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 9bf9a6e46a330890be932f60d1d996dd166426c4
author ebi-gxa
date Wed, 03 Apr 2019 11:07:51 -0400
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children e541f264fad2
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1dda36e73482 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
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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@+galaxy1">
1dda36e73482 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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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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5 <import>scanpy_macros.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[
1dda36e73482 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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9 ln -s '${input_obj_file}' input.h5 &&
1dda36e73482 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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10 PYTHONIOENCODING=utf-8 scanpy-normalise-data.py
1dda36e73482 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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11 -i input.h5
1dda36e73482 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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12 -f '${input_format}'
1dda36e73482 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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13 -o output.h5
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14 -F '${output_format}'
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15 -s '${scale_factor}'
1dda36e73482 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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16 #if $save_raw
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17 '${save_raw}'
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18 #end if
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19 @EXPORT_MTX_OPTS@
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20 ]]></command>
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21
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22 <inputs>
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23 <expand macro="input_object_params"/>
1dda36e73482 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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24 <expand macro="output_object_params"/>
1dda36e73482 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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25 <param name="scale_factor" argument="--scale-factor" type="float" value="1e4" label="Target number to normalise to" help="Aimed counts per cell after normalisation, default: 1e4"/>
1dda36e73482 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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26 <param name="save_raw" argument="--save-raw" type="boolean" truevalue="--save-raw" falsevalue="" checked="true" label="Save pre-normalised data" help="Save raw quantification in log scale before normalisation."/>
1dda36e73482 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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27 <expand macro="export_mtx_params"/>
1dda36e73482 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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28 </inputs>
1dda36e73482 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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29
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30 <outputs>
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31 <data name="output_h5" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: Normalized data" />
1dda36e73482 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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32 <expand macro="export_mtx_outputs"/>
1dda36e73482 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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33 </outputs>
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34
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35 <tests>
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36 <test>
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37 <param name="input_obj_file" value="filter_genes.h5"/>
1dda36e73482 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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38 <param name="input_format" value="anndata"/>
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39 <param name="output_format" value="anndata"/>
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40 <param name="scale_factor" value="1e4"/>
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41 <param name="save_raw" value="false"/>
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42 <output name="output_h5" file="normalise_data.h5" ftype="h5" compare="sim_size"/>
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43 </test>
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44 </tests>
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45
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46 <help><![CDATA[
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47 =========================================================
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48 Normalize total counts per cell (`pp.normalize_per_cell`)
1dda36e73482 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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49 =========================================================
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50
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51 Normalize each cell by total counts over all genes, so that every cell has
1dda36e73482 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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52 the same total count after normalization.
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53
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54 Similar functions are used, for example, by Seurat, Cell Ranger or SPRING.
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55
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56 @HELP@
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57
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58 @VERSION_HISTORY@
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59 ]]></help>
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60 <expand macro="citations"/>
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61 </tool>