hidden test parameter enables this will make Metaphlan +# download the data to the JWD +mpa_vJan21_TOY_CHOCOPhlAnSGB mpa_vJan21_TOY_CHOCOPhlAnSGB mpa_vJan21_TOY_CHOCOPhlAnSGB_202103 ./ SGB +# mpa_vJun23_CHOCOPhlAnSGB_202403 mpa_vJun23_CHOCOPhlAnSGB_202403 mpa_vJun23_CHOCOPhlAnSGB_202403 ${__HERE__}/mpa_vJun23_CHOCOPhlAnSGB_202403/ SGB |
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| diff -r 289b3807e80c -r b6897977d13e tool_data_table_conf.xml.test --- a/tool_data_table_conf.xml.test Tue Apr 30 09:09:32 2024 +0000 +++ b/tool_data_table_conf.xml.test Mon Jul 29 07:14:21 2024 +0000 |
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| @@ -2,6 +2,6 @@ <tables> <table name="metaphlan_database_versioned" comment_char="#"> <columns>value, name, dbkey, path, db_version</columns> - <file path="${__HERE__}/test-data/test_database_versioned.loc"/> + <file path="${__HERE__}/test-data/test_database_versioned.loc.test"/> </table> </tables> |