| Previous changeset 6:7ad420b1be89 (2019-11-26) Next changeset 8:fe740b19e3b9 (2020-02-20) |
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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 d52bedbcef249117567014584058429525883ef7-dirty |
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modified:
scanpy-neighbours.xml scanpy_macros2.xml |
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removed:
scanpy-filter-genes.xml.bak |
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| diff -r 7ad420b1be89 -r 75240f9a8c96 scanpy-filter-genes.xml.bak --- a/scanpy-filter-genes.xml.bak Tue Nov 26 05:54:48 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 7ad420b1be89 -r 75240f9a8c96 scanpy-neighbours.xml --- a/scanpy-neighbours.xml Tue Nov 26 05:54:48 2019 -0500 +++ b/scanpy-neighbours.xml Wed Feb 19 11:53:12 2020 -0500 |
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| @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="utf-8"?> -<tool id="scanpy_compute_graph" name="Scanpy ComputeGraph" version="@TOOL_VERSION@+galaxy0"> +<tool id="scanpy_compute_graph" name="Scanpy ComputeGraph" version="@TOOL_VERSION@+galaxy8" profile="@PROFILE@"> <description>to derive kNN graph</description> <macros> <import>scanpy_macros2.xml</import> |
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| diff -r 7ad420b1be89 -r 75240f9a8c96 scanpy_macros2.xml --- a/scanpy_macros2.xml Tue Nov 26 05:54:48 2019 -0500 +++ b/scanpy_macros2.xml Wed Feb 19 11:53:12 2020 -0500 |
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| @@ -1,9 +1,12 @@ <macros> <token name="@TOOL_VERSION@">1.4.3</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** +1.4.3+galaxy8: Use profile 18.01 for modules. + 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). |