Mercurial > repos > iuc > drug2cell

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planemo upload for repository https://github.com/Teichlab/drug2cell commit 9c3372b3af7b42d66e740f07ab16fed3035783cc
author iuc
date Thu, 20 Feb 2025 20:23:05 +0000
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b0ea90bddf66 planemo upload for repository https://github.com/Teichlab/drug2cell commit 9c3372b3af7b42d66e740f07ab16fed3035783cc
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1 <tool id="drug2cell" name="drug2cell" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
b0ea90bddf66 planemo upload for repository https://github.com/Teichlab/drug2cell commit 9c3372b3af7b42d66e740f07ab16fed3035783cc
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2 <description>Collection of utility functions for gene group activity evaluation in scanpy</description>
b0ea90bddf66 planemo upload for repository https://github.com/Teichlab/drug2cell commit 9c3372b3af7b42d66e740f07ab16fed3035783cc
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3 <macros>
b0ea90bddf66 planemo upload for repository https://github.com/Teichlab/drug2cell commit 9c3372b3af7b42d66e740f07ab16fed3035783cc
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4 <token name="@TOOL_VERSION@">0.1.2</token>
b0ea90bddf66 planemo upload for repository https://github.com/Teichlab/drug2cell commit 9c3372b3af7b42d66e740f07ab16fed3035783cc
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5 <token name="@VERSION_SUFFIX@">0</token>
b0ea90bddf66 planemo upload for repository https://github.com/Teichlab/drug2cell commit 9c3372b3af7b42d66e740f07ab16fed3035783cc
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6 </macros>
b0ea90bddf66 planemo upload for repository https://github.com/Teichlab/drug2cell commit 9c3372b3af7b42d66e740f07ab16fed3035783cc
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7 <requirements>
b0ea90bddf66 planemo upload for repository https://github.com/Teichlab/drug2cell commit 9c3372b3af7b42d66e740f07ab16fed3035783cc
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8 <requirement type="package" version="0.1.2">drug2cell</requirement>
b0ea90bddf66 planemo upload for repository https://github.com/Teichlab/drug2cell commit 9c3372b3af7b42d66e740f07ab16fed3035783cc
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9 <requirement type="package" version="1.10.4">scanpy</requirement>
b0ea90bddf66 planemo upload for repository https://github.com/Teichlab/drug2cell commit 9c3372b3af7b42d66e740f07ab16fed3035783cc
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10 </requirements>
b0ea90bddf66 planemo upload for repository https://github.com/Teichlab/drug2cell commit 9c3372b3af7b42d66e740f07ab16fed3035783cc
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b0ea90bddf66 planemo upload for repository https://github.com/Teichlab/drug2cell commit 9c3372b3af7b42d66e740f07ab16fed3035783cc
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12 <command>
b0ea90bddf66 planemo upload for repository https://github.com/Teichlab/drug2cell commit 9c3372b3af7b42d66e740f07ab16fed3035783cc
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13 <![CDATA[
b0ea90bddf66 planemo upload for repository https://github.com/Teichlab/drug2cell commit 9c3372b3af7b42d66e740f07ab16fed3035783cc
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14 python3 '$script' --adata '${adata}' --output '${d2c_output}'
b0ea90bddf66 planemo upload for repository https://github.com/Teichlab/drug2cell commit 9c3372b3af7b42d66e740f07ab16fed3035783cc
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15 ]]>
b0ea90bddf66 planemo upload for repository https://github.com/Teichlab/drug2cell commit 9c3372b3af7b42d66e740f07ab16fed3035783cc
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16 </command>
b0ea90bddf66 planemo upload for repository https://github.com/Teichlab/drug2cell commit 9c3372b3af7b42d66e740f07ab16fed3035783cc
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17 <configfiles>
b0ea90bddf66 planemo upload for repository https://github.com/Teichlab/drug2cell commit 9c3372b3af7b42d66e740f07ab16fed3035783cc
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18 <configfile name="script">
b0ea90bddf66 planemo upload for repository https://github.com/Teichlab/drug2cell commit 9c3372b3af7b42d66e740f07ab16fed3035783cc
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19 <![CDATA[
b0ea90bddf66 planemo upload for repository https://github.com/Teichlab/drug2cell commit 9c3372b3af7b42d66e740f07ab16fed3035783cc
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20 import drug2cell as d2c
b0ea90bddf66 planemo upload for repository https://github.com/Teichlab/drug2cell commit 9c3372b3af7b42d66e740f07ab16fed3035783cc
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21 import scanpy as sc
b0ea90bddf66 planemo upload for repository https://github.com/Teichlab/drug2cell commit 9c3372b3af7b42d66e740f07ab16fed3035783cc
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b0ea90bddf66 planemo upload for repository https://github.com/Teichlab/drug2cell commit 9c3372b3af7b42d66e740f07ab16fed3035783cc
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23 # Load AnnData object
b0ea90bddf66 planemo upload for repository https://github.com/Teichlab/drug2cell commit 9c3372b3af7b42d66e740f07ab16fed3035783cc
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24 adata = sc.read_h5ad("${adata}")
b0ea90bddf66 planemo upload for repository https://github.com/Teichlab/drug2cell commit 9c3372b3af7b42d66e740f07ab16fed3035783cc
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b0ea90bddf66 planemo upload for repository https://github.com/Teichlab/drug2cell commit 9c3372b3af7b42d66e740f07ab16fed3035783cc
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26 # Run drug2cell
b0ea90bddf66 planemo upload for repository https://github.com/Teichlab/drug2cell commit 9c3372b3af7b42d66e740f07ab16fed3035783cc
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27 d2c.score(adata)
b0ea90bddf66 planemo upload for repository https://github.com/Teichlab/drug2cell commit 9c3372b3af7b42d66e740f07ab16fed3035783cc
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b0ea90bddf66 planemo upload for repository https://github.com/Teichlab/drug2cell commit 9c3372b3af7b42d66e740f07ab16fed3035783cc
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29 # Get the drug2cell results
b0ea90bddf66 planemo upload for repository https://github.com/Teichlab/drug2cell commit 9c3372b3af7b42d66e740f07ab16fed3035783cc
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30 d2cell = adata.uns["drug2cell"]
b0ea90bddf66 planemo upload for repository https://github.com/Teichlab/drug2cell commit 9c3372b3af7b42d66e740f07ab16fed3035783cc
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b0ea90bddf66 planemo upload for repository https://github.com/Teichlab/drug2cell commit 9c3372b3af7b42d66e740f07ab16fed3035783cc
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32 # Save the drug2cell results to a new .h5ad file
b0ea90bddf66 planemo upload for repository https://github.com/Teichlab/drug2cell commit 9c3372b3af7b42d66e740f07ab16fed3035783cc
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33 d2cell.write("${d2c_output}")
b0ea90bddf66 planemo upload for repository https://github.com/Teichlab/drug2cell commit 9c3372b3af7b42d66e740f07ab16fed3035783cc
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34 ]]>
b0ea90bddf66 planemo upload for repository https://github.com/Teichlab/drug2cell commit 9c3372b3af7b42d66e740f07ab16fed3035783cc
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35 </configfile>
b0ea90bddf66 planemo upload for repository https://github.com/Teichlab/drug2cell commit 9c3372b3af7b42d66e740f07ab16fed3035783cc
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36 </configfiles>
b0ea90bddf66 planemo upload for repository https://github.com/Teichlab/drug2cell commit 9c3372b3af7b42d66e740f07ab16fed3035783cc
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b0ea90bddf66 planemo upload for repository https://github.com/Teichlab/drug2cell commit 9c3372b3af7b42d66e740f07ab16fed3035783cc
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38 <inputs>
b0ea90bddf66 planemo upload for repository https://github.com/Teichlab/drug2cell commit 9c3372b3af7b42d66e740f07ab16fed3035783cc
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39 <param name="adata" type="data" format="h5ad" label="AnnData Object" help="Select the processed AnnData object file containing your single-cell RNA-seq data"/>
b0ea90bddf66 planemo upload for repository https://github.com/Teichlab/drug2cell commit 9c3372b3af7b42d66e740f07ab16fed3035783cc
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40 </inputs>
b0ea90bddf66 planemo upload for repository https://github.com/Teichlab/drug2cell commit 9c3372b3af7b42d66e740f07ab16fed3035783cc
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b0ea90bddf66 planemo upload for repository https://github.com/Teichlab/drug2cell commit 9c3372b3af7b42d66e740f07ab16fed3035783cc
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42 <outputs>
b0ea90bddf66 planemo upload for repository https://github.com/Teichlab/drug2cell commit 9c3372b3af7b42d66e740f07ab16fed3035783cc
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43 <data name="d2c_output" format="h5ad" label="drug2cell Results" />
b0ea90bddf66 planemo upload for repository https://github.com/Teichlab/drug2cell commit 9c3372b3af7b42d66e740f07ab16fed3035783cc
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44 </outputs>
b0ea90bddf66 planemo upload for repository https://github.com/Teichlab/drug2cell commit 9c3372b3af7b42d66e740f07ab16fed3035783cc
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b0ea90bddf66 planemo upload for repository https://github.com/Teichlab/drug2cell commit 9c3372b3af7b42d66e740f07ab16fed3035783cc
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46 <tests>
b0ea90bddf66 planemo upload for repository https://github.com/Teichlab/drug2cell commit 9c3372b3af7b42d66e740f07ab16fed3035783cc
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47 <test>
b0ea90bddf66 planemo upload for repository https://github.com/Teichlab/drug2cell commit 9c3372b3af7b42d66e740f07ab16fed3035783cc
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48 <param name="adata" value="tiny_adata.h5ad"/>
b0ea90bddf66 planemo upload for repository https://github.com/Teichlab/drug2cell commit 9c3372b3af7b42d66e740f07ab16fed3035783cc
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49 <output name="d2c_output" file="d2c_output.h5ad">
b0ea90bddf66 planemo upload for repository https://github.com/Teichlab/drug2cell commit 9c3372b3af7b42d66e740f07ab16fed3035783cc
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50 <assert_contents>
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51 <has_h5_keys keys="obs,var"/>
b0ea90bddf66 planemo upload for repository https://github.com/Teichlab/drug2cell commit 9c3372b3af7b42d66e740f07ab16fed3035783cc
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52 </assert_contents>
b0ea90bddf66 planemo upload for repository https://github.com/Teichlab/drug2cell commit 9c3372b3af7b42d66e740f07ab16fed3035783cc
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53 </output>
b0ea90bddf66 planemo upload for repository https://github.com/Teichlab/drug2cell commit 9c3372b3af7b42d66e740f07ab16fed3035783cc
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54 </test>
b0ea90bddf66 planemo upload for repository https://github.com/Teichlab/drug2cell commit 9c3372b3af7b42d66e740f07ab16fed3035783cc
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55 </tests>
b0ea90bddf66 planemo upload for repository https://github.com/Teichlab/drug2cell commit 9c3372b3af7b42d66e740f07ab16fed3035783cc
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b0ea90bddf66 planemo upload for repository https://github.com/Teichlab/drug2cell commit 9c3372b3af7b42d66e740f07ab16fed3035783cc
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57 <help>
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58 <![CDATA[
b0ea90bddf66 planemo upload for repository https://github.com/Teichlab/drug2cell commit 9c3372b3af7b42d66e740f07ab16fed3035783cc
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59 This tool uses the drug2cell package to score gene groups based on drug-target data from the ChEMBL database.
b0ea90bddf66 planemo upload for repository https://github.com/Teichlab/drug2cell commit 9c3372b3af7b42d66e740f07ab16fed3035783cc
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60 It performs differential expression analysis to identify gene groups up-regulated in particular clusters.
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61 ]]>
b0ea90bddf66 planemo upload for repository https://github.com/Teichlab/drug2cell commit 9c3372b3af7b42d66e740f07ab16fed3035783cc
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62 </help>
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65 <citations>
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66 <citation type="doi">10.1038/s41586-023-06311-1</citation>
b0ea90bddf66 planemo upload for repository https://github.com/Teichlab/drug2cell commit 9c3372b3af7b42d66e740f07ab16fed3035783cc
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67 </citations>
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68 </tool>
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