Mercurial > repos > iuc > scater_filter

annotate scater-filter.xml @ 2:7a365ec81b52 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 154318f74839a4481c7c68993c4fb745842c4cce"
author iuc
date Thu, 09 Sep 2021 12:24:17 +0000
parents b7ea9f09c02f
children 652923ce664f
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7a365ec81b52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 154318f74839a4481c7c68993c4fb745842c4cce"
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1 <tool id="scater_filter" name="Scater: filter SCE" version="@TOOL_VERSION@" profile="@PROFILE@">
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2 <description>with user-defined parameters or PCA</description>
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3 <expand macro="bio_tools"/>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements">
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8 <requirement type="package" version="0.93_8">r-robustbase</requirement>
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9 </expand>
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10 <command detect_errors="exit_code"><![CDATA[
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11 #if $filter_type.filter_type_selector == 'manual':
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12 Rscript '$__tool_directory__/scater-manual-filter.R'
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13 -i '$input_loom'
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14 #if str($filter_type.library_size):
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15 --library-size ${filter_type.library_size}
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16 #end if
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17 #if str($filter_type.percent_counts_MT):
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18 --percent-counts-MT ${filter_type.percent_counts_MT}
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19 #end if
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20 #if str($filter_type.expressed_features):
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21 --expressed-features ${filter_type.expressed_features}
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22 #end if
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23 #if str($filter_type.detection_limit):
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24 --detection-limit ${filter_type.detection_limit}
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25 #end if
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26 #if str($filter_type.min_cells_expressed):
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27 --min-cells-expressed ${filter_type.min_cells_expressed}
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28 #end if
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29 #else:
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30 Rscript '$__tool_directory__/scater-pca-filter.R'
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31 -i '$input_loom'
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32 #end if
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33 -o '$output_loom'
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34 ]]></command>
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35 <inputs>
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36 <param name="input_loom" type="data" format="loom" label="Input SingleCellLoomExperiment dataset" />
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37 <conditional name="filter_type">
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38 <param name="filter_type_selector" type="select" label="Type of filter">
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39 <option value="manual">manual</option>
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40 <option value="pca">PCA</option>
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41 </param>
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42 <when value="manual">
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43 <param name="library_size" argument="--library-size" type="integer" optional="true" label="Minimum library size (mapped reads) to filter cells on" help="Raising this number will raise the stringency and may lower the number of included cells" />
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44 <param name="percent_counts_MT" argument="--percent-counts-MT" type="float" min="0" max="100" optional="true" label="Maximum % of mitochondrial genes expressed per cell" help="Cells that exceed this value will be filtered out" />
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45 <param name="expressed_features" type="integer" value="100" optional="true" label="Remove cells that have less than the given number of expressed features" />
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46 <param name="detection_limit" argument="--detection-limit" type="float" optional="true" label="Number of reads mapped to a feature above which it to be deemed as expressed" help="Raising this number will raise the stringency and may lower the number of expressed genes" />
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47 <param name="min_cells_expressed" argument="---min-cells-expressed" type="integer" optional="true" label="Remove features that occur in less than the given number of cells" help="Features that exceed this value will be filtered out" />
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48 </when>
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49 <when value="pca" />
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50 </conditional>
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51 </inputs>
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52 <outputs>
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53 <data name="output_loom" format="loom" label="${tool.name} on ${on_string}" />
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54 </outputs>
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55 <tests>
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56 <test>
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57 <param name="input_loom" value="scater_qcready.loom" ftype="loom" />
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58 <param name="filter_type_selector" value="manual" />
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59 <param name="detection_limit" value="4" />
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60 <param name="library_size" value="100000" />
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61 <param name="percent_counts_MT" value="33.0" />
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62 <param name="min_cells_expressed" value="3" />
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63 <output name="output_loom" file="scater_manual_filtered.loom" compare="sim_size" />
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64 </test>
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65 <test>
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66 <param name="input_loom" value="scater_qcready.loom" ftype="loom" />
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67 <param name="filter_type_selector" value="pca" />
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68 <output name="output_loom" file="scater_pca_filtered.loom" compare="sim_size" />
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69 </test>
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70 </tests>
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71 <help><![CDATA[
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72 Filter a SingleCellLoomExperiment object with Scater using one of the following methods:
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73
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74 - user-defined parameters
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75 - PCA to automatically removes outliers.
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76 ]]></help>
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77 <expand macro="citations" />
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78 </tool>