Mercurial > repos > ebi-gxa > scanpy_filter_genes

annotate scanpy-filter-genes.xml @ 11:6ac8b9a3a279 draft

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planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit cbe12e02ee9ff5692be7547bdbe28fd1cd013a92
author ebi-gxa
date Thu, 20 Feb 2020 10:18:01 -0500
parents 6d571e4e5839
children c678f671e151
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d1b97a5d5a8d planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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1 <?xml version="1.0" encoding="utf-8"?>
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6ac8b9a3a279 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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2 <tool id="scanpy_filter_genes" name="Scanpy FilterGenes" version="@TOOL_VERSION@+galaxy9" profile="@PROFILE@">
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3 <description>based on counts and numbers of cells expressed</description>
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4 <macros>
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5 <import>scanpy_macros2.xml</import>
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6 </macros>
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7 <expand macro="requirements"/>
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8 <command detect_errors="exit_code"><![CDATA[
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9 ln -s '${input_obj_file}' input.h5 &&
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10 PYTHONIOENCODING=utf-8 scanpy-filter-genes
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11 #if $parameters
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12 #for $p in $parameters
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13 #set $min = $p.min
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14 #set $max = $p.max
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15 #if $p.name.startswith('pct_')
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16 #set $min = float($min) / 100
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17 #set $max = float($max) / 100
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18 #end if
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19 --param 'g:$p.name' $min $max
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20 #end for
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21 #end if
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22 #if $categories
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23 #set cats = ' '.join(["--category 'g:{name}' '{negate}{values}'".format(**$c) for $c in $categories])
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24 ${cats}
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25 #end if
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26 #if $subsets
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27 #set subs = ' '.join(["--subset 'g:{name}' '{subset}'".format(**$s) for $s in $subsets])
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28 ${subs}
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29 #end if
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30 $force_recalc
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31 @INPUT_OPTS@
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32 @OUTPUT_OPTS@
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33 @EXPORT_MTX_OPTS@
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34 ]]></command>
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36 <inputs>
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37 <expand macro="input_object_params"/>
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38 <expand macro="output_object_params"/>
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39
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40 <repeat name="parameters" title="Parameters to select genes to keep" min="1">
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41 <param name="name" type="text" value="n_cells" label="Name of parameter to filter on" help="for example n_genes or n_counts">
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42 <option value="n_cells">n_cells</option>
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43 <option value="n_counts">n_counts</option>
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44 </param>
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45 <param name="min" type="float" min="0" value="0" label="Min value" help="Genes with value below min will be discarded."/>
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46 <param name="max" type="float" min="0" value="1e9" label="Max value" help="Genes with value above max will be discarded."/>
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47 </repeat>
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48
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49 <repeat name="categories" title="Categories to select genes to keep (unless negate is checked)" min="0">
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50 <param name="name" type="text" value="" label="Name of the categorical variable to filter on"/>
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51 <param name="values" type="text" value="" label="Comma-separated list of categories"/>
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52 <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."/>
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53 </repeat>
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54
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55 <repeat name="subsets" title="Subsets to select genes to keep" min="0">
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56 <param name="name" type="text" value="" label="Name of the categorical variable to filter on"/>
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57 <param name="subset" type="data" format="tabular" label="List of values to keep" help="A one-column headerless text file is required"/>
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58 </repeat>
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59 <param name="force_recalc" label="Force recalculation of QC vars" type="boolean" truevalue="--force-recalc" falsevalue="" help="If set, it will recalculate pcts and other existing QC vars, overwriting existing ones."/>
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60 <expand macro="export_mtx_params"/>
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61 </inputs>
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63 <outputs>
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64 <expand macro="output_data_obj" description="Filtered cells"/>
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65 <expand macro="export_mtx_outputs"/>
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66 </outputs>
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67
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68 <tests>
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69 <test>
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70 <param name="input_obj_file" value="filter_cells.h5"/>
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71 <param name="input_format" value="anndata"/>
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72 <param name="output_format" value="anndata"/>
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73 <repeat name="parameters">
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74 <param name="name" value="n_cells"/>
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75 <param name="min" value="3"/>
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76 <param name="max" value="1e9"/>
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77 </repeat>
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78 <repeat name="parameters">
3
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79 <param name="name" value="n_counts"/>
0
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80 <param name="min" value="0"/>
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81 <param name="max" value="1e9"/>
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82 </repeat>
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83 <output name="output_h5" file="filter_genes.h5" ftype="h5" compare="sim_size"/>
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84 </test>
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85 </tests>
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86
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87 <help><![CDATA[
3
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88 =====================================================================
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89 Filter genes based on arbitrary attributes (`scanpy.pp.filter_genes`)
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90 =====================================================================
0
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91
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92 Keep genes that have at least `min_counts` counts or are expressed in at
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93 least `min_cells` cells or have at most `max_counts` counts or are expressed
3
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94 in at most `max_cells` cells. Other gene attributes can be used for filtering
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95 too if available.
0
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96
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97
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98 @HELP@
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99
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100 @VERSION_HISTORY@
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101 ]]></help>
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102 <expand macro="citations"/>
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103 </tool>