| Previous changeset 7:8abb1680e8ca (2020-02-19) Next changeset 9:e4006a341f74 (2020-03-11) |
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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 cbe12e02ee9ff5692be7547bdbe28fd1cd013a92 |
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modified:
scanpy-find-cluster.xml scanpy_macros2.xml |
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added:
scanpy-filter-genes.xml.bak |
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| diff -r 8abb1680e8ca -r 6a9e2be28b07 scanpy-filter-genes.xml.bak --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scanpy-filter-genes.xml.bak Thu Feb 20 10:16:59 2020 -0500 |
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| @@ -0,0 +1,94 @@ +<?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 8abb1680e8ca -r 6a9e2be28b07 scanpy-find-cluster.xml --- a/scanpy-find-cluster.xml Wed Feb 19 11:49:18 2020 -0500 +++ b/scanpy-find-cluster.xml Thu Feb 20 10:16:59 2020 -0500 |
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| @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="utf-8"?> -<tool id="scanpy_find_cluster" name="Scanpy FindCluster" version="@TOOL_VERSION@+galaxy8" profile="@PROFILE@"> +<tool id="scanpy_find_cluster" name="Scanpy FindCluster" version="@TOOL_VERSION@+galaxy9" profile="@PROFILE@"> <description>based on community detection on KNN graph</description> <macros> <import>scanpy_macros2.xml</import> |
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| diff -r 8abb1680e8ca -r 6a9e2be28b07 scanpy_macros2.xml --- a/scanpy_macros2.xml Wed Feb 19 11:49:18 2020 -0500 +++ b/scanpy_macros2.xml Thu Feb 20 10:16:59 2020 -0500 |
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| @@ -5,7 +5,9 @@ <token name="@VERSION_HISTORY@"><![CDATA[ **Version history** -1.4.3+galaxy8: Use profile 18.01 for modules. +1.4.3+galaxy9: Update to scanpy-scripts 0.2.9 (running scanpy ==1.4.3) to address bugfixes in find-variable-genes. + +1.4.3+galaxy9: 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. @@ -42,7 +44,7 @@ <xml name="requirements"> <requirements> - <requirement type="package" version="0.2.8">scanpy-scripts</requirement> + <requirement type="package" version="0.2.9">scanpy-scripts</requirement> <yield/> </requirements> </xml> |