Mercurial > repos > ebi-gxa > scanpy_parameter_iterator

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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 62f47287c7e8449c59a1f1f454852ddc669b1b1e-dirty"
author ebi-gxa
date Mon, 07 Sep 2020 13:13:08 +0000
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7c4d44c14ceb "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit dcb8b19d34c3e2bf822996ca2e80de111c30b27e"
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1 <tool id="scanpy_parameter_iterator" name="Scanpy ParameterIterator" version="0.0.1+galaxy2">
0
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2 <description>produce an iteration over a defined parameter</description>
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3 <macros>
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4 <import>scanpy_macros.xml</import>
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5 </macros>
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6 <requirements>
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7 <requirement type="package" version="1.42.1">bioconductor-rtracklayer</requirement>
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8 </requirements>
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9 <command detect_errors="exit_code"><![CDATA[
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10 mkdir outputs;
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11 #if str( $input_type.parameter_values ) == "list_comma_separated_values":
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12 for param in \$(echo '$input_type.input_values' | sed 's/,/ /g'); do
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13 echo \$param > outputs/'$parameter_name'_\$param\.txt;
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14 done
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15 #else if str( $input_type.parameter_values ) == "step_increase_values":
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16 for param in \$(seq '$input_type.start_value' '$input_type.step' '$input_type.end_value'); do
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17 echo \$param > outputs/'$parameter_name'_\$param\.txt;
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18 done
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19 #end if
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20 ]]></command>
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21
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22 <inputs>
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7c4d44c14ceb "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit dcb8b19d34c3e2bf822996ca2e80de111c30b27e"
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23 <param type="select" name="parameter_name" label="Parameter name" help="Select a type of parameter">
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24 <option value="perplexity" selected="True">Perplexity</option>
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25 <option value="resolution">Resolution</option>
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7c4d44c14ceb "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit dcb8b19d34c3e2bf822996ca2e80de111c30b27e"
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26 <option value="n_neighbors">Number of neighbors</option>
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27 </param>
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28 <conditional name="input_type">
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29 <param type="select" name="parameter_values" label="Choose the format of the input values" help="step increase values or list of all the parameter values">
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30 <option value="list_comma_separated_values" selected="True">List of all parameter values to be iterated</option>
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31 <option value="step_increase_values">Step increase values to be iterated</option>
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32 </param>
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33 <when value="list_comma_separated_values">
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34 <param type="text" value="0.1, 0.3, 0.5, 0.7, 1.0, 2.0, 3.0, 4.0, 5.0" name="input_values" label="User input values" help="List of all comma separated values for the parameter"/>
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35 </when>
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36 <when value="step_increase_values">
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37 <param type="float" value="1" name="start_value" label="Starting value" help="Initial value for the parameter"/>
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38 <param type="float" value="2" name="step" label="Step" help="Increment to use from first to last value"/>
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39 <param type="float" value="10" name="end_value" label="Ending value" help="Final value for the parameter. The final value is not included if increments of step don't match the last value."/>
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40 </when>
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41 </conditional>
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42 </inputs>
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43
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44 <outputs>
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45 <collection name="parameter_iteration" type="list" label="Parameter iterated">
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46 <discover_datasets pattern="__name_and_ext__" directory="outputs"/>
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47 </collection>
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48 </outputs>
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49
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50 <tests>
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51 <test>
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52 <param name="parameter_name" value="perplexity"/>
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53 <conditional name="input_type">
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54 <param name="parameter_values" value="list_comma_separated_values"/>
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55 <param name="input_values" value="1, 5, 10"/>
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56 </conditional>
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57 <output_collection name="parameter_iteration" count="3">
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58 <element name="perplexity_1" file="perplexity_1.txt" ftype="txt" compare="sim_size"/>
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59 <element name="perplexity_5" file="perplexity_5.txt" ftype="txt" compare="sim_size"/>
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60 <element name="perplexity_10" file="perplexity_10.txt" ftype="txt" compare="sim_size"/>
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61 </output_collection>
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62 </test>
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63 </tests>
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64
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65 <help><![CDATA[
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66 .. class:: infomark
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67
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68 **What it does**
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69
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7c4d44c14ceb "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit dcb8b19d34c3e2bf822996ca2e80de111c30b27e"
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70 Given start, step and end, it will iterate parameters for either perplexity (for t-SNE), resolution (clustering)
7c4d44c14ceb "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit dcb8b19d34c3e2bf822996ca2e80de111c30b27e"
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71 or number of neighbours (neighbour graph construction).
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1a30a61effea 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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72
1a30a61effea 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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73 **Inputs**
1a30a61effea 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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74
1a30a61effea 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 * Parameter name: either Resolution or Perplexity.
1a30a61effea 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 * Starting value: float for Resolution, integer for Perplexity.
1a30a61effea 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 * Step: float for Resolution, integer for Perplexity.
1a30a61effea 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 * End value: float for Resolution, integer for Perplexity.
1a30a61effea 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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79
1a30a61effea 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 **Outputs**
1a30a61effea 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
1a30a61effea 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 * Collection of parameters to be passed to either Scanpy run tSNE (perplexity) or Scanpy find clusters (resolution).
1a30a61effea 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
1a30a61effea 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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84 @VERSION_HISTORY@
1a30a61effea 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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85 ]]></help>
1a30a61effea 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 <expand macro="citations"/>
1a30a61effea 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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87 </tool>