Mercurial > repos > goeckslab > scimap_anndata_to_csv

annotate anndata_to_csv.xml @ 0:199b5f278356 draft

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planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
author goeckslab
date Mon, 10 Jun 2024 18:44:49 +0000
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199b5f278356 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
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1 <tool id="scimap_anndata_to_csv" name="Convert Anndata to CSV" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>with Scimap</description>
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3 <macros>
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4 <import>main_macros.xml</import>
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5 </macros>
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6 <expand macro="scimap_requirements" />
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7 <expand macro="macro_stdio" />
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8 <version_command>echo "@VERSION@"</version_command>
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9 <command detect_errors="aggressive">
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10 <![CDATA[
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11 python '$__tool_directory__/anndata_to_csv.py'
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12 --inputs '$inputs'
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13 --outfile '$outfile'
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14
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15 ]]>
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16 </command>
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17 <configfiles>
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18 <inputs name="inputs" data_style="paths"/>
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19 </configfiles>
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20 <inputs>
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21 <param name="anndata" type="data" format="h5ad" label="Select the input anndata" />
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22 <param name="layer" type="select" label="Select the Anndata layer to export">
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23 <option value="x">adata.X</option>
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24 <option value="raw">adata.raw.X</option>
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25 </param>
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26 <param name="cellid" type="text" value="CellID" label="Name of column containing Cell IDs" />
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27 </inputs>
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28 <outputs>
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29 <data format="csv" name="outfile" />
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30 </outputs>
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31 <tests>
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32 <test>
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33 <param name="anndata" value="tutorial_data.h5ad" />
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34 <param name="layer" value="x" />
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35 <output name="outfile" ftype="csv">
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36 <assert_contents>
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37 <has_n_columns n="41" sep="," />
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38 <has_n_lines n="500" />
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39 </assert_contents>
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40 </output>
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41 </test>
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42 </tests>
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43 <help>
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44 <![CDATA[
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45 **What it does**
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46
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47 This scimap function converts from Anndata format to CSV.
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48 There are three options for the data matrix returned:
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49 1) the current contents of adata.X
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50 2) the current contents of adata.raw.X
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51 3) the current contents of adata.raw.X with a log+1 transformation applied
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52
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53 ]]>
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54 </help>
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55 <expand macro="citations" />
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56 </tool>