| Previous changeset 5:1442daff0c7c (2019-11-20) Next changeset 7:9681ec095ed5 (2019-11-26) |
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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 400799f99ee36ad12b990b1ccabf4be16a26c003 |
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modified:
scanpy-normalise-data.xml scanpy_macros2.xml |
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removed:
scanpy-filter-genes.xml.bak |
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| diff -r 1442daff0c7c -r 9e42d8795385 scanpy-filter-genes.xml.bak --- a/scanpy-filter-genes.xml.bak Wed Nov 20 05:11:20 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,94 +0,0 @@ -<?xml version="1.0" encoding="utf-8"?> -<tool id="scanpy_filter_genes" name="Scanpy FilterGenes" version="@TOOL_VERSION@+galaxy3"> - <description>based on counts and numbers of cells expressed</description> - <macros> - <import>scanpy_macros2.xml</import> - </macros> - <expand macro="requirements"/> - <command detect_errors="exit_code"><![CDATA[ -ln -s '${input_obj_file}' input.h5 && -PYTHONIOENCODING=utf-8 scanpy-filter-genes -#if $parameters - #set pars = ' '.join(['--param g:{name} {min} {max}'.format(**$p) for $p in $parameters]) - ${pars} -#end if -#if $categories - #set cats = ' '.join(['--category g:{name} {negate}{values}'.format(**$c) for $c in $categories]) - ${cats} -#end if -#if $subsets - #set subs = ' '.join(['--subset g:{name} {subset}'.format(**$s) for $s in $subsets]) - ${subs} -#end if - @INPUT_OPTS@ - @OUTPUT_OPTS@ - @EXPORT_MTX_OPTS@ -]]></command> - - <inputs> - <expand macro="input_object_params"/> - <expand macro="output_object_params"/> - - <repeat name="parameters" title="Parameters used to filter genes" min="1"> - <param name="name" type="text" value="n_cells" label="Name of parameter to filter on" help="for example n_genes or n_counts"> - <option value="n_cells">n_cells</option> - <option value="n_counts">n_counts</option> - </param> - <param name="min" type="float" min="0" value="0" label="Min value"/> - <param name="max" type="float" min="0" value="1e9" label="Max value"/> - </repeat> - - <repeat name="categories" title="Categories used to filter genes" min="0"> - <param name="name" type="text" value="" label="Name of the categorical variable to filter on"/> - <param name="values" type="text" value="" label="Comma-separated list of categories"/> - <param name="negate" type="boolean" truevalue="!" falsevalue="" checked="false" label="Apply as negative filter" help="If enabled, specified categories will be removed rather than retained."/> - </repeat> - - <repeat name="subsets" title="Subsets used to filter genes" min="0"> - <param name="name" type="text" value="" label="Name of the categorical variable to filter on"/> - <param name="subset" type="data" format="tabular" label="List of values to keep" help="A one-column headerless text file is required"/> - </repeat> - <expand macro="export_mtx_params"/> - </inputs> - - <outputs> - <data name="output_h5" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: Filtered genes"/> - <expand macro="export_mtx_outputs"/> - </outputs> - - <tests> - <test> - <param name="input_obj_file" value="filter_cells.h5"/> - <param name="input_format" value="anndata"/> - <param name="output_format" value="anndata"/> - <repeat name="parameters"> - <param name="name" value="n_cells"/> - <param name="min" value="3"/> - <param name="max" value="1e9"/> - </repeat> - <repeat name="parameters"> - <param name="name" value="n_counts"/> - <param name="min" value="0"/> - <param name="max" value="1e9"/> - </repeat> - <output name="output_h5" file="filter_genes.h5" ftype="h5" compare="sim_size"/> - </test> - </tests> - - <help><![CDATA[ -===================================================================== -Filter genes based on arbitrary attributes (`scanpy.pp.filter_genes`) -===================================================================== - -Keep genes that have at least `min_counts` counts or are expressed in at -least `min_cells` cells or have at most `max_counts` counts or are expressed -in at most `max_cells` cells. Other gene attributes can be used for filtering -too if available. - - -@HELP@ - -@VERSION_HISTORY@ -]]></help> - <expand macro="citations"/> -</tool> |
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| diff -r 1442daff0c7c -r 9e42d8795385 scanpy-normalise-data.xml --- a/scanpy-normalise-data.xml Wed Nov 20 05:11:20 2019 -0500 +++ b/scanpy-normalise-data.xml Mon Nov 25 14:36:21 2019 -0500 |
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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@+galaxy3"> +<tool id="scanpy_normalise_data" name="Scanpy NormaliseData" version="@TOOL_VERSION@+galaxy6"> <description>to make all cells having the same total expression</description> <macros> <import>scanpy_macros2.xml</import> @@ -25,7 +25,7 @@ <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" + <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."/> @@ -33,7 +33,7 @@ </inputs> <outputs> - <data name="output_h5" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: Normalised data"/> + <expand macro="output_data_obj" description="Normalised data"/> <expand macro="export_mtx_outputs"/> </outputs> |
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| diff -r 1442daff0c7c -r 9e42d8795385 scanpy_macros2.xml --- a/scanpy_macros2.xml Wed Nov 20 05:11:20 2019 -0500 +++ b/scanpy_macros2.xml Mon Nov 25 14:36:21 2019 -0500 |
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| @@ -4,6 +4,8 @@ <token name="@VERSION_HISTORY@"><![CDATA[ **Version history** +1.4.3+galaxy6: Update to scanpy-scripts 0.2.8 (running scanpy ==1.4.3) and wider compatibility with other Galaxy modules. Bug fixes in filtering and plotting improvements. + 1.4.3+galaxy0: Update to scanpy-scripts 0.2.5 (running scanpy ==1.4.3). 1.4.2+galaxy0: Update to scanpy-scripts 0.2.4 (requires scanpy >=1.4.2). @@ -17,7 +19,11 @@ --input-format '${input_format}' input.h5 </token> <token name="@OUTPUT_OPTS@"> - --show-obj stdout --output-format '${output_format}' output.h5 +#if str($output_format).startswith('anndata') + --show-obj stdout --output-format anndata output.h5 +#else + --show-obj stdout --output-format loom output.h5 +#end if </token> <token name="@PLOT_OPTS@"> #if $fig_title @@ -33,7 +39,7 @@ <xml name="requirements"> <requirements> - <requirement type="package" version="0.2.6">scanpy-scripts</requirement> + <requirement type="package" version="0.2.8">scanpy-scripts</requirement> <yield/> </requirements> </xml> @@ -55,7 +61,7 @@ </xml> <xml name="input_object_params"> - <param name="input_obj_file" argument="input-object-file" type="data" format="h5" label="Input object in hdf5 format"/> + <param name="input_obj_file" argument="input-object-file" type="data" format="h5,h5ad" label="Input object in AnnData/Loom format"/> <param name="input_format" argument="--input-format" type="select" label="Format of input object"> <option value="anndata" selected="true">AnnData format hdf5</option> <option value="loom">Loom format hdf5</option> @@ -64,11 +70,44 @@ <xml name="output_object_params"> <param name="output_format" argument="--output-format" type="select" label="Format of output object"> - <option value="anndata" selected="true">AnnData format hdf5</option> - <option value="loom">Loom format hdf5</option> + <option value="anndata_h5ad" selected="true">AnnData format</option> + <option value="anndata">AnnData format (h5 for older versions)</option> + <option value="loom">Loom format</option> + <option value="loom_legacy">Loom format (h5 for older versions)</option> + </param> + </xml> + + <xml name="output_object_params_no_loom"> + <param name="output_format" argument="--output-format" type="select" label="Format of output object"> + <option value="anndata_h5ad" selected="true">AnnData format</option> + <option value="anndata">AnnData format (h5 for older versions)</option> </param> </xml> + <xml name="output_data_obj_no_loom" token_description="operation"> + <data name="output_h5ad" format="h5ad" from_work_dir="output.h5" label="${tool.name} on ${on_string}: @DESCRIPTION@ AnnData"> + <filter>output_format == 'anndata_h5ad'</filter> + </data> + <data name="output_h5" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: @DESCRIPTION@ AnnData"> + <filter>output_format == 'anndata'</filter> + </data> + </xml> + + <xml name="output_data_obj" token_description="operation"> + <data name="output_h5ad" format="h5ad" from_work_dir="output.h5" label="${tool.name} on ${on_string}: @DESCRIPTION@ AnnData"> + <filter>output_format == 'anndata_h5ad'</filter> + </data> + <data name="output_h5" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: @DESCRIPTION@ AnnData"> + <filter>output_format == 'anndata'</filter> + </data> + <data name="output_loom_legacy" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: @DESCRIPTION@ Loom"> + <filter>output_format == 'loom_legacy'</filter> + </data> + <data name="output_loom" format="loom" from_work_dir="output.h5" label="${tool.name} on ${on_string}: @DESCRIPTION@ Loom"> + <filter>output_format == 'loom'</filter> + </data> + </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'"/> |