| Previous changeset 18:28ab1cdd0cf5 (2021-04-12) Next changeset 20:8d9c22419c56 (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-normalise-data.xml scanpy_macros2.xml |
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| diff -r 28ab1cdd0cf5 -r 3a4564b9d685 scanpy-normalise-data.xml --- a/scanpy-normalise-data.xml Mon Apr 12 14:43:58 2021 +0000 +++ b/scanpy-normalise-data.xml Wed May 05 12:11:45 2021 +0000 |
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| @@ -21,12 +21,10 @@ #if $settings.exclude.exclude_highly_expressed --exclude-highly-expressed --max-fraction '${settings.exclude.max_fraction}' #end if - #if $settings.save_raw - --save-raw ${settings.save_raw} - #end if #end if @INPUT_OPTS@ @OUTPUT_OPTS@ + @SAVE_MATRIX_OPTS@ @EXPORT_MTX_OPTS@ ]]></command> @@ -34,6 +32,7 @@ <expand macro="input_object_params"/> <expand macro="output_object_params"/> <expand macro="export_mtx_params"/> + <expand macro="save_matrix_params"/> <conditional name="settings"> <param name="default" type="boolean" checked="true" label="Use programme defaults"/> <when value="true"/> @@ -42,8 +41,6 @@ label="Target number to normalise to" help="Aimed counts per cell after normalisation."/> <param name="log_transform" argument="--no-log-transform" type="boolean" truevalue="" falsevalue="--no-log-transform" checked="True" label="Apply log transform?" help="If enabled, will apply a log transformation following normalisation."/> - <param name="save_raw" argument="--save-raw" type="boolean" truevalue="yes" falsevalue="no" checked="true" - label="Save normalised data in `.raw`" help="The saved normalised data are log1p transformed."/> <conditional name="exclude"> <param name="exclude_highly_expressed" argument="--exclude-highly-expressed" type="boolean" checked="False" label="Exclude highly expressed genes?" help="Exclude (very) highly expressed genes for the computation of the normalization factor (size factor) for each cell. A gene is considered highly expressed, if it has more than max_fraction of the total counts in at least one cell. The not-excluded genes will sum up to the number specified by --normalize-to."/> |
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| diff -r 28ab1cdd0cf5 -r 3a4564b9d685 scanpy_macros2.xml --- a/scanpy_macros2.xml Mon Apr 12 14:43:58 2021 +0000 +++ b/scanpy_macros2.xml Wed May 05 12:11:45 2021 +0000 |
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| @@ -30,6 +30,14 @@ <token name="@INPUT_OPTS@"> --input-format '${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'"/> |