Mercurial > repos > ebi-gxa > scanpy_filter_genes

annotate scanpy-filter-genes.xml @ 2:a797a810d7e9 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 21b38b449c453762966dfbe55ec3bf7d39377c86
author ebi-gxa
date Tue, 22 Oct 2019 08:01:01 -0400
parents 7aebd6265a97
children 77fbe74247c2
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1 <?xml version="1.0" encoding="utf-8"?>
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a797a810d7e9 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 21b38b449c453762966dfbe55ec3bf7d39377c86
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2 <tool id="scanpy_filter_genes" name="Scanpy FilterGenes" version="@TOOL_VERSION@+galaxy2">
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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 $parameters
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12 #set pars = ' '.join(['--param {name} {min} {max}'.format(**$p) for $p in $parameters])
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13 ${pars}
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14 #end if
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15 #if $categories
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16 #set cats = ' '.join(['--category {name} {values}'.format(**$c) for $c in $categories])
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17 ${cats}
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18 #end if
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19 #if $subsets
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20 #set subs = ' '.join(['--subsets {name} {subset}'.format(**$s) for $s in $subsets])
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21 ${subs}
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22 #end if
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23 @INPUT_OPTS@
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24 @OUTPUT_OPTS@
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25 ]]></command>
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27 <inputs>
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28 <expand macro="input_object_params"/>
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29 <expand macro="output_object_params"/>
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31 <repeat name="parameters" title="Parameters used to filter cells" min="1">
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32 <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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33 <option value="n_cells">n_cells</option>
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34 <option value="gene:n_counts">n_counts</option>
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35 </param>
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36 <param name="min" type="float" min="0" value="0" label="Min value"/>
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37 <param name="max" type="float" min="0" value="1e9" label="Max value"/>
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38 </repeat>
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39
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40 <repeat name="categories" title="Categories used to filter genes" min="0">
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41 <param name="name" type="text" value="" label="Name of the categorical variable to filter on"/>
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42 <param name="values" type="text" value="" label="Comma-separated values"/>
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43 </repeat>
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45 <repeat name="subsets" title="Subsets used to filter genes" min="0">
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46 <param name="name" type="text" value="" label="Name of the categorical variable to filter on"/>
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47 <param name="subset" type="data" format="tabular" label="List of values"/>
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48 </repeat>
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49 <expand macro="export_mtx_params"/>
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50 </inputs>
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51
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52 <outputs>
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53 <data name="output_h5" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: Filtered genes"/>
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54 <expand macro="export_mtx_outputs"/>
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55 </outputs>
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56
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57 <tests>
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58 <test>
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59 <param name="input_obj_file" value="filter_cells.h5"/>
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60 <param name="input_format" value="anndata"/>
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61 <param name="output_format" value="anndata"/>
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62 <repeat name="parameters">
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63 <param name="name" value="n_cells"/>
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64 <param name="min" value="3"/>
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65 <param name="max" value="1e9"/>
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66 </repeat>
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67 <repeat name="parameters">
1
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68 <param name="name" value="gene:n_counts"/>
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69 <param name="min" value="0"/>
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70 <param name="max" value="1e9"/>
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71 </repeat>
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72 <output name="output_h5" file="filter_genes.h5" ftype="h5" compare="sim_size"/>
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73 </test>
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74 </tests>
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75
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76 <help><![CDATA[
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77 ===================================================================
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78 Filter genes based on number of cells or counts (`pp.filter_genes`)
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79 ===================================================================
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80
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81 Keep genes that have at least `min_counts` counts or are expressed in at
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82 least `min_cells` cells or have at most `max_counts` counts or are expressed
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83 in at most `max_cells` cells.
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84
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85 Only provide one of the optional parameters `min_counts`, `min_cells`,
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86 `max_counts`, `max_cells` per call.
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87
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88
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89 @HELP@
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90
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91 @VERSION_HISTORY@
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92 ]]></help>
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93 <expand macro="citations"/>
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94 </tool>