| Previous changeset 0:367b1ed91207 (2016-06-07) Next changeset 2:e3cbd2287f63 (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_add_metadata.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 367b1ed91207 -r 28ad7ac9c193 biom_add_metadata.xml --- a/biom_add_metadata.xml Tue Jun 07 17:25:44 2016 -0400 +++ b/biom_add_metadata.xml Wed Sep 11 12:41:29 2019 -0400 |
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| @@ -1,75 +1,68 @@ -<tool id="biom_add_metadata" name="BIOM metadata" version="@VERSION@.0"> - <description>add-metadata</description> +<tool id="biom_add_metadata" name="Add metadata" version="@VERSION@.1"> + <description>to a BIOM table</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements" /> - <expand macro="stdio" /> <expand macro="version_command" /> - <command> + <command detect_errors="exit_code"> <![CDATA[ biom add-metadata - -i "${input_table}" - -o "${output_table}" - #if $input_sample_metadata: - --sample-metadata-fp "${input_sample_metadata}" + --input-fp '$input_fp' + --output-fp '$output_fp' + #if $sample_metadata_fp + --sample-metadata-fp '$sample_metadata_fp' #end if - #if $input_observation_metadata: - --observation-metadata-fp "${input_observation_metadata}" + #if $observation_metadata_fp + --observation-metadata-fp '$observation_metadata_fp' #end if - #if $sc_separated: - --sc-separated "${sc_separated}" + #if $sc_separated + --sc-separated '$sc_separated' #end if - #if $sc_pipe_separated: - --sc-pipe-separated "${sc_pipe_separated}" + #if $sc_pipe_separated + --sc-pipe-separated '$sc_pipe_separated' #end if - #if $int_fields: - --int-fields "${int_fields}" + #if $int_fields + --int-fields '$int_fields' #end if - #if $float_fields: - --float-fields "${float_fields}" + #if $float_fields + --float-fields '$float_fields' #end if - #if $sample_header: - --sample-header "${sample_header}" + #if $sample_header + --sample-header '$sample_header' #end if - #if $observation_header: - --observation-header "${observation_header}" + #if $observation_header + --observation-header '$observation_header' #end if - ${output_as_json} + $output_as_json ]]> </command> <inputs> - <param name="input_table" type="data" format="biom1" label="BIOM File" argument="--input-fp"/> - <param name="input_sample_metadata" type="data" format="tabular" optional="True" label="Sample Metadata Tabular File" argument="--sample-metadata-fp PATH"/> - <param name="input_observation_metadata" type="data" format="tabular" optional="True" label="Observation Metadata Tabular File" argument="--observation-metadata-fp"/> - <param name="sc_separated" type="text" value="" label="Comma-separated list of the metadata fields to split on semicolons" argument="--sc-separated"/> - <param name="sc_pipe_separated" type="text" value="" label="Comma-separated list of the metadata fields to split on semicolons and pipes (|)" argument="--sc-pipe-separated"/> - <param name="int_fields" type="text" value="" label="Comma-separated list of the metadata fields to cast to integers" argument="--int-fields"/> - <param name="float_fields" type="text" value="" label="Comma-separated list of the metadata fields to cast to floating point numbers" argument="--float-fields"/> - <param name="sample_header" type="text" value="" label="Comma-separated list of the sample metadata field names" argument="--sample-header"/> - <param name="observation_header" type="text" value="" label="Comma-separated list of the observation metadata field names" argument="--observation-header"/> - <param name="output_as_json" type="boolean" checked="True" truevalue="--output-as-json" falsevalue="" label="Write the output file in JSON format (biom1)" argument="--output-as-json"/> + <param name="input_fp" argument="--input-fp" type="data" format="biom1" label="BIOM File"/> + <param name="sample_metadata_fp" argument="--sample-metadata-fp" type="data" format="tabular" optional="True" label="Sample Metadata Tabular File" /> + <param name="observation_metadata_fp" argument="--observation-metadata-fp" type="data" format="tabular" optional="True" label="Observation Metadata Tabular File"/> + <param name="sc_separated" argument="--sc-separated" type="text" value="" label="Comma-separated list of the metadata fields to split on semicolons" /> + <param name="sc_pipe_separated" argument="--sc-pipe-separated" type="text" value="" label="Comma-separated list of the metadata fields to split on semicolons and pipes (|)"/> + <param name="int_fields" argument="--int-fields" type="text" value="" label="Comma-separated list of the metadata fields to cast to integers" /> + <param name="float_fields" argument="--float-fields" type="text" value="" label="Comma-separated list of the metadata fields to cast to floating point numbers" /> + <param name="sample_header" argument="--sample-header" type="text" value="" label="Comma-separated list of the sample metadata field names" /> + <param name="observation_header" argument="--observation-header" type="text" value="" label="Comma-separated list of the observation metadata field names" /> + <param name="output_as_json" argument="--output-as-json" type="boolean" checked="True" truevalue="--output-as-json" falsevalue="" label="Write the output file in JSON format (biom1)" /> </inputs> <outputs> - <data format="biom1" name="output_table"> + <data format="biom1" name="output_fp"> <change_format> - <when input="${str( $output_as_json )}" value="" format="biom2" /> + <when input="${str( $output_as_json )}" value="" format="h5" /> </change_format> </data> </outputs> <tests> <test> - <param name="input_table" value="input_abundance_1.biom1" ftype="biom1"/> - <param name="input_observation_metadata" value="input_taxonomy_1.tabular" ftype="tabular"/> + <param name="input_fp" value="input_abundance_1.biom1" ftype="biom1"/> + <param name="observation_metadata_fp" value="input_taxonomy_1.tabular" ftype="tabular"/> <param name="sc_separated" value="taxonomy"/> - <param name="input_sample_metadata"/> - <param name="sc_pipe_separated" value=""/> - <param name="int_fields" value=""/> - <param name="float_fields" value=""/> - <param name="sample_header" value=""/> - <param name="observation_header" value=""/> - <param name="output_as_json" value="True"/> - <output name="output_table" file="output_taxonomy_1.biom1.re" ftype="biom1" compare="re_match"/> + <param name="output_as_json" value="--output-as-json"/> + <output name="output_fp" file="output_taxonomy_1.biom1.re" ftype="biom1" compare="re_match"/> </test> </tests> <help><![CDATA[ @@ -127,8 +120,6 @@ provided here. --output-as-json Write the output file in JSON format. --help Show this message and exit. - - ]]></help> <expand macro="citations" /> </tool> |
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| diff -r 367b1ed91207 -r 28ad7ac9c193 macros.xml --- a/macros.xml Tue Jun 07 17:25:44 2016 -0400 +++ b/macros.xml Wed Sep 11 12:41:29 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 367b1ed91207 -r 28ad7ac9c193 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 367b1ed91207 -r 28ad7ac9c193 test-data/input_abundance_1.tabular --- a/test-data/input_abundance_1.tabular Tue Jun 07 17:25:44 2016 -0400 +++ b/test-data/input_abundance_1.tabular Wed Sep 11 12:41:29 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 367b1ed91207 -r 28ad7ac9c193 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 367b1ed91207 -r 28ad7ac9c193 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 367b1ed91207 -r 28ad7ac9c193 test-data/observation_subsetting --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/observation_subsetting Wed Sep 11 12:41:29 2019 -0400 |
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| @@ -0,0 +1,2 @@ +11 +23 \ No newline at end of file |
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| diff -r 367b1ed91207 -r 28ad7ac9c193 test-data/sample_subsetting --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sample_subsetting Wed Sep 11 12:41:29 2019 -0400 |
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| @@ -0,0 +1,1 @@ +SAMPLE_1 \ No newline at end of file |
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| diff -r 367b1ed91207 -r 28ad7ac9c193 test-data/subset_observations.biom --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/subset_observations.biom Wed Sep 11 12:41:29 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 367b1ed91207 -r 28ad7ac9c193 test-data/subset_samples.biom --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/subset_samples.biom Wed Sep 11 12:41:29 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 367b1ed91207 -r 28ad7ac9c193 test-data/summarize --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summarize Wed Sep 11 12:41:29 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 367b1ed91207 -r 28ad7ac9c193 test-data/summarize_qualitative_observations --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summarize_qualitative_observations Wed Sep 11 12:41:29 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 367b1ed91207 -r 28ad7ac9c193 test-data/uc_table.uc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/uc_table.uc Wed Sep 11 12:41:29 2019 -0400 |
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