Mercurial > repos > iuc > biom_add_metadata
changeset 0:367b1ed91207 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
| author | iuc |
|---|---|
| date | Tue, 07 Jun 2016 17:25:44 -0400 |
| parents | |
| children | 28ad7ac9c193 |
| files | biom_add_metadata.xml macros.xml test-data/input_abundance_1.biom1 test-data/input_abundance_1.tabular test-data/input_abundance_taxonomy_1.tabular test-data/input_taxonomy_1.tabular test-data/output_1.biom1.re test-data/output_taxonomy_1.biom1.re |
| diffstat | 8 files changed, 221 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/biom_add_metadata.xml Tue Jun 07 17:25:44 2016 -0400 @@ -0,0 +1,134 @@ +<tool id="biom_add_metadata" name="BIOM metadata" version="@VERSION@.0"> + <description>add-metadata</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <expand macro="stdio" /> + <expand macro="version_command" /> + <command> + <![CDATA[ + biom add-metadata + -i "${input_table}" + -o "${output_table}" + #if $input_sample_metadata: + --sample-metadata-fp "${input_sample_metadata}" + #end if + #if $input_observation_metadata: + --observation-metadata-fp "${input_observation_metadata}" + #end if + #if $sc_separated: + --sc-separated "${sc_separated}" + #end if + #if $sc_pipe_separated: + --sc-pipe-separated "${sc_pipe_separated}" + #end if + #if $int_fields: + --int-fields "${int_fields}" + #end if + #if $float_fields: + --float-fields "${float_fields}" + #end if + #if $sample_header: + --sample-header "${sample_header}" + #end if + #if $observation_header: + --observation-header "${observation_header}" + #end if + ${output_as_json} + ]]> + </command> + <inputs> + <param name="input_table" type="data" format="biom1" label="BIOM File" argument="--input-fp"/> + <param name="input_sample_metadata" type="data" format="tabular" optional="True" label="Sample Metadata Tabular File" argument="--sample-metadata-fp PATH"/> + <param name="input_observation_metadata" type="data" format="tabular" optional="True" label="Observation Metadata Tabular File" argument="--observation-metadata-fp"/> + <param name="sc_separated" type="text" value="" label="Comma-separated list of the metadata fields to split on semicolons" argument="--sc-separated"/> + <param name="sc_pipe_separated" type="text" value="" label="Comma-separated list of the metadata fields to split on semicolons and pipes (|)" argument="--sc-pipe-separated"/> + <param name="int_fields" type="text" value="" label="Comma-separated list of the metadata fields to cast to integers" argument="--int-fields"/> + <param name="float_fields" type="text" value="" label="Comma-separated list of the metadata fields to cast to floating point numbers" argument="--float-fields"/> + <param name="sample_header" type="text" value="" label="Comma-separated list of the sample metadata field names" argument="--sample-header"/> + <param name="observation_header" type="text" value="" label="Comma-separated list of the observation metadata field names" argument="--observation-header"/> + <param name="output_as_json" type="boolean" checked="True" truevalue="--output-as-json" falsevalue="" label="Write the output file in JSON format (biom1)" argument="--output-as-json"/> + </inputs> + <outputs> + <data format="biom1" name="output_table"> + <change_format> + <when input="${str( $output_as_json )}" value="" format="biom2" /> + </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="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"/> + </test> + </tests> + <help><![CDATA[ + +Usage: biom add-metadata [OPTIONS] + + Add metadata to a BIOM table. + + Add sample and/or observation metadata to BIOM-formatted files. See + examples here: http://biom-format.org/documentation/adding_metadata.html + + Example usage: + + Add sample metadata to a BIOM table: + + $ biom add-metadata -i otu_table.biom -o table_with_sample_metadata.biom + -m sample_metadata.txt + +Options: + -i, --input-fp PATH The input BIOM table [required] + -o, --output-fp PATH The output BIOM table [required] + -m, --sample-metadata-fp PATH The sample metadata mapping file (will add + sample metadata to the input BIOM table, if + provided). + --observation-metadata-fp PATH The observation metadata mapping file (will + add observation metadata to the input BIOM + table, if provided). + --sc-separated TEXT Comma-separated list of the metadata fields + to split on semicolons. This is useful for + hierarchical data such as taxonomy or + functional categories. + --sc-pipe-separated TEXT Comma-separated list of the metadata fields + to split on semicolons and pipes ("|"). This + is useful for hierarchical data such as + functional categories with one-to-many + mappings (e.g. x;y;z|x;y;w)). + --int-fields TEXT Comma-separated list of the metadata fields + to cast to integers. This is useful for + integer data such as "DaysSinceStart". + --float-fields TEXT Comma-separated list of the metadata fields + to cast to floating point numbers. This is + useful for real number data such as "pH". + --sample-header TEXT Comma-separated list of the sample metadata + field names. This is useful if a header line + is not provided with the metadata, if you + want to rename the fields, or if you want to + include only the first n fields where n is + the number of entries provided here. + --observation-header TEXT Comma-separated list of the observation + metadata field names. This is useful if a + header line is not provided with the + metadata, if you want to rename the fields, + or if you want to include only the first n + fields where n is the number of entries + provided here. + --output-as-json Write the output file in JSON format. + --help Show this message and exit. + + + ]]></help> + <expand macro="citations" /> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Tue Jun 07 17:25:44 2016 -0400 @@ -0,0 +1,24 @@ +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="2.1.5">biom-format</requirement> + <yield/> + </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> + <xml name="citations"> + <citations> + <citation type="doi">10.1186/2047-217X-1-7</citation> + <yield/> + </citations> + </xml> +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input_abundance_1.biom1 Tue Jun 07 17:25:44 2016 -0400 @@ -0,0 +1,1 @@ +{"id": "None","format": "Biological Observation Matrix 1.0.0","format_url": "http://biom-format.org","matrix_type": "sparse","generated_by": "BIOM-Format 2.1.5","date": "2016-05-26T17:20:40.263567","type": "OTU table","matrix_element_type": "float","shape": [19, 2],"data": [[1,0,160.0],[1,1,242.0],[6,0,1.0],[6,1,1.0],[7,0,3.0],[7,1,4.0],[12,0,13.0],[12,1,36.0],[14,0,1.0],[14,1,5.0],[15,0,1.0],[16,0,1.0],[16,1,3.0]],"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}],"columns": [{"id": "SAMPLE_1", "metadata": null},{"id": "SAMPLE_2", "metadata": null}]} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input_abundance_1.tabular Tue Jun 07 17:25:44 2016 -0400 @@ -0,0 +1,20 @@ +#ID SAMPLE_1 SAMPLE_2 +2 0 0 +3 160 242 +4 0 0 +5 0 0 +8 0 0 +9 0 0 +10 1 1 +11 3 4 +12 0 0 +14 0 0 +15 0 0 +16 0 0 +17 13 36 +18 0 0 +22 1 5 +23 1 0 +25 1 3 +28 0 0 +29 0 0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input_abundance_taxonomy_1.tabular Tue Jun 07 17:25:44 2016 -0400 @@ -0,0 +1,20 @@ +#ID SAMPLE_1 SAMPLE_2 taxonomy +2 0 0 d__Archaea +3 160 242 d__Bacteria +4 0 0 d__Archaea;p__Crenarchaeota +5 0 0 d__Archaea;p__Euryarchaeota +8 0 0 d__Bacteria;p__AC1 +9 0 0 d__Bacteria;p__AD3 +10 1 1 d__Bacteria;p__Acidobacteria +11 3 4 d__Bacteria;p__Actinobacteria +12 0 0 d__Bacteria;p__AncK6 +14 0 0 d__Bacteria;p__Armatimonadetes +15 0 0 d__Bacteria;p__BHI80-139 +16 0 0 d__Bacteria;p__BRC1 +17 13 36 d__Bacteria;p__Bacteroidetes +18 0 0 d__Bacteria;p__CD12 +22 1 5 d__Bacteria;p__Chlorobi +23 1 0 d__Bacteria;p__Chloroflexi +25 1 3 d__Bacteria;p__Cyanobacteria +28 0 0 d__Bacteria;p__EM19 +29 0 0 d__Bacteria;p__EM3
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input_taxonomy_1.tabular Tue Jun 07 17:25:44 2016 -0400 @@ -0,0 +1,20 @@ +#ID taxonomy +2 d__Archaea +3 d__Bacteria +4 d__Archaea;p__Crenarchaeota +5 d__Archaea;p__Euryarchaeota +8 d__Bacteria;p__AC1 +9 d__Bacteria;p__AD3 +10 d__Bacteria;p__Acidobacteria +11 d__Bacteria;p__Actinobacteria +12 d__Bacteria;p__AncK6 +14 d__Bacteria;p__Armatimonadetes +15 d__Bacteria;p__BHI80-139 +16 d__Bacteria;p__BRC1 +17 d__Bacteria;p__Bacteroidetes +18 d__Bacteria;p__CD12 +22 d__Bacteria;p__Chlorobi +23 d__Bacteria;p__Chloroflexi +25 d__Bacteria;p__Cyanobacteria +28 d__Bacteria;p__EM19 +29 d__Bacteria;p__EM3
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_1.biom1.re Tue Jun 07 17:25:44 2016 -0400 @@ -0,0 +1,1 @@ +\{\"id\"\:\ \"None\"\,\"format\"\:\ \"Biological\ Observation\ Matrix\ 1\.0\.0\"\,\"format\_url\"\:\ \"http\:\/\/biom\-format\.org\"\,\"matrix\_type\"\:\ \"sparse\"\,\"generated\_by\"\:\ \"BIOM\-Format\ 2\.1\.5\"\,\"date\"\:\ \".*\"\,\"type\"\:\ \"OTU\ table\"\,\"matrix\_element\_type\"\:\ \"float\"\,\"shape\"\:\ \[19\,\ 2\]\,\"data\"\:\ \[\[1\,0\,160\.0\]\,\[1\,1\,242\.0\]\,\[6\,0\,1\.0\]\,\[6\,1\,1\.0\]\,\[7\,0\,3\.0\]\,\[7\,1\,4\.0\]\,\[12\,0\,13\.0\]\,\[12\,1\,36\.0\]\,\[14\,0\,1\.0\]\,\[14\,1\,5\.0\]\,\[15\,0\,1\.0\]\,\[16\,0\,1\.0\]\,\[16\,1\,3\.0\]\]\,\"rows\"\:\ \[\{\"id\"\:\ \"2\"\,\ \"metadata\"\:\ null\}\,\{\"id\"\:\ \"3\"\,\ \"metadata\"\:\ null\}\,\{\"id\"\:\ \"4\"\,\ \"metadata\"\:\ null\}\,\{\"id\"\:\ \"5\"\,\ \"metadata\"\:\ null\}\,\{\"id\"\:\ \"8\"\,\ \"metadata\"\:\ null\}\,\{\"id\"\:\ \"9\"\,\ \"metadata\"\:\ null\}\,\{\"id\"\:\ \"10\"\,\ \"metadata\"\:\ null\}\,\{\"id\"\:\ \"11\"\,\ \"metadata\"\:\ null\}\,\{\"id\"\:\ \"12\"\,\ \"metadata\"\:\ null\}\,\{\"id\"\:\ \"14\"\,\ \"metadata\"\:\ null\}\,\{\"id\"\:\ \"15\"\,\ \"metadata\"\:\ null\}\,\{\"id\"\:\ \"16\"\,\ \"metadata\"\:\ null\}\,\{\"id\"\:\ \"17\"\,\ \"metadata\"\:\ null\}\,\{\"id\"\:\ \"18\"\,\ \"metadata\"\:\ null\}\,\{\"id\"\:\ \"22\"\,\ \"metadata\"\:\ null\}\,\{\"id\"\:\ \"23\"\,\ \"metadata\"\:\ null\}\,\{\"id\"\:\ \"25\"\,\ \"metadata\"\:\ null\}\,\{\"id\"\:\ \"28\"\,\ \"metadata\"\:\ null\}\,\{\"id\"\:\ \"29\"\,\ \"metadata\"\:\ null\}\]\,\"columns\"\:\ \[\{\"id\"\:\ \"SAMPLE\_1\"\,\ \"metadata\"\:\ null\}\,\{\"id\"\:\ \"SAMPLE\_2\"\,\ \"metadata\"\:\ null\}\]\}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_taxonomy_1.biom1.re Tue Jun 07 17:25:44 2016 -0400 @@ -0,0 +1,1 @@ +\{\"id\"\:\ \"None\"\,\"format\"\:\ \"Biological\ Observation\ Matrix\ 1\.0\.0\"\,\"format\_url\"\:\ \"http\:\/\/biom\-format\.org\"\,\"matrix\_type\"\:\ \"sparse\"\,\"generated\_by\"\:\ \"BIOM\-Format\ 2\.1\.5\"\,\"date\"\:\ \".*\"\,\"type\"\:\ \"OTU\ table\"\,\"matrix\_element\_type\"\:\ \"float\"\,\"shape\"\:\ \[19\,\ 2\]\,\"data\"\:\ \[\[1\,0\,160\.0\]\,\[1\,1\,242\.0\]\,\[6\,0\,1\.0\]\,\[6\,1\,1\.0\]\,\[7\,0\,3\.0\]\,\[7\,1\,4\.0\]\,\[12\,0\,13\.0\]\,\[12\,1\,36\.0\]\,\[14\,0\,1\.0\]\,\[14\,1\,5\.0\]\,\[15\,0\,1\.0\]\,\[16\,0\,1\.0\]\,\[16\,1\,3\.0\]\]\,\"rows\"\:\ \[\{\"id\"\:\ \"2\"\,\ \"metadata\"\:\ \{\"taxonomy\"\:\ \[\"d\_\_Archaea\"\]\}\}\,\{\"id\"\:\ \"3\"\,\ \"metadata\"\:\ \{\"taxonomy\"\:\ \[\"d\_\_Bacteria\"\]\}\}\,\{\"id\"\:\ \"4\"\,\ \"metadata\"\:\ \{\"taxonomy\"\:\ \[\"d\_\_Archaea\"\,\ \"p\_\_Crenarchaeota\"\]\}\}\,\{\"id\"\:\ \"5\"\,\ \"metadata\"\:\ \{\"taxonomy\"\:\ \[\"d\_\_Archaea\"\,\ \"p\_\_Euryarchaeota\"\]\}\}\,\{\"id\"\:\ \"8\"\,\ \"metadata\"\:\ \{\"taxonomy\"\:\ \[\"d\_\_Bacteria\"\,\ \"p\_\_AC1\"\]\}\}\,\{\"id\"\:\ \"9\"\,\ \"metadata\"\:\ \{\"taxonomy\"\:\ \[\"d\_\_Bacteria\"\,\ \"p\_\_AD3\"\]\}\}\,\{\"id\"\:\ \"10\"\,\ \"metadata\"\:\ \{\"taxonomy\"\:\ \[\"d\_\_Bacteria\"\,\ \"p\_\_Acidobacteria\"\]\}\}\,\{\"id\"\:\ \"11\"\,\ \"metadata\"\:\ \{\"taxonomy\"\:\ \[\"d\_\_Bacteria\"\,\ \"p\_\_Actinobacteria\"\]\}\}\,\{\"id\"\:\ \"12\"\,\ \"metadata\"\:\ \{\"taxonomy\"\:\ \[\"d\_\_Bacteria\"\,\ \"p\_\_AncK6\"\]\}\}\,\{\"id\"\:\ \"14\"\,\ \"metadata\"\:\ \{\"taxonomy\"\:\ \[\"d\_\_Bacteria\"\,\ \"p\_\_Armatimonadetes\"\]\}\}\,\{\"id\"\:\ \"15\"\,\ \"metadata\"\:\ \{\"taxonomy\"\:\ \[\"d\_\_Bacteria\"\,\ \"p\_\_BHI80\-139\"\]\}\}\,\{\"id\"\:\ \"16\"\,\ \"metadata\"\:\ \{\"taxonomy\"\:\ \[\"d\_\_Bacteria\"\,\ \"p\_\_BRC1\"\]\}\}\,\{\"id\"\:\ \"17\"\,\ \"metadata\"\:\ \{\"taxonomy\"\:\ \[\"d\_\_Bacteria\"\,\ \"p\_\_Bacteroidetes\"\]\}\}\,\{\"id\"\:\ \"18\"\,\ \"metadata\"\:\ \{\"taxonomy\"\:\ \[\"d\_\_Bacteria\"\,\ \"p\_\_CD12\"\]\}\}\,\{\"id\"\:\ \"22\"\,\ \"metadata\"\:\ \{\"taxonomy\"\:\ \[\"d\_\_Bacteria\"\,\ \"p\_\_Chlorobi\"\]\}\}\,\{\"id\"\:\ \"23\"\,\ \"metadata\"\:\ \{\"taxonomy\"\:\ \[\"d\_\_Bacteria\"\,\ \"p\_\_Chloroflexi\"\]\}\}\,\{\"id\"\:\ \"25\"\,\ \"metadata\"\:\ \{\"taxonomy\"\:\ \[\"d\_\_Bacteria\"\,\ \"p\_\_Cyanobacteria\"\]\}\}\,\{\"id\"\:\ \"28\"\,\ \"metadata\"\:\ \{\"taxonomy\"\:\ \[\"d\_\_Bacteria\"\,\ \"p\_\_EM19\"\]\}\}\,\{\"id\"\:\ \"29\"\,\ \"metadata\"\:\ \{\"taxonomy\"\:\ \[\"d\_\_Bacteria\"\,\ \"p\_\_EM3\"\]\}\}\]\,\"columns\"\:\ \[\{\"id\"\:\ \"SAMPLE\_1\"\,\ \"metadata\"\:\ null\}\,\{\"id\"\:\ \"SAMPLE\_2\"\,\ \"metadata\"\:\ null\}\]\}