Mercurial > repos > ebi-gxa > score_genes_aucell
annotate decoupler_aucell_score.xml @ 1:e024d8280886 draft
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 56273bcfbc0de8f6ab093f1131a7d22c05a70f25
author | ebi-gxa |
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date | Thu, 16 Nov 2023 20:05:21 +0000 |
parents | 1e8697931d73 |
children | e887a7e8c5b4 |
rev | line source |
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1e8697931d73
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c8c39f14eeee6e7a6d097fd0cb9430b12793eb8b
ebi-gxa
parents:
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1 <?xml version="1.0"?> |
1
e024d8280886
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 56273bcfbc0de8f6ab093f1131a7d22c05a70f25
ebi-gxa
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2 <tool id="score_genes_aucell" name="Decoupler AUCell" version="1.4.0+galaxy1" profile="20.05"> |
0
1e8697931d73
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c8c39f14eeee6e7a6d097fd0cb9430b12793eb8b
ebi-gxa
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3 <description> |
1e8697931d73
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c8c39f14eeee6e7a6d097fd0cb9430b12793eb8b
ebi-gxa
parents:
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4 scores cells using the AUCell method for gene sets. |
1e8697931d73
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c8c39f14eeee6e7a6d097fd0cb9430b12793eb8b
ebi-gxa
parents:
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5 </description> |
1e8697931d73
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c8c39f14eeee6e7a6d097fd0cb9430b12793eb8b
ebi-gxa
parents:
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6 <requirements> |
1e8697931d73
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c8c39f14eeee6e7a6d097fd0cb9430b12793eb8b
ebi-gxa
parents:
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7 <requirement type="package" version="1.4.0">decoupler</requirement> |
1e8697931d73
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c8c39f14eeee6e7a6d097fd0cb9430b12793eb8b
ebi-gxa
parents:
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8 </requirements> |
1e8697931d73
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c8c39f14eeee6e7a6d097fd0cb9430b12793eb8b
ebi-gxa
parents:
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9 <command> |
1e8697931d73
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c8c39f14eeee6e7a6d097fd0cb9430b12793eb8b
ebi-gxa
parents:
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10 python '$__tool_directory__/decoupler_aucell_score.py' |
1e8697931d73
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c8c39f14eeee6e7a6d097fd0cb9430b12793eb8b
ebi-gxa
parents:
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11 --input_file '$input_file' |
1e8697931d73
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c8c39f14eeee6e7a6d097fd0cb9430b12793eb8b
ebi-gxa
parents:
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12 #if $gene_lists_source.source == "gmt" |
1
e024d8280886
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 56273bcfbc0de8f6ab093f1131a7d22c05a70f25
ebi-gxa
parents:
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13 --gmt_file '$gene_lists_source.gmt_file' |
e024d8280886
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 56273bcfbc0de8f6ab093f1131a7d22c05a70f25
ebi-gxa
parents:
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14 #if $gene_lists_source.gene_sets_to_score |
e024d8280886
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 56273bcfbc0de8f6ab093f1131a7d22c05a70f25
ebi-gxa
parents:
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15 --gene_sets_to_score '$gene_lists_source.gene_sets_to_score' |
e024d8280886
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 56273bcfbc0de8f6ab093f1131a7d22c05a70f25
ebi-gxa
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16 #end if |
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1e8697931d73
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c8c39f14eeee6e7a6d097fd0cb9430b12793eb8b
ebi-gxa
parents:
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17 #else: |
1
e024d8280886
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 56273bcfbc0de8f6ab093f1131a7d22c05a70f25
ebi-gxa
parents:
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18 --gene_lists_to_score '$gene_lists_source.gene_lists_to_score' |
e024d8280886
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 56273bcfbc0de8f6ab093f1131a7d22c05a70f25
ebi-gxa
parents:
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19 --score_names '$gene_lists_source.score_names' |
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1e8697931d73
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c8c39f14eeee6e7a6d097fd0cb9430b12793eb8b
ebi-gxa
parents:
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20 #end if |
1e8697931d73
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c8c39f14eeee6e7a6d097fd0cb9430b12793eb8b
ebi-gxa
parents:
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21 --gene_symbols_field '$gene_symbols_field' |
1e8697931d73
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c8c39f14eeee6e7a6d097fd0cb9430b12793eb8b
ebi-gxa
parents:
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22 $use_raw |
1e8697931d73
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c8c39f14eeee6e7a6d097fd0cb9430b12793eb8b
ebi-gxa
parents:
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23 #if $write_anndata: |
1e8697931d73
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c8c39f14eeee6e7a6d097fd0cb9430b12793eb8b
ebi-gxa
parents:
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24 --write_anndata |
1e8697931d73
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c8c39f14eeee6e7a6d097fd0cb9430b12793eb8b
ebi-gxa
parents:
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25 --output_file anndata_aucell.h5ad |
1e8697931d73
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c8c39f14eeee6e7a6d097fd0cb9430b12793eb8b
ebi-gxa
parents:
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26 #else: |
1e8697931d73
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c8c39f14eeee6e7a6d097fd0cb9430b12793eb8b
ebi-gxa
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27 --output_file anndata_aucell_per_cell.tsv |
1e8697931d73
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c8c39f14eeee6e7a6d097fd0cb9430b12793eb8b
ebi-gxa
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28 #end if |
1e8697931d73
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c8c39f14eeee6e7a6d097fd0cb9430b12793eb8b
ebi-gxa
parents:
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29 </command> |
1e8697931d73
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c8c39f14eeee6e7a6d097fd0cb9430b12793eb8b
ebi-gxa
parents:
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30 <inputs> |
1e8697931d73
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c8c39f14eeee6e7a6d097fd0cb9430b12793eb8b
ebi-gxa
parents:
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31 <param name="input_file" type="data" format="h5ad" label="Input AnnData file" /> |
1e8697931d73
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c8c39f14eeee6e7a6d097fd0cb9430b12793eb8b
ebi-gxa
parents:
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32 <conditional name="gene_lists_source"> |
1e8697931d73
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c8c39f14eeee6e7a6d097fd0cb9430b12793eb8b
ebi-gxa
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33 <param name="source" type="select" label="Source of gene lists to score" help="Choose between using a GMT file and specified gene sets or enumerated genes and gene set names."> |
1e8697931d73
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c8c39f14eeee6e7a6d097fd0cb9430b12793eb8b
ebi-gxa
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34 <option value="gmt" selected="true">Gene sets from GMT file</option> |
1e8697931d73
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c8c39f14eeee6e7a6d097fd0cb9430b12793eb8b
ebi-gxa
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35 <option value="enumerated">Gene sets enumerated manually</option> |
1e8697931d73
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c8c39f14eeee6e7a6d097fd0cb9430b12793eb8b
ebi-gxa
parents:
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36 </param> |
1e8697931d73
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c8c39f14eeee6e7a6d097fd0cb9430b12793eb8b
ebi-gxa
parents:
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37 <when value="gmt"> |
1e8697931d73
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c8c39f14eeee6e7a6d097fd0cb9430b12793eb8b
ebi-gxa
parents:
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38 <param name="gmt_file" type="data" format="txt" label="GMT file with gene sets" /> |
1
e024d8280886
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 56273bcfbc0de8f6ab093f1131a7d22c05a70f25
ebi-gxa
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39 <param name="gene_sets_to_score" type="text" optional="true" label="Gene sets to score within the GMT file" /> |
0
1e8697931d73
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c8c39f14eeee6e7a6d097fd0cb9430b12793eb8b
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40 </when> |
1e8697931d73
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c8c39f14eeee6e7a6d097fd0cb9430b12793eb8b
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41 <when value="enumerated"> |
1e8697931d73
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c8c39f14eeee6e7a6d097fd0cb9430b12793eb8b
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42 <param name="gene_lists_to_score" type="text" label="Genes to score" /> |
1e8697931d73
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c8c39f14eeee6e7a6d097fd0cb9430b12793eb8b
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43 <param name="score_names" type="text" label="Score names" /> |
1e8697931d73
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c8c39f14eeee6e7a6d097fd0cb9430b12793eb8b
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44 </when> |
1e8697931d73
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c8c39f14eeee6e7a6d097fd0cb9430b12793eb8b
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45 </conditional> |
1e8697931d73
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c8c39f14eeee6e7a6d097fd0cb9430b12793eb8b
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46 <param name="gene_symbols_field" type="text" label="Gene symbols field" help="The field in the AnnData var table where gene symbols are stored."/> |
1e8697931d73
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c8c39f14eeee6e7a6d097fd0cb9430b12793eb8b
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47 <param name="use_raw" type="boolean" value="false" truevalue="--use_raw" falsevalue="" label="Use raw data" help="Use RAW data in the AnnData instead of the X matrix."/> |
1e8697931d73
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c8c39f14eeee6e7a6d097fd0cb9430b12793eb8b
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48 <param name="write_anndata" type="boolean" value="false" truevalue="--write_anndata" falsevalue="" label="Write the modified AnnData object" help="Whether to write or not the same AnnData file again with the signatures on it. If unselected, a text files of cells in rows and signatures in columns (as in Obs) is produced."/> |
1e8697931d73
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c8c39f14eeee6e7a6d097fd0cb9430b12793eb8b
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49 </inputs> |
1e8697931d73
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c8c39f14eeee6e7a6d097fd0cb9430b12793eb8b
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50 <outputs> |
1e8697931d73
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c8c39f14eeee6e7a6d097fd0cb9430b12793eb8b
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51 <data name="output_ad" format="h5ad" from_work_dir="anndata_aucell.h5ad" label="${tool.name} on ${on_string}: Output AnnData file"> |
1e8697931d73
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c8c39f14eeee6e7a6d097fd0cb9430b12793eb8b
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52 <filter>write_anndata</filter> |
1e8697931d73
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c8c39f14eeee6e7a6d097fd0cb9430b12793eb8b
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53 </data> |
1e8697931d73
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c8c39f14eeee6e7a6d097fd0cb9430b12793eb8b
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54 <data name="output_table" format="tabular" from_work_dir="anndata_aucell_per_cell.tsv" label="${tool.name} on ${on_string}: Output AUCell table"> |
1e8697931d73
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c8c39f14eeee6e7a6d097fd0cb9430b12793eb8b
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55 <filter>not write_anndata</filter> |
1e8697931d73
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c8c39f14eeee6e7a6d097fd0cb9430b12793eb8b
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56 </data> |
1e8697931d73
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c8c39f14eeee6e7a6d097fd0cb9430b12793eb8b
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57 </outputs> |
1e8697931d73
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c8c39f14eeee6e7a6d097fd0cb9430b12793eb8b
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58 <tests> |
1e8697931d73
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c8c39f14eeee6e7a6d097fd0cb9430b12793eb8b
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59 <test expect_num_outputs="1"> |
1e8697931d73
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c8c39f14eeee6e7a6d097fd0cb9430b12793eb8b
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60 <param name="input_file" value="mito_counted_anndata.h5ad"/> |
1e8697931d73
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c8c39f14eeee6e7a6d097fd0cb9430b12793eb8b
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61 <param name="gene_symbols_field" value="Symbol"/> |
1e8697931d73
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c8c39f14eeee6e7a6d097fd0cb9430b12793eb8b
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62 <param name="write_anndata" value="true"/> |
1e8697931d73
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c8c39f14eeee6e7a6d097fd0cb9430b12793eb8b
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63 <conditional name="gene_lists_source"> |
1
e024d8280886
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 56273bcfbc0de8f6ab093f1131a7d22c05a70f25
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64 <param name="gene_sets_to_score" value="HALLMARK_NOTCH_SIGNALING,HALLMARK_APICAL_SURFACE"/> |
e024d8280886
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 56273bcfbc0de8f6ab093f1131a7d22c05a70f25
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65 <param name="gmt_file" value="mouse_hallmark_ss.gmt"/> |
0
1e8697931d73
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c8c39f14eeee6e7a6d097fd0cb9430b12793eb8b
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66 <param name="source" value="gmt"/> |
1e8697931d73
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c8c39f14eeee6e7a6d097fd0cb9430b12793eb8b
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67 </conditional> |
1e8697931d73
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c8c39f14eeee6e7a6d097fd0cb9430b12793eb8b
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68 <output name="output_ad"> |
1e8697931d73
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c8c39f14eeee6e7a6d097fd0cb9430b12793eb8b
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69 <assert_contents> |
1e8697931d73
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c8c39f14eeee6e7a6d097fd0cb9430b12793eb8b
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70 <has_h5_keys keys="obs/AUCell_HALLMARK_NOTCH_SIGNALING"/> |
1e8697931d73
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c8c39f14eeee6e7a6d097fd0cb9430b12793eb8b
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71 <has_h5_keys keys="obs/AUCell_HALLMARK_APICAL_SURFACE"/> |
1e8697931d73
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c8c39f14eeee6e7a6d097fd0cb9430b12793eb8b
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72 </assert_contents> |
1e8697931d73
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c8c39f14eeee6e7a6d097fd0cb9430b12793eb8b
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73 </output> |
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74 </test> |
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75 <test expect_num_outputs="1"> |
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76 <param name="input_file" value="mito_counted_anndata.h5ad"/> |
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77 <param name="gene_symbols_field" value="Symbol"/> |
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78 <param name="write_anndata" value="true"/> |
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79 <conditional name="gene_lists_source"> |
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80 <param name="source" value="gmt"/> |
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81 <param name="gmt_file" value="mouse_hallmark_ss.gmt"/> |
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82 </conditional> |
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83 <output name="output_ad"> |
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84 <assert_contents> |
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85 <has_h5_keys keys="obs/AUCell_HALLMARK_NOTCH_SIGNALING"/> |
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86 <has_h5_keys keys="obs/AUCell_HALLMARK_APICAL_SURFACE"/> |
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87 </assert_contents> |
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88 </output> |
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89 </test> |
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90 <test expect_num_outputs="1"> |
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91 <param name="input_file" value="mito_counted_anndata.h5ad"/> |
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92 <param name="gene_symbols_field" value="Symbol"/> |
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93 <param name="write_anndata" value="true"/> |
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94 <conditional name="gene_lists_source"> |
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95 <param name="source" value="enumerated"/> |
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96 <param name="gene_lists_to_score" value="Cd8b1,Cd8b2,Cd8a,Cd4,Nrp1,Cd80:Il1a,Il1b,Il6,Nos2,Tlr2,Tlr4,Cd80"/> |
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97 <param name="score_names" value="TCell,Macro"/> |
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98 </conditional> |
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99 <output name="output_ad"> |
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100 <assert_contents> |
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101 <has_h5_keys keys="obs/AUCell_TCell"/> |
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102 <has_h5_keys keys="obs/AUCell_Macro"/> |
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103 </assert_contents> |
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104 </output> |
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105 </test> |
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106 <test expect_num_outputs="1"> |
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107 <param name="input_file" value="mito_counted_anndata.h5ad"/> |
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108 <param name="gene_symbols_field" value="Symbol"/> |
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109 <param name="write_anndata" value="False"/> |
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110 <conditional name="gene_lists_source"> |
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111 <param name="source" value="gmt"/> |
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112 <param name="gene_sets_to_score" value="HALLMARK_NOTCH_SIGNALING,HALLMARK_APICAL_SURFACE"/> |
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113 <param name="gmt_file" value="mouse_hallmark_ss.gmt"/> |
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114 </conditional> |
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115 <output name="output_table"> |
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116 <assert_contents> |
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117 <has_n_columns n="3"/> |
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118 <has_text_matching expression="AUCell_HALLMARK_NOTCH_SIGNALING"/> |
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119 </assert_contents> |
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120 </output> |
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121 </test> |
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122 </tests> |
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123 <help> |
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124 **Description** |
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125 |
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126 This tool scores cells using the AUCell method for gene sets. |
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127 |
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128 **Input** |
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129 |
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130 The input file should be an AnnData object in H5AD format. The tool accepts an H5AD file containing raw or normalized data. |
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131 |
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132 The tool takes one of two input formats for specifying the gene sets to score: |
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133 |
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134 1. A GMT file containing gene sets. You can specify which gene sets to use within the GMT file using the "gene_sets_to_score" parameter. |
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135 2. A list of genes and their associated score names. You can specify the genes to score using the "gene_lists_to_score" parameter, and their associated score names using the "score_names" parameter. |
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136 |
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137 In both cases, you must specify the name of the field in the AnnData object that contains the gene symbols using the "gene_symbols_field" parameter. |
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138 |
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139 You can also specify whether to use the raw data in the AnnData object instead of the X matrix using the "use_raw" parameter. |
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140 |
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141 **Output** |
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142 |
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143 The tool outputs an AnnData object containing the scores in the "obs" field, or a tab-separated text file containing the scores for each cell. |
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144 |
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145 If the "write_anndata" parameter is set to "true", the tool will write the modified AnnData object to an H5AD file. Otherwise, it will output a tab-separated text file containing the scores for each cell. |
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146 |
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147 **Example** |
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148 |
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149 |
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150 </help> |
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151 <citations> |
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planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c8c39f14eeee6e7a6d097fd0cb9430b12793eb8b
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152 <citation type="doi">10.1093/bioadv/vbac016</citation> |
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planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c8c39f14eeee6e7a6d097fd0cb9430b12793eb8b
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153 </citations> |
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planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c8c39f14eeee6e7a6d097fd0cb9430b12793eb8b
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154 </tool> |