| Previous changeset 17:796cd21bb304 (2021-04-12) Next changeset 19:5605f8452eb3 (2021-07-22) |
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Commit message:
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty" |
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modified:
scanpy-scale-data.xml scanpy_macros2.xml |
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| diff -r 796cd21bb304 -r 22f2957da902 scanpy-scale-data.xml --- a/scanpy-scale-data.xml Mon Apr 12 14:47:48 2021 +0000 +++ b/scanpy-scale-data.xml Wed May 05 12:15:30 2021 +0000 |
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| @@ -12,6 +12,7 @@ --max-value '${scale_max}' #end if ${zero_center} + @SAVE_MATRIX_OPTS@ @INPUT_OPTS@ @OUTPUT_OPTS@ ]]></command> @@ -22,6 +23,7 @@ <param name="zero_center" type="boolean" checked="true" truevalue="" falsevalue="--no-zero-center" label="Zero center data before scaling"/> <param name="scale_max" argument="--max-value" type="float" min="0" optional="true" label="Truncate to this value after scaling"/> + <expand macro="save_matrix_params"/> </inputs> <outputs> |
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| diff -r 796cd21bb304 -r 22f2957da902 scanpy_macros2.xml --- a/scanpy_macros2.xml Mon Apr 12 14:47:48 2021 +0000 +++ b/scanpy_macros2.xml Wed May 05 12:15:30 2021 +0000 |
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| @@ -30,6 +30,14 @@ <token name="@INPUT_OPTS@"> --input-format '${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'"/> |