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annotate scater-filter.xml @ 0:eca7cdc36e1e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
author iuc
date Thu, 18 Jul 2019 11:09:31 -0400
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eca7cdc36e1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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1 <tool id="scater_filter" name="Scater: filter SCE" version="@TOOL_VERSION@">
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2 <description>with user-defined parameters or PCA</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements">
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7 <requirement type="package" version="2.0.9">r-mvoutlier</requirement>
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8 </expand>
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9 <command detect_errors="exit_code"><![CDATA[
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10 #if $filter_type.filter_type_selector == 'manual':
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11 Rscript '$__tool_directory__/scater-manual-filter.R'
eca7cdc36e1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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12 -i '$input_loom'
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13 #if str($filter_type.detection_limit):
eca7cdc36e1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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14 --detection-limit ${filter_type.detection_limit}
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15 #end if
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16 #if str($filter_type.library_size):
eca7cdc36e1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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17 --library-size ${filter_type.library_size}
eca7cdc36e1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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18 #end if
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19 #if str($filter_type.percent_counts_MT):
eca7cdc36e1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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20 --percent-counts-MT ${filter_type.percent_counts_MT}
eca7cdc36e1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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21 #end if
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22 #else:
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23 Rscript '$__tool_directory__/scater-pca-filter.R'
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24 -i '$input_loom'
eca7cdc36e1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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25 #end if
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26 -o '$output_loom'
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27 ]]></command>
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28 <inputs>
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29 <param name="input_loom" type="data" format="loom" label="Input SingleCellLoomExperiment dataset" />
eca7cdc36e1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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30 <conditional name="filter_type">
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31 <param name="filter_type_selector" type="select" label="Type of filter">
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32 <option value="manual">manual</option>
eca7cdc36e1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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33 <option value="pca">PCA</option>
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34 </param>
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35 <when value="manual">
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36 <param name="detection_limit" argument="--detection-limit" type="float" optional="true" label="Number of reads mapped to a gene for it to be counted as expressed" help="Raising this number will raise the stringency and may lower the number of expressed genes" />
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37 <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" />
eca7cdc36e1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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38 <param name="percent_counts_MT" argument="--percent-counts-MT" type="float" optional="true" label="Maximum % of mitochondrial genes expressed per cell" help="Cells that exceed this value will be filtered out" />
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39 </when>
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40 <when value="pca" />
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41 </conditional>
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42 </inputs>
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43 <outputs>
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44 <data name="output_loom" format="loom" label="${tool.name} on ${on_string}" />
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45 </outputs>
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46 <tests>
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47 <test>
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48 <param name="input_loom" value="scater_qcready.loom" ftype="loom" />
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49 <param name="filter_type_selector" value="manual" />
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50 <param name="detection_limit" value="4" />
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51 <param name="library_size" value="100000" />
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52 <param name="percent_counts_MT" value="33.0" />
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53 <output name="output_loom" file="scater_manual_filtered.loom" compare="sim_size" />
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54 </test>
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55 <test>
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56 <param name="input_loom" value="scater_qcready.loom" ftype="loom" />
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57 <param name="filter_type_selector" value="pca" />
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58 <output name="output_loom" file="scater_pca_filtered.loom" compare="sim_size" />
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59 </test>
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60 </tests>
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61 <help><![CDATA[
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62 Filter a SingleCellLoomExperiment object with Scater using one of the following methods:
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63
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64 - user-defined parameters
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65 - PCA to automatically removes outliers.
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66 ]]></help>
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67 <expand macro="citations" />
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68 </tool>