Mercurial > repos > ebi-gxa > scanpy_filter_genes
changeset 3:77fbe74247c2 draft
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ccd9b839849600b1aa3b6cf54f667575a5f2da9d
author | ebi-gxa |
---|---|
date | Fri, 25 Oct 2019 08:21:35 -0400 |
parents | a797a810d7e9 |
children | fa6c08064fc1 |
files | dataset_102795.dat dataset_102795.dat.zip input.h5 input.h5.zip scanpy-filter-genes.xml scanpy_macros2.xml |
diffstat | 6 files changed, 32537 insertions(+), 17 deletions(-) [+] |
line wrap: on
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/dataset_102795.dat Fri Oct 25 08:21:35 2019 -0400 @@ -0,0 +1,32520 @@ +ENSDARG00000102141 +ENSDARG00000102123 +ENSDARG00000114503 +ENSDARG00000115971 +ENSDARG00000098311 +ENSDARG00000104839 +ENSDARG00000100143 +ENSDARG00000102474 +ENSDARG00000104049 +ENSDARG00000102226 +ENSDARG00000103095 +ENSDARG00000102128 +ENSDARG00000110470 +ENSDARG00000100422 +ENSDARG00000104632 +ENSDARG00000100660 +ENSDARG00000113107 +ENSDARG00000099787 +ENSDARG00000112451 +ENSDARG00000070546 +ENSDARG00000045914 +ENSDARG00000045913 +ENSDARG00000045911 +ENSDARG00000045910 +ENSDARG00000045909 +ENSDARG00000025073 +ENSDARG00000084828 +ENSDARG00000095951 +ENSDARG00000093924 +ENSDARG00000108269 +ENSDARG00000084451 +ENSDARG00000031737 +ENSDARG00000099652 +ENSDARG00000101047 +ENSDARG00000102104 +ENSDARG00000099833 +ENSDARG00000103870 +ENSDARG00000096118 +ENSDARG00000045900 +ENSDARG00000016968 +ENSDARG00000102878 +ENSDARG00000059311 +ENSDARG00000017386 +ENSDARG00000045898 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--- a/scanpy-filter-genes.xml Tue Oct 22 08:01:01 2019 -0400 +++ b/scanpy-filter-genes.xml Fri Oct 25 08:21:35 2019 -0400 @@ -9,15 +9,15 @@ ln -s '${input_obj_file}' input.h5 && PYTHONIOENCODING=utf-8 scanpy-filter-genes #if $parameters - #set pars = ' '.join(['--param {name} {min} {max}'.format(**$p) for $p in $parameters]) + #set pars = ' '.join(['--param g:{name} {min} {max}'.format(**$p) for $p in $parameters]) ${pars} #end if #if $categories - #set cats = ' '.join(['--category {name} {values}'.format(**$c) for $c in $categories]) + #set cats = ' '.join(['--category g:{name} {values}'.format(**$c) for $c in $categories]) ${cats} #end if #if $subsets - #set subs = ' '.join(['--subsets {name} {subset}'.format(**$s) for $s in $subsets]) + #set subs = ' '.join(['--subset g:{name} {subset}'.format(**$s) for $s in $subsets]) ${subs} #end if @INPUT_OPTS@ @@ -28,10 +28,10 @@ <expand macro="input_object_params"/> <expand macro="output_object_params"/> - <repeat name="parameters" title="Parameters used to filter cells" min="1"> + <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="gene:n_counts">n_counts</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"/> @@ -39,12 +39,12 @@ <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 values"/> + <param name="values" type="text" value="" label="Comma-separated values to keep"/> </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"/> + <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> @@ -65,7 +65,7 @@ <param name="max" value="1e9"/> </repeat> <repeat name="parameters"> - <param name="name" value="gene:n_counts"/> + <param name="name" value="n_counts"/> <param name="min" value="0"/> <param name="max" value="1e9"/> </repeat> @@ -74,16 +74,14 @@ </tests> <help><![CDATA[ -=================================================================== -Filter genes based on number of cells or counts (`pp.filter_genes`) -=================================================================== +===================================================================== +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. - -Only provide one of the optional parameters `min_counts`, `min_cells`, -`max_counts`, `max_cells` per call. +in at most `max_cells` cells. Other gene attributes can be used for filtering +too if available. @HELP@
--- a/scanpy_macros2.xml Tue Oct 22 08:01:01 2019 -0400 +++ b/scanpy_macros2.xml Fri Oct 25 08:21:35 2019 -0400 @@ -1,9 +1,11 @@ <macros> - <token name="@TOOL_VERSION@">1.4.2</token> + <token name="@TOOL_VERSION@">1.4.3</token> <token name="@HELP@">More information can be found at https://scanpy.readthedocs.io</token> <token name="@VERSION_HISTORY@"><![CDATA[ **Version history** +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). 1.3.2+galaxy1: Normalise-data and filter-genes: Exposes ability to output 10x files. @@ -31,7 +33,7 @@ <xml name="requirements"> <requirements> - <requirement type="package" version="0.2.4.post4">scanpy-scripts</requirement> + <requirement type="package" version="0.2.5.post1">scanpy-scripts</requirement> <yield/> </requirements> </xml>