Mercurial > repos > ebi-gxa > scanpy_parameter_iterator

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author ebi-gxa
date Wed, 13 Mar 2019 11:48:57 -0400
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1 <tool id="scanpy_parameter_iterator" name="Scanpy ParameterIterator" version="0.0.1+galaxy0">
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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 for param in \$(seq '$start_value' '$step' '$end_value'); do
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12 echo \$param > outputs/'$parameter_name'_\$param\.txt;
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13 done
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14 ]]></command>
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16 <inputs>
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17 <param type="select" name="parameter_name" label="Choose the format of the expression data" help="Use compressed txt, Scanpy or Seurat objects">
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18 <option value="resolution" selected="true">Resolution</option>
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19 <option value="perplexity">Perplexity</option>
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20 </param>
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21 <param type="float" value="0" name="start_value" label="Starting value" help="Initial value for the parameter"/>
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22 <param type="float" value="1" name="step" label="Step" help="Increment to use from first to last value"/>
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23 <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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24 </inputs>
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25
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26 <outputs>
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27 <collection name="parameter_iteration" type="list" label="Parameter iterated">
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28 <discover_datasets pattern="__name_and_ext__" directory="outputs" />
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29 </collection>
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30 </outputs>
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31
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32 <tests>
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33 <test>
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34 <param name="parameter_name" value="perplexity"/>
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35 <param name="start_value" value="1"/>
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36 <param name="step" value="1"/>
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37 <param name="end_value" value="2"/>
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38 <output_collection name="parameter_iteration">
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39 <element name="perplexity_1"/>
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40 <element name="perplexity_2">
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41 <assert_contents>
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42 <has_line line="2" />
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43 </assert_contents>
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44 </element>
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45 </output_collection>
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46 </test>
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47 </tests>
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48
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49 <help><![CDATA[
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50 .. class:: infomark
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51
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52 **What it does**
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53
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54 Given start, step and end, it will iterate parameters for either perplexity or
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55 resolution.
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56
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57 **Inputs**
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58
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59 * Parameter name: either Resolution or Perplexity.
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60 * Starting value: float for Resolution, integer for Perplexity.
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61 * Step: float for Resolution, integer for Perplexity.
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62 * End value: float for Resolution, integer for Perplexity.
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63
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64 **Outputs**
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65
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66 * Collection of parameters to be passed to either Scanpy run tSNE (perplexity) or Scanpy find clusters (resolution).
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67
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68 @VERSION_HISTORY@
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69 ]]></help>
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70 <expand macro="citations"/>
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71 </tool>