Mercurial > repos > goeckslab > scimap_phenotyping

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author goeckslab
date Tue, 30 Jul 2024 18:21:08 +0000
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1 <tool id="scimap_phenotyping" name="Single Cell Phenotyping" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>using scimap</description>
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3 <macros>
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4 <import>main_macros.xml</import>
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5 </macros>
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7 <expand macro="scimap_requirements"/>
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8 <expand macro="macro_stdio" />
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9 <version_command>echo "@VERSION@"</version_command>
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10 <command detect_errors="aggressive">
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11 <![CDATA[
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12 python '$__tool_directory__/scimap_phenotyping.py'
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13 --adata '$anndata'
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14 #if $log
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15 --log
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16 #end if
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17 #if $manual_gates
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18 --manual_gates '$manual_gates'
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19 --manual_gates_ext '${manual_gates.ext}'
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20 #end if
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21 --gating_workflow '$gating_workflow'
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22 --gating_workflow_ext '${gating_workflow.ext}'
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23 --random_state '$random_state'
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24 --output '$output'
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25
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26 ]]>
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27 </command>
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28 <configfiles>
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29 <inputs name="inputs" />
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30 </configfiles>
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31 <inputs>
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32 <param name="anndata" type="data" format="h5ad" label="Select the input anndata" />
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33 <param name="log" type="boolean" checked="true" label="Whether to log the data prior to rescaling" />
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34 <param name="manual_gates" type="data" format="tabular,csv" optional="true" label="Select the dataset containing manual gate information" help="First column as markers and second column as the gate values in log1p scale. If a marker is not included, auto gating
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35 based on gaussian mixture modeling will be executed. Optional."/>
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36 <param name="gating_workflow" type="data" format="tabular,csv" label="Select the dataset containing gating workflow" />
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37 <param name="random_state" type="integer" value="0" optional="true" label="Set seed used by the random number generator for GMM" />
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38 </inputs>
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39 <outputs>
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40 <data format="h5ad" name="output" />
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41 </outputs>
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42 <tests>
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43 <test>
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44 <param name="anndata" value="tutorial_data.h5ad" ftype="h5ad" />
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45 <param name="manual_gates" value="manual_gates.csv" ftype="csv" />
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46 <param name="gating_workflow" value="phenotype_workflow.csv" ftype="csv" />
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47 <output name="output">
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48 <assert_contents>
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49 <has_h5_keys keys="obs/phenotype" />
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50 </assert_contents>
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51 </output>
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52 </test>
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53 </tests>
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54 <help>
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55 <![CDATA[
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56 **What it does**
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57
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58 This tool generates single cell phenotyping using either manual gating or auto gating (gaussian mixture modeling) implemented in Scimap.
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59
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60 **Input**
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61
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62 AnnData.
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63
2
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64 **Important Note**
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65
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66 If adata.raw.X exists, it will be used. If adata.raw.X does not exist, adata.X is used
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67
0
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68 **Output**
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69
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70 Anndata with "obs/phenotype" added.
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71
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72
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73 ]]>
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74 </help>
2
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75 <expand macro="citations" />
0
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76 </tool>