Mercurial > repos > ebi-gxa > scanpy_integrate_harmony
changeset 6:1d92cea73607 draft
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
| author | ebi-gxa |
|---|---|
| date | Wed, 05 May 2021 12:10:53 +0000 |
| parents | 3f61bf17ca50 |
| children | bf824765919c |
| files | scanpy_macros2.xml |
| diffstat | 1 files changed, 16 insertions(+), 1 deletions(-) [+] |
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--- a/scanpy_macros2.xml Mon Apr 12 14:43:07 2021 +0000 +++ b/scanpy_macros2.xml Wed May 05 12:10:53 2021 +0000 @@ -30,6 +30,14 @@ <token name="@INPUT_OPTS@"> --input-format '${input_format}' input.h5 </token> + <token name="@SAVE_MATRIX_OPTS@"> + #if $save_raw + --save-raw + #end if + #if $save_layer + --save-layer ${settings.save_layer} + #end if + </token> <token name="@OUTPUT_OPTS@"> #if str($output_format).startswith('anndata') --show-obj stdout --output-format anndata output.h5 @@ -51,7 +59,7 @@ <xml name="requirements"> <requirements> - <requirement type="package" version="0.3.3">scanpy-scripts</requirement> + <requirement type="package" version="0.4.0">scanpy-scripts</requirement> <yield/> </requirements> </xml> @@ -122,6 +130,13 @@ </data> </xml> + <xml name="save_matrix_params"> + <param name="save_raw" argument="--save-raw" type="boolean" truevalue="yes" falsevalue="no" checked="false" + label="Save adata to adata.raw before processing?" /> + <param name="save_layer" argument="--save-layer" type="text" optional="true" + label="Save adata.X to the specified layer before processing."/> + </xml> + <xml name="output_plot_params"> <param name="fig_title" argument="--title" type="text" label="Figure title"/> <param name="fig_size" argument="--fig-size" type="text" value="4,4" label="Figure size as 'width,height', e.g, '7,7'"/>