Mercurial > repos > ebi-gxa > scanpy_normalise_data

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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 ba0c88ab1b077a0b1c60c8d3c529e72ca6946226"
author ebi-gxa
date Thu, 12 Mar 2020 09:08:10 +0000
parents 19805a556cd6
children
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19805a556cd6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48-dirty
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1 <?xml version="1.0" encoding="utf-8"?>
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2 <tool id="scanpy_normalise_data" name="Scanpy NormaliseData" version="@TOOL_VERSION@+galaxy10" profile="@PROFILE@">
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3 <description>to make all cells having the same total expression</description>
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4 <macros>
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5704635cef67 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ba0c88ab1b077a0b1c60c8d3c529e72ca6946226"
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5 <import>scanpy_macros2.xml</import>
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6 </macros>
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7 <expand macro="requirements"/>
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8 <command detect_errors="exit_code"><![CDATA[
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9 ln -s '${input_obj_file}' input.h5 &&
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10 PYTHONIOENCODING=utf-8 scanpy-normalise-data
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11 --normalize-to ${scale_factor}
5704635cef67 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ba0c88ab1b077a0b1c60c8d3c529e72ca6946226"
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12 --fraction ${fraction}
5704635cef67 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ba0c88ab1b077a0b1c60c8d3c529e72ca6946226"
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13 --save-raw ${save_raw}
5704635cef67 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ba0c88ab1b077a0b1c60c8d3c529e72ca6946226"
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14 ${log_transform}
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15 @INPUT_OPTS@
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16 @OUTPUT_OPTS@
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17 @EXPORT_MTX_OPTS@
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18 ]]></command>
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20 <inputs>
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21 <expand macro="input_object_params"/>
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22 <expand macro="output_object_params"/>
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5704635cef67 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ba0c88ab1b077a0b1c60c8d3c529e72ca6946226"
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23 <param name="scale_factor" argument="--normalize-to" type="float" value="1e4" min="0"
5704635cef67 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ba0c88ab1b077a0b1c60c8d3c529e72ca6946226"
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24 label="Target number to normalise to" help="Aimed counts per cell after normalisation."/>
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25 <param name="fraction" argument="--fraction" type="float" value="1" min="0" max="1"
5704635cef67 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ba0c88ab1b077a0b1c60c8d3c529e72ca6946226"
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26 label="Exclude top expressed genes until the remaining account for no greater than specified fraction of total counts"
5704635cef67 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ba0c88ab1b077a0b1c60c8d3c529e72ca6946226"
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27 help="Only non-excluded genes will sum up the target number."/>
5704635cef67 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ba0c88ab1b077a0b1c60c8d3c529e72ca6946226"
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28 <param name="log_transform" argument="--no-log-transform" type="boolean" truevalue="" falsevalue="--no-log-transform" checked="True"
5704635cef67 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ba0c88ab1b077a0b1c60c8d3c529e72ca6946226"
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29 label="Apply log transform?" help="If enabled, will apply a log transformation following normalisation."/>
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30 <param name="save_raw" argument="--save-raw" type="boolean" truevalue="yes" falsevalue="no" checked="true"
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31 label="Save normalised data in `.raw`" help="The saved normalised data are log1p transformed."/>
5704635cef67 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ba0c88ab1b077a0b1c60c8d3c529e72ca6946226"
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32 <expand macro="export_mtx_params"/>
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33 </inputs>
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35 <outputs>
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36 <expand macro="output_data_obj" description="Normalised data"/>
5704635cef67 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ba0c88ab1b077a0b1c60c8d3c529e72ca6946226"
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37 <expand macro="export_mtx_outputs"/>
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38 </outputs>
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40 <tests>
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41 <test>
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42 <param name="input_obj_file" value="filter_genes.h5"/>
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43 <param name="input_format" value="anndata"/>
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44 <param name="output_format" value="anndata"/>
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45 <param name="scale_factor" value="1e4"/>
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46 <param name="save_raw" value="false"/>
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47 <output name="output_h5" file="normalise_data.h5" ftype="h5" compare="sim_size"/>
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48 </test>
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49 </tests>
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50
19805a556cd6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48-dirty
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51 <help><![CDATA[
1
5704635cef67 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ba0c88ab1b077a0b1c60c8d3c529e72ca6946226"
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52 =============================================================
5704635cef67 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ba0c88ab1b077a0b1c60c8d3c529e72ca6946226"
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53 Normalise total counts per cell (`scanpy.pp.normalize_total`)
5704635cef67 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ba0c88ab1b077a0b1c60c8d3c529e72ca6946226"
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54 =============================================================
0
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55
1
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56 Normalise each cell by total counts over all genes (excluding top expressed
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57 genes if so required), so that every cell has the same total count after
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58 normalisation.
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59
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60 Similar functions are used, for example, by Seurat, Cell Ranger or SPRING.
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61
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62 @HELP@
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63
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64 @VERSION_HISTORY@
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65 ]]></help>
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66 <expand macro="citations"/>
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67 </tool>