| Previous changeset 12:47c747351d62 (2020-06-05) Next changeset 14:e81a4512a057 (2020-09-10) |
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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 62f47287c7e8449c59a1f1f454852ddc669b1b1e-dirty" |
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modified:
scanpy-normalise-data.xml scanpy_macros2.xml |
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| diff -r 47c747351d62 -r 6aa97861fdfd scanpy-normalise-data.xml --- a/scanpy-normalise-data.xml Fri Jun 05 09:03:47 2020 -0400 +++ b/scanpy-normalise-data.xml Mon Sep 07 13:13:49 2020 +0000 |
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| @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="utf-8"?> -<tool id="scanpy_normalise_data" name="Scanpy NormaliseData" version="@TOOL_VERSION@+galaxy10" profile="@PROFILE@"> +<tool id="scanpy_normalise_data" name="Scanpy NormaliseData" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> <description>to make all cells having the same total expression</description> <macros> <import>scanpy_macros2.xml</import> @@ -8,10 +8,23 @@ <command detect_errors="exit_code"><![CDATA[ ln -s '${input_obj_file}' input.h5 && PYTHONIOENCODING=utf-8 scanpy-normalise-data - --normalize-to ${scale_factor} - --fraction ${fraction} - --save-raw ${save_raw} - ${log_transform} + #if not $settings.default + #if not $settings.log_transform + ${settings.log_transform} + #end if + #if $settings.scale_factor + --normalize-to '${settings.scale_factor}' + #end if + #if $settings.key_added + --key-added '${settings.key_added}' + #end if + #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@ @EXPORT_MTX_OPTS@ @@ -20,16 +33,37 @@ <inputs> <expand macro="input_object_params"/> <expand macro="output_object_params"/> - <param name="scale_factor" argument="--normalize-to" type="float" value="1e4" min="0" - label="Target number to normalise to" help="Aimed counts per cell after normalisation."/> - <param name="fraction" argument="--fraction" type="float" value="1" min="0" max="1" - label="Exclude top expressed genes until the remaining account for no greater than specified fraction of total counts" - help="Only non-excluded genes will sum up the target number."/> - <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."/> <expand macro="export_mtx_params"/> + <conditional name="settings"> + <param name="default" type="boolean" checked="true" label="Use programme defaults"/> + <when value="true"/> + <when value="false"> + <param name="scale_factor" argument="--normalize-to" type="float" value="1e4" min="0" + 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."/> + <when value="true"> + <param name="max_fraction" argument="--max-fraction" type="float" value="0.05" min="0" max="1" + label="Consider cells as highly expressed that have more counts than max_fraction of the original total counts in at least one cell." /> + </when> + </conditional> + <param name="layers" argument="--layers" type="text" optional="true" + label="Comma-separated list of layers to normalize. Set to 'all' to normalize all layers."/> + <param name="layer_norm" type="select" label="How to normalise layers" help="If None, after normalization, for each layer in layers each cell has a total count equal to the median of the counts_per_cell before normalization of the layer. If 'after', for each layer in layers each cell has a total count equal to the value of --normalize-to. If 'X', for each layer in layers each cell has a total count equal to the median of total counts for observations (cells) of adata.X before normalization." > + <option value="" selected="true">None</option> + <option value="X">X</option> + <option value="after">after</option> + </param> + + <param name="key_added" argument="--key-added" type="text" optional="true" + label="Name of the field in adata.obs where the normalization factor is stored. Default: don't store."/> + </when> + </conditional> </inputs> <outputs> |
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| diff -r 47c747351d62 -r 6aa97861fdfd scanpy_macros2.xml --- a/scanpy_macros2.xml Fri Jun 05 09:03:47 2020 -0400 +++ b/scanpy_macros2.xml Mon Sep 07 13:13:49 2020 +0000 |
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| @@ -1,10 +1,13 @@ <macros> - <token name="@TOOL_VERSION@">1.4.3</token> + <token name="@TOOL_VERSION@">1.6.0</token> <token name="@HELP@">More information can be found at https://scanpy.readthedocs.io</token> <token name="@PROFILE@">18.01</token> <token name="@VERSION_HISTORY@"><![CDATA[ **Version history** +1.6.0+galaxy0: Update to scanpy-scripts 0.2.13 (running scanpy ==1.6.0) to incorporate new options, code simplifications, and batch integration methods. Jonathan Manning, Expression Atlas team https://www.ebi.ac.uk/gxa/home at +EMBL-EBI https://www.ebi.ac.uk/ + 1.4.3+galaxy10: Update to scanpy-scripts 0.2.10 (running scanpy ==1.4.3) to address bugfixes in run-pca. 1.4.3+galaxy10: Update to scanpy-scripts 0.2.9 (running scanpy ==1.4.3) to address bugfixes in find-variable-genes. @@ -46,7 +49,7 @@ <xml name="requirements"> <requirements> - <requirement type="package" version="0.2.10">scanpy-scripts</requirement> + <requirement type="package" version="0.3.0">scanpy-scripts</requirement> <yield/> </requirements> </xml> |