Mercurial > repos > ebi-gxa > scanpy_run_dpt

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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 ee197a80b2d591c393e1662854bc119b2ecab11e-dirty
author ebi-gxa
date Tue, 27 Feb 2024 16:43:43 +0000
parents 2f569aa8c920
children
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f57f57c459d8 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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1 <?xml version="1.0" encoding="utf-8"?>
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03921aa8b29c planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ee197a80b2d591c393e1662854bc119b2ecab11e-dirty
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2 <tool id="scanpy_run_dpt" name="Scanpy DPT" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
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3 <description>diffusion pseudotime inference</description>
f57f57c459d8 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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4 <macros>
f57f57c459d8 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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5 <import>scanpy_macros2.xml</import>
f57f57c459d8 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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6 </macros>
f57f57c459d8 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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7 <expand macro="requirements"/>
f57f57c459d8 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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8 <command detect_errors="exit_code"><![CDATA[
f57f57c459d8 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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9 ln -s '${input_obj_file}' input.h5 &&
f57f57c459d8 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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10 PYTHONIOENCODING=utf-8 scanpy-cli dpt
f57f57c459d8 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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11 --n-dcs $n_dcs
f57f57c459d8 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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12 --root '${root_attr}' '${root_value}'
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13 #if $n_branchings > 0
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14 --n-branchings ${n_branchings}
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15 --min-group-size ${min_group_size}
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16 #end if
f57f57c459d8 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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17 #if $use_graph
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18 --neighbors-key '${use_graph}'
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19 #end if
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20 #if $key_added
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21 --key-added '${key_added}'
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22 #end if
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23 #if not $allow_kendall_tau_shift
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24 --disallow-kendall-tau-shift
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25 #end if
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26 @INPUT_OPTS@
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27 @OUTPUT_OPTS@
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28 ]]></command>
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30 <inputs>
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31 <expand macro="input_object_params"/>
f57f57c459d8 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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32 <expand macro="output_object_params"/>
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33
f57f57c459d8 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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34 <param name="n_dcs" argument="--n-dcs" type="integer" min="2" value="10"
f57f57c459d8 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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35 label="Number of diffusion components to use"/>
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36 <param name="n_branchings" argument="--n-branchings" min="0" type="integer" value="0"
f57f57c459d8 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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37 label="Number of branchings to detect"/>
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38 <param name="min_group_size" argument="--min-group-size" type="float" min="0" max="1" value="0"
f57f57c459d8 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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39 label="The fraction of total cells under which further splitting is skipped during recursive splitting of branches"
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40 help="Ignored when `Number of branchings to detect` is 0"/>
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41 <param name="root_attr" argument="--root {attr} value" type="text"
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42 label="Name of attribute that defines clustering"/>
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43 <param name="root_value" argument="--root attr {value}" type="text"
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44 label="Name of the clustering that defines the root cell type"/>
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45 <param name="use_graph" argument="--neighbors-key" value="neighbors" type="text"
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46 label="Name of the slot that holds the KNN graph"/>
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47 <param name="key_added" argument="--key-added" type="text" optional="true"
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48 label="Additional suffix to the name of the slot to save the calculated pseudo-time"/>
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49 <param name="allow_kendall_tau_shift" type="boolean" checked="true" label="Allow Kendall Tau shift" help="If a very small branch is detected upon splitting, shift away from maximum correlation in Kendall tau criterion of [Haghverdi16] to stabilize the splitting" />
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50 </inputs>
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51
f57f57c459d8 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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52 <outputs>
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53 <expand macro="output_data_obj" description="Diffussion pseudotime inference"/>
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54 </outputs>
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55
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56 <tests>
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57 <test>
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58 <param name="input_obj_file" value="diffmap.h5"/>
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59 <param name="input_format" value="anndata"/>
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60 <param name="output_format" value="anndata"/>
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61 <param name="n_dcs" value="10"/>
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62 <param name="root_attr" value="louvain"/>
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63 <param name="root_value" value="1"/>
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64 <param name="use_graph" value="neighbors"/>
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65 <output name="output_h5" ftype="h5">
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66 <assert_contents>
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67 <has_h5_keys keys="obs/dpt_pseudotime"/>
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68 </assert_contents>
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69 </output>
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70 </test>
f57f57c459d8 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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71 </tests>
f57f57c459d8 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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72
f57f57c459d8 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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73 <help><![CDATA[
f57f57c459d8 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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74 ================================================
f57f57c459d8 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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75 Calculate Diffusion Pseudotime (`scanpy.tl.dpt`)
f57f57c459d8 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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76 ================================================
f57f57c459d8 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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77
f57f57c459d8 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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78 Calculate diffusion pseudotime from single cell KNN graphs.
f57f57c459d8 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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79
f57f57c459d8 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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80 This requires to run `Scanpy DiffusionMap` and `Scanpy FindCluster`, first.
f57f57c459d8 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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81
f57f57c459d8 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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82 It yields `dpt_pseudotime`, diffusion pseudotime as an attribute for each cell.
f57f57c459d8 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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83
f57f57c459d8 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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84 @HELP@
f57f57c459d8 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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85
f57f57c459d8 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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86 @VERSION_HISTORY@
f57f57c459d8 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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87 ]]></help>
f57f57c459d8 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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88 <expand macro="citations">
f57f57c459d8 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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89 <citation type="doi">10.1186/s13059-019-1663-x</citation>
f57f57c459d8 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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90 </expand>
f57f57c459d8 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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91 </tool>