# HG changeset patch # User ebi-gxa # Date 1620216757 0 # Node ID 1bc31f0f3aea98caf482db2461427bac8f218e16 # Parent 2fe4b4cba31228b28f60d888b3ac362980bcd985 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty" diff -r 2fe4b4cba312 -r 1bc31f0f3aea scanpy_macros2.xml --- a/scanpy_macros2.xml Mon Apr 12 14:44:49 2021 +0000 +++ b/scanpy_macros2.xml Wed May 05 12:12:37 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'"/>