Mercurial > repos > ebi-gxa > scanpy_plot_embed

annotate scanpy-filter-genes.xml.bak @ 3:b2410da4e381 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 1d069e25584e436d7628694cb8853a15f1f85604
author ebi-gxa
date Wed, 20 Nov 2019 05:17:27 -0500
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3
b2410da4e381 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1d069e25584e436d7628694cb8853a15f1f85604
ebi-gxa
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1 <?xml version="1.0" encoding="utf-8"?>
b2410da4e381 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1d069e25584e436d7628694cb8853a15f1f85604
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2 <tool id="scanpy_filter_genes" name="Scanpy FilterGenes" version="@TOOL_VERSION@+galaxy3">
b2410da4e381 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1d069e25584e436d7628694cb8853a15f1f85604
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3 <description>based on counts and numbers of cells expressed</description>
b2410da4e381 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1d069e25584e436d7628694cb8853a15f1f85604
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4 <macros>
b2410da4e381 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1d069e25584e436d7628694cb8853a15f1f85604
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5 <import>scanpy_macros2.xml</import>
b2410da4e381 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1d069e25584e436d7628694cb8853a15f1f85604
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6 </macros>
b2410da4e381 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1d069e25584e436d7628694cb8853a15f1f85604
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7 <expand macro="requirements"/>
b2410da4e381 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1d069e25584e436d7628694cb8853a15f1f85604
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8 <command detect_errors="exit_code"><![CDATA[
b2410da4e381 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1d069e25584e436d7628694cb8853a15f1f85604
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9 ln -s '${input_obj_file}' input.h5 &&
b2410da4e381 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1d069e25584e436d7628694cb8853a15f1f85604
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10 PYTHONIOENCODING=utf-8 scanpy-filter-genes
b2410da4e381 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1d069e25584e436d7628694cb8853a15f1f85604
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11 #if $parameters
b2410da4e381 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1d069e25584e436d7628694cb8853a15f1f85604
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12 #set pars = ' '.join(['--param g:{name} {min} {max}'.format(**$p) for $p in $parameters])
b2410da4e381 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1d069e25584e436d7628694cb8853a15f1f85604
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13 ${pars}
b2410da4e381 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1d069e25584e436d7628694cb8853a15f1f85604
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14 #end if
b2410da4e381 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1d069e25584e436d7628694cb8853a15f1f85604
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15 #if $categories
b2410da4e381 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1d069e25584e436d7628694cb8853a15f1f85604
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16 #set cats = ' '.join(['--category g:{name} {negate}{values}'.format(**$c) for $c in $categories])
b2410da4e381 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1d069e25584e436d7628694cb8853a15f1f85604
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17 ${cats}
b2410da4e381 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1d069e25584e436d7628694cb8853a15f1f85604
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18 #end if
b2410da4e381 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1d069e25584e436d7628694cb8853a15f1f85604
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19 #if $subsets
b2410da4e381 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1d069e25584e436d7628694cb8853a15f1f85604
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20 #set subs = ' '.join(['--subset g:{name} {subset}'.format(**$s) for $s in $subsets])
b2410da4e381 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1d069e25584e436d7628694cb8853a15f1f85604
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21 ${subs}
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22 #end if
b2410da4e381 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1d069e25584e436d7628694cb8853a15f1f85604
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23 @INPUT_OPTS@
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24 @OUTPUT_OPTS@
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25 @EXPORT_MTX_OPTS@
b2410da4e381 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1d069e25584e436d7628694cb8853a15f1f85604
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26 ]]></command>
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27
b2410da4e381 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1d069e25584e436d7628694cb8853a15f1f85604
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28 <inputs>
b2410da4e381 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1d069e25584e436d7628694cb8853a15f1f85604
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29 <expand macro="input_object_params"/>
b2410da4e381 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1d069e25584e436d7628694cb8853a15f1f85604
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30 <expand macro="output_object_params"/>
b2410da4e381 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1d069e25584e436d7628694cb8853a15f1f85604
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31
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32 <repeat name="parameters" title="Parameters used to filter genes" min="1">
b2410da4e381 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1d069e25584e436d7628694cb8853a15f1f85604
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33 <param name="name" type="text" value="n_cells" label="Name of parameter to filter on" help="for example n_genes or n_counts">
b2410da4e381 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1d069e25584e436d7628694cb8853a15f1f85604
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34 <option value="n_cells">n_cells</option>
b2410da4e381 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1d069e25584e436d7628694cb8853a15f1f85604
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35 <option value="n_counts">n_counts</option>
b2410da4e381 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1d069e25584e436d7628694cb8853a15f1f85604
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36 </param>
b2410da4e381 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1d069e25584e436d7628694cb8853a15f1f85604
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37 <param name="min" type="float" min="0" value="0" label="Min value"/>
b2410da4e381 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1d069e25584e436d7628694cb8853a15f1f85604
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38 <param name="max" type="float" min="0" value="1e9" label="Max value"/>
b2410da4e381 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1d069e25584e436d7628694cb8853a15f1f85604
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39 </repeat>
b2410da4e381 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1d069e25584e436d7628694cb8853a15f1f85604
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40
b2410da4e381 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1d069e25584e436d7628694cb8853a15f1f85604
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41 <repeat name="categories" title="Categories used to filter genes" min="0">
b2410da4e381 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1d069e25584e436d7628694cb8853a15f1f85604
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42 <param name="name" type="text" value="" label="Name of the categorical variable to filter on"/>
b2410da4e381 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1d069e25584e436d7628694cb8853a15f1f85604
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43 <param name="values" type="text" value="" label="Comma-separated list of categories"/>
b2410da4e381 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1d069e25584e436d7628694cb8853a15f1f85604
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44 <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."/>
b2410da4e381 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1d069e25584e436d7628694cb8853a15f1f85604
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45 </repeat>
b2410da4e381 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1d069e25584e436d7628694cb8853a15f1f85604
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46
b2410da4e381 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1d069e25584e436d7628694cb8853a15f1f85604
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47 <repeat name="subsets" title="Subsets used to filter genes" min="0">
b2410da4e381 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1d069e25584e436d7628694cb8853a15f1f85604
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48 <param name="name" type="text" value="" label="Name of the categorical variable to filter on"/>
b2410da4e381 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1d069e25584e436d7628694cb8853a15f1f85604
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49 <param name="subset" type="data" format="tabular" label="List of values to keep" help="A one-column headerless text file is required"/>
b2410da4e381 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1d069e25584e436d7628694cb8853a15f1f85604
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50 </repeat>
b2410da4e381 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1d069e25584e436d7628694cb8853a15f1f85604
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51 <expand macro="export_mtx_params"/>
b2410da4e381 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1d069e25584e436d7628694cb8853a15f1f85604
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52 </inputs>
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53
b2410da4e381 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1d069e25584e436d7628694cb8853a15f1f85604
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54 <outputs>
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55 <data name="output_h5" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: Filtered genes"/>
b2410da4e381 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1d069e25584e436d7628694cb8853a15f1f85604
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56 <expand macro="export_mtx_outputs"/>
b2410da4e381 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1d069e25584e436d7628694cb8853a15f1f85604
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57 </outputs>
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58
b2410da4e381 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1d069e25584e436d7628694cb8853a15f1f85604
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59 <tests>
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60 <test>
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61 <param name="input_obj_file" value="filter_cells.h5"/>
b2410da4e381 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1d069e25584e436d7628694cb8853a15f1f85604
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62 <param name="input_format" value="anndata"/>
b2410da4e381 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1d069e25584e436d7628694cb8853a15f1f85604
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63 <param name="output_format" value="anndata"/>
b2410da4e381 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1d069e25584e436d7628694cb8853a15f1f85604
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64 <repeat name="parameters">
b2410da4e381 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1d069e25584e436d7628694cb8853a15f1f85604
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65 <param name="name" value="n_cells"/>
b2410da4e381 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1d069e25584e436d7628694cb8853a15f1f85604
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66 <param name="min" value="3"/>
b2410da4e381 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1d069e25584e436d7628694cb8853a15f1f85604
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67 <param name="max" value="1e9"/>
b2410da4e381 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1d069e25584e436d7628694cb8853a15f1f85604
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68 </repeat>
b2410da4e381 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1d069e25584e436d7628694cb8853a15f1f85604
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69 <repeat name="parameters">
b2410da4e381 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1d069e25584e436d7628694cb8853a15f1f85604
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70 <param name="name" value="n_counts"/>
b2410da4e381 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1d069e25584e436d7628694cb8853a15f1f85604
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71 <param name="min" value="0"/>
b2410da4e381 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1d069e25584e436d7628694cb8853a15f1f85604
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72 <param name="max" value="1e9"/>
b2410da4e381 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1d069e25584e436d7628694cb8853a15f1f85604
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73 </repeat>
b2410da4e381 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1d069e25584e436d7628694cb8853a15f1f85604
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74 <output name="output_h5" file="filter_genes.h5" ftype="h5" compare="sim_size"/>
b2410da4e381 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1d069e25584e436d7628694cb8853a15f1f85604
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75 </test>
b2410da4e381 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1d069e25584e436d7628694cb8853a15f1f85604
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76 </tests>
b2410da4e381 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1d069e25584e436d7628694cb8853a15f1f85604
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77
b2410da4e381 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1d069e25584e436d7628694cb8853a15f1f85604
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78 <help><![CDATA[
b2410da4e381 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1d069e25584e436d7628694cb8853a15f1f85604
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79 =====================================================================
b2410da4e381 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1d069e25584e436d7628694cb8853a15f1f85604
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80 Filter genes based on arbitrary attributes (`scanpy.pp.filter_genes`)
b2410da4e381 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1d069e25584e436d7628694cb8853a15f1f85604
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81 =====================================================================
b2410da4e381 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1d069e25584e436d7628694cb8853a15f1f85604
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82
b2410da4e381 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1d069e25584e436d7628694cb8853a15f1f85604
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83 Keep genes that have at least `min_counts` counts or are expressed in at
b2410da4e381 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1d069e25584e436d7628694cb8853a15f1f85604
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84 least `min_cells` cells or have at most `max_counts` counts or are expressed
b2410da4e381 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1d069e25584e436d7628694cb8853a15f1f85604
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85 in at most `max_cells` cells. Other gene attributes can be used for filtering
b2410da4e381 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1d069e25584e436d7628694cb8853a15f1f85604
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86 too if available.
b2410da4e381 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1d069e25584e436d7628694cb8853a15f1f85604
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87
b2410da4e381 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1d069e25584e436d7628694cb8853a15f1f85604
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88
b2410da4e381 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1d069e25584e436d7628694cb8853a15f1f85604
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89 @HELP@
b2410da4e381 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1d069e25584e436d7628694cb8853a15f1f85604
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90
b2410da4e381 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1d069e25584e436d7628694cb8853a15f1f85604
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91 @VERSION_HISTORY@
b2410da4e381 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1d069e25584e436d7628694cb8853a15f1f85604
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92 ]]></help>
b2410da4e381 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1d069e25584e436d7628694cb8853a15f1f85604
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93 <expand macro="citations"/>
b2410da4e381 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1d069e25584e436d7628694cb8853a15f1f85604
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94 </tool>