Mercurial > repos > iuc > anndata_export
diff export.xml @ 0:fcb7370e827f draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
| author | iuc |
|---|---|
| date | Wed, 10 Apr 2019 03:24:14 -0400 |
| parents | |
| children | 8623710d083c |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/export.xml Wed Apr 10 03:24:14 2019 -0400 @@ -0,0 +1,82 @@ +<tool id="anndata_export" name="Export AnnData" version="@VERSION@+@GALAXY_VERSION@"> + <description>to different formats</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <expand macro="version_command"/> + <command detect_errors="exit_code"><![CDATA[ +@CMD@ + ]]></command> + <configfiles> + <configfile name="script_file"><![CDATA[ +@CMD_imports@ + +adata = ad.read('$input') +#if $output_format == 'loom' +adata.write_loom('anndata.loom') +#else if $output_format == 'tabular' +adata.write_csvs('.', sep="\t", skip_data = False) +#end if +]]></configfile> + </configfiles> + <inputs> + <param name="input" type="data" format="h5ad" label="Annotated data matrix"/> + <param name="output_format" type="select" label="Format to write the annotated data matrix"> + <option value="loom">loom</option> + <option value="tabular">Tabular</option> + </param> + </inputs> + <outputs> + <data name="loom_output" format="loom" from_work_dir="anndata.loom" label="${tool.name} on ${on_string}: Annotated data matrix"> + <filter>output_format == 'loom'</filter> + </data> + <data name="tabular_x" format="tabular" from_work_dir="X.csv" label="${tool.name} on ${on_string}: Matrix table (X)"> + <filter>output_format == 'tabular'</filter> + </data> + <data name="tabular_obs" format="tabular" from_work_dir="obs.csv" label="${tool.name} on ${on_string}: Key-indexed one-dimensional observations annotation (obs)"> + <filter>output_format == 'tabular'</filter> + </data> + <data name="tabular_obsm" format="tabular" from_work_dir="obsm.csv" label="${tool.name} on ${on_string}: Key-indexed multi-dimensional observations annotation (obsm)"> + <filter>output_format == 'tabular'</filter> + </data> + <data name="tabular_var" format="tabular" from_work_dir="var.csv" label="${tool.name} on ${on_string}: Key-indexed one-dimensional variables annotation (var)"> + <filter>output_format == 'tabular'</filter> + </data> + <data name="tabular_varm" format="tabular" from_work_dir="varm.csv" label="${tool.name} on ${on_string}: Key-indexed multi-dimensional variables annotation (varm)"> + <filter>output_format == 'tabular'</filter> + </data> + </outputs> + <tests> + <test> + <param name="input" value="krumsiek11.h5ad"/> + <param name="output_format" value="loom"/> + <assert_stdout> + <has_text_matching expression="adata.write_loom"/> + </assert_stdout> + <output name="loom_output" value="export.krumsiek11.loom" ftype="loom" compare="sim_size"/> + </test> + <test> + <param name="input" value="krumsiek11.h5ad"/> + <param name="output_format" value="tabular"/> + <assert_stdout> + <has_text_matching expression="adata.write_csvs"/> + </assert_stdout> + <output name="tabular_x" value="export.krumsiek11.X.tabular" ftype="tabular"/> + <output name="tabular_obs" value="export.krumsiek11.obs.tabular" ftype="tabular"/> + <output name="tabular_obsm" value="export.krumsiek11.obsm.tabular" ftype="tabular"/> + <output name="tabular_var" value="export.krumsiek11.var.tabular" ftype="tabular"/> + <output name="tabular_varm" value="export.krumsiek11.varm.tabular" ftype="tabular"/> + </test> + </tests> + <help><![CDATA[ +**What it does** + +This tool exports a AnnData dataset to a Loom file +(`write_loom method <https://anndata.readthedocs.io/en/latest/anndata.AnnData.write_loom.html>`__) +or a Tabular file (`write_csvs method <https://anndata.readthedocs.io/en/latest/anndata.AnnData.write_csvs.html>`__) + +@HELP@ + ]]></help> + <expand macro="citations"/> +</tool>