Mercurial > repos > ebi-gxa > scanpy_parameter_iterator

annotate scanpy-parameter-iterator.xml @ 17:4bb2ca8e2bd3 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 0cba7758ff1591240bdc81d8075fd90b46951c2d-dirty"
author ebi-gxa
date Fri, 13 Nov 2020 14:57:26 +0000
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children 328e7846309d
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ae4debc68f4a "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1fc1a5ce4636be4672c65e1765012af3b71d2d13-dirty"
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1 <tool id="scanpy_parameter_iterator" name="Scanpy ParameterIterator" version="0.0.1+galaxy3">
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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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ae4debc68f4a "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1fc1a5ce4636be4672c65e1765012af3b71d2d13-dirty"
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23 <param type="text" name="parameter_name" value='perplexity' label="Parameter type" help="This is a value that will be prefixed to output file names" />
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24 <conditional name="input_type">
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25 <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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26 <option value="list_comma_separated_values" selected="True">List of all parameter values to be iterated</option>
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27 <option value="step_increase_values">Step increase values to be iterated</option>
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28 </param>
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29 <when value="list_comma_separated_values">
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30 <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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31 </when>
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32 <when value="step_increase_values">
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33 <param type="float" value="1" name="start_value" label="Starting value" help="Initial value for the parameter"/>
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34 <param type="float" value="2" name="step" label="Step" help="Increment to use from first to last value"/>
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35 <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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36 </when>
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37 </conditional>
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38 </inputs>
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39
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40 <outputs>
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41 <collection name="parameter_iteration" type="list" label="Parameter iterated">
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42 <discover_datasets pattern="__name_and_ext__" directory="outputs"/>
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43 </collection>
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44 </outputs>
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45
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46 <tests>
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47 <test>
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48 <param name="parameter_name" value="perplexity"/>
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49 <conditional name="input_type">
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50 <param name="parameter_values" value="list_comma_separated_values"/>
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51 <param name="input_values" value="1, 5, 10"/>
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52 </conditional>
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53 <output_collection name="parameter_iteration" count="3">
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54 <element name="perplexity_1" file="perplexity_1.txt" ftype="txt" compare="sim_size"/>
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55 <element name="perplexity_5" file="perplexity_5.txt" ftype="txt" compare="sim_size"/>
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56 <element name="perplexity_10" file="perplexity_10.txt" ftype="txt" compare="sim_size"/>
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57 </output_collection>
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58 </test>
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59 </tests>
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60
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61 <help><![CDATA[
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62 .. class:: infomark
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63
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64 **What it does**
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65
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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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66 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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67 or number of neighbours (neighbour graph construction).
0
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68
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69 **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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70
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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71 * 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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72 * 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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73 * 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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74 * 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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75
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 **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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77
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 * 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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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 @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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81 ]]></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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82 <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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83 </tool>