Mercurial > repos > ebi-gxa > scanpy_filter_cells

annotate scanpy-filter-cells.xml @ 24:b28ba58033ea 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 9748fb7ca203206ecac97461f60ce75890d00fa4-dirty"
author ebi-gxa
date Fri, 15 Oct 2021 15:02:05 +0000
parents 7fd39eb52f38
children e9283529cba1
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1 <?xml version="1.0" encoding="utf-8"?>
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2 <tool id="scanpy_filter_cells" name="Scanpy FilterCells" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@" >
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3 <description>based on counts and numbers of genes 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[
9f0ca1641ab2 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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9 ln -s '${input_obj_file}' input.h5 &&
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10 PYTHONIOENCODING=utf-8 scanpy-filter-cells
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11 #if $gene_name
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12 --gene-name '${gene_name}'
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13 #end if
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14 #if $parameters
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15 #for $p in $parameters
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16 #set $min = $p.min
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17 #set $max = $p.max
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18 #if $p.name.startswith('pct_')
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19 #set $min = float($min) / 100
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20 #set $max = float($max) / 100
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21 #end if
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22 --param 'c:$p.name' $min $max
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23 #end for
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24 #end if
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25 #if $categories
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26 #set cats = ' '.join(["--category 'c:{name}' '{negate}{values}'".format(**$c) for $c in $categories])
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27 ${cats}
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28 #end if
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29 #if $subsets
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30 #set subs = ' '.join(["--subset 'c:{name}' '{subset}'".format(**$s) for $s in $subsets])
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31 ${subs}
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32 #end if
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33 @SAVE_MATRIX_OPTS@
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34 @INPUT_OPTS@
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35 @OUTPUT_OPTS@
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36 @EXPORT_MTX_OPTS@
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37 ]]></command>
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38
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39 <inputs>
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40 <expand macro="input_object_params"/>
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41 <expand macro="output_object_params"/>
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42
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43 <param name="gene_name" type="text" optional="true" label="Name of the column in `anndata.var` that contains gene name"
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44 help="Used for flagging mitochondria genes (starting with 'MT-'). Leave empty if gene table already has a boolean column called 'mito' that flags MT genes"/>
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45
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46 <repeat name="parameters" title="Parameters to select cells to keep" min="1">
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47 <param name="name" type="text" value="n_genes" label="Name of parameter to filter on" help="for example n_genes or n_counts">
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48 <option value="n_genes">n_genes</option>
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49 <option value="n_counts">n_counts</option>
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50 <option value="pct_counts_mito">pct_counts_mito (only usable if MT genes are flagged or has been pre-calculated)</option>
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51 </param>
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52 <param name="min" type="float" value="0" min="0" label="Min value" help="Cells with value below min will be discarded."/>
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53 <param name="max" type="float" value="1e9" label="Max value" help="Cells with value above max will be discarded."/>
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54 </repeat>
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55
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56 <repeat name="categories" title="Categories to select cells to keep (unless negate is checked)" min="0">
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57 <param name="name" type="text" value="" label="Name of the categorical variable to filter on"/>
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58 <param name="values" type="text" value="" label="Comma-separated list of categories" help="Cells with these values in this categorical variable will be kept."/>
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59 <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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60 </repeat>
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61
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62 <repeat name="subsets" title="Subsets to select cells to keep" min="0">
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63 <param name="name" type="text" value="" label="Name of the categorical variable to filter on"/>
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64 <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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65 </repeat>
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66 <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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67 <expand macro="save_matrix_params"/>
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68 <expand macro="export_mtx_params"/>
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69 </inputs>
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70
9f0ca1641ab2 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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71 <outputs>
7
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72 <expand macro="output_data_obj" description="Filtered cells"/>
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73 <expand macro="export_mtx_outputs"/>
0
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74 </outputs>
9f0ca1641ab2 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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75
9f0ca1641ab2 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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76 <tests>
9f0ca1641ab2 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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77 <test>
9f0ca1641ab2 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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78 <param name="input_obj_file" value="read_10x.h5"/>
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79 <param name="input_format" value="anndata"/>
9f0ca1641ab2 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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80 <param name="output_format" value="anndata"/>
9f0ca1641ab2 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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81 <repeat name="parameters">
9f0ca1641ab2 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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82 <param name="name" value="n_genes"/>
9f0ca1641ab2 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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83 <param name="min" value="200"/>
14
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84 <param name="max" value="20000"/>
0
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85 </repeat>
9f0ca1641ab2 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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86 <repeat name="parameters">
2
c23d0ff783d4 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ccd9b839849600b1aa3b6cf54f667575a5f2da9d
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87 <param name="name" value="n_counts"/>
0
9f0ca1641ab2 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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88 <param name="min" value="0"/>
9f0ca1641ab2 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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89 <param name="max" value="1e9"/>
9f0ca1641ab2 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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90 </repeat>
14
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91 <output name="output_h5" file="filter_cells.h5" ftype="h5" compare="sim_size"/>
0
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92 </test>
9f0ca1641ab2 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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93 </tests>
9f0ca1641ab2 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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94
9f0ca1641ab2 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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95 <help><![CDATA[
1
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96 ===================================================================
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97 Filter cells based on various QC metrics (`scanpy.pp.filter_cells`)
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98 ===================================================================
0
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99
1
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100 For instance, only keep cells with at least `min_counts` and at most
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101 `max_counts` UMI and/or at least `min_genes` expressed genes and/or at most
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102 `max_mito_percent` mitocondria expression. This is to filter measurement
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103 outliers, i.e., "unreliable" observations.
0
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104
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105 @HELP@
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106
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107 @VERSION_HISTORY@
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108 ]]></help>
9f0ca1641ab2 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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109 <expand macro="citations"/>
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110 </tool>