Mercurial > repos > iuc > intermine_galaxy_exchange
changeset 0:3d09554c8a47 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange commit 562a034dbd23e37f1a994b1987a7cc0ec08be1a2
| author | iuc |
|---|---|
| date | Mon, 09 Jul 2018 14:11:23 -0400 |
| parents | |
| children | 5673140f2d5a |
| files | intermine_galaxy_exchange.xml test-data/intermine-format-example.tsv |
| diffstat | 2 files changed, 91 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/intermine_galaxy_exchange.xml Mon Jul 09 14:11:23 2018 -0400 @@ -0,0 +1,88 @@ +<tool id="galaxy_intermine_exchange" name="Create InterMine Interchange" version="0.0.1"> + <description>Dataset</description> + <requirements> + <requirement type="package" version="8.25">coreutils</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + awk -F \$'\t' ' { + #if str($feature_text): + f = "${feature_text}"; + #else: + f = \$${feature_column}; + #end if + + #if str($feature_id_text): + i = "${feature_id_text}"; + #else: + i = \$${feature_id_column}; + #end if + + #if str($organism_text): + o = "${organism_text}"; + #elif $organism_column: + o = \$${organism_column}; + #else: + o= ""; + #end if + + print f, i, o; } ' OFS=\$'\t' '${input_tabular}' > '${intermine_output}' + ]]> + </command> + <inputs> + <param name="input_tabular" type="data" format="txt" multiple="False" optional="False" label="Tabular file"/> + <param name="feature_column" type="data_column" data_ref="input_tabular" optional="False" label="Feature Type column" value="1"/> + <param name="feature_text" type="text" value="" optional="True" label="Feature Type" help="Optional, will override column selection with static text value"/> + <param name="feature_id_column" type="data_column" data_ref="input_tabular" optional="False" label="Feature column Identifier" value="2"/> + <param name="feature_id_text" type="text" value="" optional="True" label="Feature Type" help="Optional, will override column selection with static text value"/> + <param name="organism_column" type="data_column" data_ref="input_tabular" optional="True" label="Feature column Identifier" value="3"/> + <param name="organism_text" type="text" value="" optional="True" label="Feature Type" help="Optional, will override column selection with static text value"/> + </inputs> + <outputs> + <data format="intermine_tabular" name="intermine_output"/> + </outputs> + <tests> + <test> + <param name="input_tabular" value="intermine-format-example.tsv" ftype="tabular"/> + <param name="feature_column" value="1"/> + <param name="feature_id_text" value=""/> + <param name="feature_id_column" value="2"/> + <param name="feature_text" value=""/> + <param name="forganism_column" value="2"/> + <param name="organism_text" value=""/> + <output name="tabular_output" file="intermine-format-example.tsv" ftype="intermine_tabular"/> + </test> + </tests> + <help> + <![CDATA[ +InterMine-Galaxy exchange format +================================ +This file format exists as an intermediate step to import from Galaxy to InterMines and is not in itself a data format intended to be used for data storage or any purpose apart from Galaxy->InterMine interoperability. + +This file has two mandatory columns and one optional column + +Column 1 (mandatory) +-------------------- +**Type of identifier**, e.g. `Gene` or `Protein`. Must be a class in the `InterMine data model`_. Gene or Protein is always a safe option. + +Column 2 (mandatory) +-------------------- +**Identifier** this could be, as an example, a gene symbol like `GATA1` or another other identifier, e.g. `FBGN0000099` or perhaps a protein accession, or some other identifier. + +Column 3 (optional) +------------------- +**Organism name** - e.g. `H. sapiens` or `Drosophila melanogaster`. This is optional and does not have to be precise, but is good to provide if it is known. + +---- + +For additional information, please see: + +- https://github.com/intermine/galaxy-integration/blob/master/intermine-file-format/intermine-format-definition.md +- https://raw.githubusercontent.com/intermine/galaxy-integration/master/intermine-file-format/intermine-format-example.tsv + +.. _InterMine data model: http://intermine.readthedocs.io/en/latest/data-model/model/#a-short-example + ]]> + </help> + <citations> + <citation type="doi">10.1093/nar/gku301</citation> + </citations> +</tool>