Mercurial > repos > ebi-gxa > run_sccaf
changeset 1:647d34f125bc draft default tip
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 7034937deaaf56b2e6f585bb28234a86a5b5fa2e
| author | ebi-gxa |
|---|---|
| date | Mon, 25 Nov 2019 06:28:58 -0500 |
| parents | ca26d4b4b02c |
| children | |
| files | sccaf_macros.xml |
| diffstat | 1 files changed, 12 insertions(+), 8 deletions(-) [+] |
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--- a/sccaf_macros.xml Mon Oct 14 08:11:29 2019 -0400 +++ b/sccaf_macros.xml Mon Nov 25 06:28:58 2019 -0500 @@ -4,7 +4,7 @@ <requirement type="package" version="@TOOL_VERSION@">sccaf</requirement> </requirements> </xml> - <token name="@TOOL_VERSION@">0.0.7</token> + <token name="@TOOL_VERSION@">0.0.9</token> <token name="@SCCAF_INTRO@"> SCCAF explained =============== @@ -67,18 +67,22 @@ </citations> </xml> <xml name="input_object_params"> - <param name="input_obj_file" argument="--input-object-file" type="data" format="h5" label="Input object in AnnData hdf5 format" help="Normally the result of Scanpy (or equivalent), which already has both a visualisation (either tSNE, UMAP or PCA - needed) and clustering (ideally) pre-computed."/> - <param name="input_format" argument="--input-format" type="select" label="Format of input object"> - <option value="anndata" selected="true">AnnData format hdf5</option> - <option value="loom">Loom format hdf5, current support is incomplete</option> - </param> + <param name="input_obj_file" argument="--input-object-file" type="data" format="h5,h5ad" label="Input object in AnnData hdf5 format" help="Normally the result of Scanpy (or equivalent), which already has both a visualisation (either tSNE, UMAP or PCA - needed) and clustering (ideally) pre-computed."/> </xml> <xml name="output_object_params"> <param name="output_format" argument="--output-format" type="select" label="Format of output object"> - <option value="anndata" selected="true">AnnData format hdf5</option> - <option value="loom">Loom format hdf5, current support is defective</option> + <option value="anndata_h5ad" selected="true">AnnData format hdf5</option> + <option value="anndata">AnnData format (h5 for older versions)</option> </param> </xml> + <xml name="output_data_obj" token_description="operation"> + <data name="output_h5ad" format="h5ad" from_work_dir="output.h5" label="${tool.name} on ${on_string}: @DESCRIPTION@ AnnData"> + <filter>output_format == 'anndata_h5ad'</filter> + </data> + <data name="output_h5" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: @DESCRIPTION@ AnnData"> + <filter>output_format == 'anndata'</filter> + </data> + </xml> <xml name="output_plot_params"> <param name="color_by" argument="--color-by" type="text" value="n_genes" label="Color by attributes, comma separated strings"/> <param name="groups" argument="--groups" type="text" optional="ture" label="Restrict plotting to named groups, comma separated strings"/>