| Previous changeset 0:501c21cce614 (2016-06-07) Next changeset 2:584008e574b2 (2020-01-24) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab" |
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modified:
biom_convert.xml macros.xml test-data/input_abundance_1.tabular |
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added:
test-data/biom_from_uc.biom test-data/normalized_presence_absence_observations.biom test-data/normalized_relative_abund_samples.biom test-data/observation_subsetting test-data/sample_subsetting test-data/subset_observations.biom test-data/subset_samples.biom test-data/summarize test-data/summarize_qualitative_observations test-data/uc_table.uc |
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| diff -r 501c21cce614 -r 0de92f0b96ef biom_convert.xml --- a/biom_convert.xml Tue Jun 07 17:26:00 2016 -0400 +++ b/biom_convert.xml Wed Sep 11 12:40:19 2019 -0400 |
| [ |
| b'@@ -1,56 +1,63 @@\n-<tool id="biom_convert" name="Convert BIOM" version="@VERSION@.0">\n- <description>formats</description>\n+<tool id="biom_convert" name="Convert" version="@VERSION@.2">\n+ <description>between BIOM table formats</description>\n <macros>\n <import>macros.xml</import>\n </macros>\n <expand macro="requirements" />\n- <expand macro="stdio" />\n <expand macro="version_command" />\n- <command>\n+ <command detect_errors="exit_code">\n <![CDATA[\n- biom convert -i "${input_type.input_table}" -o "${output_table}"\n- #if str( $input_type.input_type_selector ) == "tsv": \n- #if $input_type.process_obs_metadata:\n- --process-obs-metadata "${input_type.process_obs_metadata}"\n- #end if\n+ ## biom convert requires the header to start with a #\n+ ## so we just add one if its missing\n+ #if $input.type_selector == "tsv"\n+ sed \'1s/^\\([^#].*\\)/#\\1/\' \'$input.input_fp\' > input &&\n+ #else\n+ ln -s \'$input.input_fp\' input &&\n #end if\n-\n- #if str( $output_type.output_type_selector ) == "tsv": \n- --to-tsv\n- #if $output_type.header_key:\n- --header-key "${output_type.header_key}"\n- #if $output_type.output_metadata_id:\n- --output-metadata-id "${output_type.output_metadata_id}"\n+ biom convert \n+ --input-fp input\n+ --output-fp \'$output_fp\'\n+ #if str( $input.type_selector ) == "tsv"\n+ #if $input.process_obs_metadata:\n+ --process-obs-metadata \'$input.process_obs_metadata\'\n #end if\n- --tsv-metadata-formatter "${output_type.tsv_metadata_formatter}"\n #end if\n- #else:\n- --table-type "${output_type.table_type}"\n- #if str( $output_type.biom_type.biom_type_selector ) == \'hdf5\':\n- --to-hdf5\n- ${output_type.biom_type.collapsed_samples}\n- ${output_type.biom_type.collapsed_observations}\n+ #if str( $output.type_selector ) == "tsv"\n+ --to-tsv\n+ #if $output_type.header_key\n+ --header-key \'$output.header_key\'\n+ #if $output_type.output_metadata_id\n+ --output-metadata-id \'$output.output_metadata_id\'\n+ #end if\n+ --tsv-metadata-formatter \'$output.tsv_metadata_formatter\'\n+ #end if\n #else:\n- --to-json\n- #end if\n- #if $output_type.sample_metadata_fp:\n- --sample-metadata-fp "${output_type.sample_metadata_fp}"\n- #end if\n- #if $output_type.observation_metadata_fp:\n- --observation-metadata-fp "${output_type.observation_metadata_fp}"\n- #end if\n- #end if \n+ --table-type \'$output.table_type\'\n+ #if str( $output.biom_type.selector ) == \'hdf5\':\n+ --to-hdf5\n+ $output.biom_type.collapsed_samples\n+ $output.biom_type.collapsed_observations\n+ #else:\n+ --to-json\n+ #end if\n+ #if $output.sample_metadata_fp\n+ --sample-metadata-fp \'$output.sample_metadata_fp\'\n+ #end if\n+ #if $output.observation_metadata_fp\n+ --observation-metadata-fp \'$output.observation_metadata_fp\'\n+ #end if\n+ #end if \n ]]>\n </command>\n <inputs>\n- <conditional name="input_type">\n- <param name="input_type_'..b'tadata mapping file" argument="--sample-metadata-fp"/>\n- <param name="observation_metadata_fp" type="data" format="tabular" optional="True" label="Add observation metadata from mapping file" argument="--observation-metadata-fp"/>\n+ <param name="sample_metadata_fp" argument="--sample-metadata-fp" type="data" format="tabular" optional="True" label="Add sample metadata from metadata mapping file" />\n+ <param name="observation_metadata_fp" argument="--observation-metadata-fp" type="data" format="tabular" optional="True" label="Add observation metadata from mapping file" />\n </when>\n </conditional>\n </inputs>\n <outputs>\n- <data format="biom1" name="output_table">\n+ <data format="biom1" name="output_fp">\n <change_format>\n- <when input="output_type.output_type_selector" value="tsv" format="tabular" />\n- <when input="output_type.biom_type" value="hdf5" format="biom2" />\n+ <when input="output.type_selector" value="tsv" format="tabular" />\n+ <when input="output.biom_type" value="hdf5" format="h5" />\n </change_format>\n </data>\n </outputs>\n <tests>\n <test>\n- <conditional name="input_type">\n- <param name="input_type_selector" value="tsv"/>\n- <param name="input_table" value="input_abundance_taxonomy_1.tabular" ftype="tabular"/>\n+ <conditional name="input">\n+ <param name="type_selector" value="tsv"/>\n+ <param name="input_fp" value="input_abundance_taxonomy_1.tabular" ftype="tabular"/>\n <param name="process_obs_metadata" value="taxonomy"/>\n </conditional>\n- <conditional name="output_type">\n- <param name="output_type_selector" value="biom"/>\n+ <conditional name="output">\n+ <param name="type_selector" value="biom"/>\n <param name="table_type" value="OTU table"/>\n <conditional name="biom_type">\n- <param name="biom_type_selector" value="json"/>\n+ <param name="selector" value="json"/>\n </conditional>\n <param name="sample_metadata_fp"/>\n <param name="observation_metadata_fp"/>\n </conditional>\n- <output name="output_table" file="output_taxonomy_1.biom1.re" ftype="biom1" compare="re_match"/>\n+ <output name="output_fp" file="output_taxonomy_1.biom1.re" ftype="biom1" compare="re_match"/>\n </test>\n <test>\n- <conditional name="input_type">\n- <param name="input_type_selector" value="tsv"/>\n- <param name="input_table" value="input_abundance_1.tabular" ftype="tabular"/>\n+ <conditional name="input">\n+ <param name="type_selector" value="tsv"/>\n+ <param name="input_fp" value="input_abundance_1.tabular" ftype="tabular"/>\n <param name="process_obs_metadata" value=""/>\n </conditional>\n- <conditional name="output_type">\n- <param name="output_type_selector" value="biom"/>\n+ <conditional name="output">\n+ <param name="type_selector" value="biom"/>\n <param name="table_type" value="OTU table"/>\n <conditional name="biom_type">\n- <param name="biom_type_selector" value="json"/>\n+ <param name="selector" value="json"/>\n </conditional>\n <param name="sample_metadata_fp"/>\n <param name="observation_metadata_fp"/>\n </conditional>\n- <output name="output_table" file="output_1.biom1.re" ftype="biom1" compare="re_match"/>\n+ <output name="output_fp" file="output_1.biom1.re" ftype="biom1" compare="re_match"/>\n </test>\n </tests>\n <help><![CDATA[\n' |
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| diff -r 501c21cce614 -r 0de92f0b96ef macros.xml --- a/macros.xml Tue Jun 07 17:26:00 2016 -0400 +++ b/macros.xml Wed Sep 11 12:40:19 2019 -0400 |
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| @@ -6,12 +6,6 @@ </requirements> </xml> <token name="@VERSION@">2.1.5</token> - <xml name="stdio"> - <stdio> - <exit_code range="1:" /> - <exit_code range=":-1" /> - </stdio> - </xml> <xml name="version_command"> <version_command>biom --version</version_command> </xml> |
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| diff -r 501c21cce614 -r 0de92f0b96ef test-data/biom_from_uc.biom |
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| Binary file test-data/biom_from_uc.biom has changed |
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| diff -r 501c21cce614 -r 0de92f0b96ef test-data/input_abundance_1.tabular --- a/test-data/input_abundance_1.tabular Tue Jun 07 17:26:00 2016 -0400 +++ b/test-data/input_abundance_1.tabular Wed Sep 11 12:40:19 2019 -0400 |
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| @@ -1,4 +1,4 @@ -#ID SAMPLE_1 SAMPLE_2 +ID SAMPLE_1 SAMPLE_2 2 0 0 3 160 242 4 0 0 |
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| diff -r 501c21cce614 -r 0de92f0b96ef test-data/normalized_presence_absence_observations.biom |
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| Binary file test-data/normalized_presence_absence_observations.biom has changed |
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| diff -r 501c21cce614 -r 0de92f0b96ef test-data/normalized_relative_abund_samples.biom |
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| Binary file test-data/normalized_relative_abund_samples.biom has changed |
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| diff -r 501c21cce614 -r 0de92f0b96ef test-data/observation_subsetting --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/observation_subsetting Wed Sep 11 12:40:19 2019 -0400 |
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| @@ -0,0 +1,2 @@ +11 +23 \ No newline at end of file |
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| diff -r 501c21cce614 -r 0de92f0b96ef test-data/sample_subsetting --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sample_subsetting Wed Sep 11 12:40:19 2019 -0400 |
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| @@ -0,0 +1,1 @@ +SAMPLE_1 \ No newline at end of file |
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| diff -r 501c21cce614 -r 0de92f0b96ef test-data/subset_observations.biom --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/subset_observations.biom Wed Sep 11 12:40:19 2019 -0400 |
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| @@ -0,0 +1,23 @@ +{ +"id": "None" +, +"format": "Biological Observation Matrix 1.0.0" +, +"format_url": "http://biom-format.org" +, +"type": "OTU table" +, +"generated_by": "BIOM-Format 2.1.5" +, +"date": "2016-05-26T17:20:40.263567" +, +"matrix_type": "sparse" +, +"matrix_element_type": "float" +, +"data": [[0,0,3.0],[0,1,4.0],[1,0,1.0]], "shape": [2, 2] +, +"rows": [{"id": "11", "metadata": null}, {"id": "23", "metadata": null}] +, +"columns": [{"id": "SAMPLE_1", "metadata": null},{"id": "SAMPLE_2", "metadata": null}] +} |
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| diff -r 501c21cce614 -r 0de92f0b96ef test-data/subset_samples.biom --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/subset_samples.biom Wed Sep 11 12:40:19 2019 -0400 |
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| @@ -0,0 +1,23 @@ +{ +"id": "None" +, +"format": "Biological Observation Matrix 1.0.0" +, +"format_url": "http://biom-format.org" +, +"type": "OTU table" +, +"generated_by": "BIOM-Format 2.1.5" +, +"date": "2016-05-26T17:20:40.263567" +, +"matrix_type": "sparse" +, +"matrix_element_type": "float" +, +"data": [[1,0,160.0],[6,0,1.0],[7,0,3.0],[12,0,13.0],[14,0,1.0],[15,0,1.0],[16,0,1.0]], "shape": [19, 1] +, +"columns": [{"id": "SAMPLE_1", "metadata": null}] +, +"rows": [{"id": "2", "metadata": null},{"id": "3", "metadata": null},{"id": "4", "metadata": null},{"id": "5", "metadata": null},{"id": "8", "metadata": null},{"id": "9", "metadata": null},{"id": "10", "metadata": null},{"id": "11", "metadata": null},{"id": "12", "metadata": null},{"id": "14", "metadata": null},{"id": "15", "metadata": null},{"id": "16", "metadata": null},{"id": "17", "metadata": null},{"id": "18", "metadata": null},{"id": "22", "metadata": null},{"id": "23", "metadata": null},{"id": "25", "metadata": null},{"id": "28", "metadata": null},{"id": "29", "metadata": null}] +} |
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| diff -r 501c21cce614 -r 0de92f0b96ef test-data/summarize --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summarize Wed Sep 11 12:40:19 2019 -0400 |
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| @@ -0,0 +1,17 @@ +Num samples: 2 +Num observations: 19 +Total count: 471 +Table density (fraction of non-zero values): 0.342 + +Counts/sample summary: + Min: 180.0 + Max: 291.0 + Median: 235.500 + Mean: 235.500 + Std. dev.: 55.500 + Sample Metadata Categories: None provided + Observation Metadata Categories: None provided + +Counts/sample detail: +SAMPLE_1: 180.0 +SAMPLE_2: 291.0 \ No newline at end of file |
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| diff -r 501c21cce614 -r 0de92f0b96ef test-data/summarize_qualitative_observations --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summarize_qualitative_observations Wed Sep 11 12:40:19 2019 -0400 |
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| @@ -0,0 +1,32 @@ +Num samples: 2 +Num observations: 19 + +Sample/observations summary: + Min: 0 + Max: 2 + Median: 0.000 + Mean: 0.684 + Std. dev.: 0.921 + Sample Metadata Categories: None provided + Observation Metadata Categories: None provided + +Observations/sample detail: +2: 0 +16: 0 +12: 0 +8: 0 +4: 0 +18: 0 +9: 0 +29: 0 +5: 0 +28: 0 +14: 0 +15: 0 +23: 1 +10: 2 +17: 2 +25: 2 +22: 2 +11: 2 +3: 2 \ No newline at end of file |
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| diff -r 501c21cce614 -r 0de92f0b96ef test-data/uc_table.uc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/uc_table.uc Wed Sep 11 12:40:19 2019 -0400 |
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