Mercurial > repos > ebi-gxa > scanpy_read_10x

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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 ee197a80b2d591c393e1662854bc119b2ecab11e-dirty
author ebi-gxa
date Tue, 27 Feb 2024 16:43:19 +0000
parents af6ecb5adcc1
children
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572b6e3b2aff 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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1 <?xml version="1.0" encoding="utf-8"?>
26
078aa23c9374 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ee197a80b2d591c393e1662854bc119b2ecab11e-dirty
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2 <tool id="scanpy_read_10x" name="Scanpy Read10x" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
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3 <description>into hdf5 object handled by scanpy</description>
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4 <macros>
1
3faf577f3e40 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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5 <import>scanpy_macros2.xml</import>
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6 </macros>
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7 <expand macro="requirements"/>
572b6e3b2aff 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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8 <command detect_errors="exit_code"><![CDATA[
572b6e3b2aff 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 '${matrix}' matrix.mtx &&
572b6e3b2aff planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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10 ln -s '${genes}' genes.tsv &&
572b6e3b2aff 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 ln -s '${barcodes}' barcodes.tsv &&
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3faf577f3e40 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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12 PYTHONIOENCODING=utf-8 scanpy-read-10x
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13 --input-10x-mtx ./
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14 --var-names '${var_names}'
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15 #if $cell_meta:
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16 --extra-obs '${cell_meta}'
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17 #end if
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18 #if $gene_meta:
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19 --extra-var '${gene_meta}'
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20 #end if
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21 @OUTPUT_OPTS@
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22 ]]></command>
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24 <inputs>
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25 <param name="matrix" type="data" format="txt" label="Expression matrix in sparse matrix format (.mtx)"/>
572b6e3b2aff 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="genes" type="data" format="tsv,tabular" label="Gene table"/>
572b6e3b2aff 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 <param name="barcodes" type="data" format="tsv,tabular" label="Barcode/cell table"/>
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28 <param name="cell_meta" type="data" format="tsv,tabular" label="Cell metadata table" optional="true"
3faf577f3e40 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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29 help="Requires a header row and index column that matches the barcode/cell table"/>
3faf577f3e40 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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30 <param name="gene_meta" type="data" format="tsv,tabular" label="Gene metadata table" optional="true"
3faf577f3e40 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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31 help="Requires a header row and index column that matches the gene table"/>
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32 <expand macro="output_object_params"/>
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33 <param name="var_names" type="select" label="Attribute used as annotation index" help="If Gene ID is selected the index will point to the gene identifiers (first columns expected) and the gene symbols will be left in a field called 'gene_symbols'.">
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34 <option value="gene_ids" selected="true">Gene ID</option>
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35 <option value="gene_symbols">Gene symbol</option>
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36 </param>
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37 </inputs>
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38
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39 <outputs>
5
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40 <expand macro="output_data_obj" description="${output_format}"/>
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41 </outputs>
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42
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43 <tests>
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44 <test>
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45 <param name="matrix" value="matrix.mtx"/>
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46 <param name="genes" value="genes.tsv"/>
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47 <param name="barcodes" value="barcodes.tsv"/>
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48 <!-- <param name="cell_meta" value=""/> -->
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49 <param name="output_format" value="anndata"/>
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50 <output name="output_h5ad" ftype="h5">
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51 <assert_contents>
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52 <has_h5_keys keys="var/gene_symbols"/>
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53 </assert_contents>
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54 </output>
0
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55 </test>
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56 </tests>
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57
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58 <help><![CDATA[
1
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59 =================================================================
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60 Read 10x-Genomics-formatted mtx directory (`scanpy.read_10x_mtx`)
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61 =================================================================
0
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62
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63 The mtx directory should contain:
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64
572b6e3b2aff 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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65 1) Raw expression quantification as a sparse matrix in Matrix Market format, where the each column is a gene and each row is a barcode/cell.
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66
572b6e3b2aff 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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67 2) A gene table of at least two columns where the first column gives the gene IDs.
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68
572b6e3b2aff 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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69 3) A barcode/cell table of at least one column giving the barcode/cell IDs.
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70
1
3faf577f3e40 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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71 The above-mentioned files can be obtained by running `EBI SCXA Data Retrieval` with a dataset accession or `Human Cell Atlas Matrix Downloader` with a project name/label/UUID.
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72
3faf577f3e40 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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73 Additionally, cell and/or gene metadata table can be provided as tab-separated text with a header row and an index column that matches the respective barcode/cell and/or gene table.
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74
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75
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76 @HELP@
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77
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78 @VERSION_HISTORY@
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79 ]]></help>
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80 <expand macro="citations"/>
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81 </tool>