Mercurial > repos > iuc > anndata_import
annotate import.xml @ 11:fb9e030ffae4 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 7decaee045e15bd71deb3bc46b81aa39caf1ed31
author | iuc |
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date | Wed, 22 Jun 2022 07:21:48 +0000 |
parents | 55e35e9203cf |
children | 93dd15e13e6a |
rev | line source |
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11
fb9e030ffae4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 7decaee045e15bd71deb3bc46b81aa39caf1ed31
iuc
parents:
10
diff
changeset
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1 <tool id="anndata_import" name="Import Anndata and loom" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.09"> |
0
69e2275406fd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff
changeset
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2 <description>from different format</description> |
69e2275406fd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff
changeset
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3 <macros> |
69e2275406fd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff
changeset
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4 <import>macros.xml</import> |
69e2275406fd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff
changeset
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5 <xml name="params_10x"> |
69e2275406fd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff
changeset
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6 <param name="barcodes" type="data" format="tabular,txt" label="Barcodes"/> |
69e2275406fd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff
changeset
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7 <param name="var_names" type="select" label="Variables index"> |
69e2275406fd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff
changeset
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8 <option value="gene_symbols">gene_symbols</option> |
69e2275406fd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff
changeset
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9 <option value="gene_ids">gene_ids</option> |
69e2275406fd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff
changeset
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10 </param> |
69e2275406fd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff
changeset
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11 <param name="make_unique" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Make the variable index unique by appending '-1', '-2'?"/> |
69e2275406fd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff
changeset
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12 <param name="gex_only" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Keep only 'Gene Expression' data and ignore other feature types?"/> |
69e2275406fd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff
changeset
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13 </xml> |
69e2275406fd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff
changeset
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14 </macros> |
69e2275406fd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
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15 <expand macro="requirements"> |
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ae1e5d9d8972
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit fe92541d2244bbe480481e2ca82fe2e81b08df47"
iuc
parents:
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16 <requirement type="package" version="1.7.0">scanpy</requirement> |
0
69e2275406fd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff
changeset
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17 </expand> |
69e2275406fd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff
changeset
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18 <expand macro="version_command"/> |
69e2275406fd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
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19 <command detect_errors="exit_code"><![CDATA[ |
3
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
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20 #if $hd5_format.filetype == 'anndata' |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
2
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21 #if $hd5_format.in.adata_format == 'mtx' |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
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22 mkdir mtx |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
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23 #if $hd5_format.in.tenx.use == 'legacy_10x' |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
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24 && cp '$hd5_format.in.matrix' 'mtx/matrix.mtx' |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
2
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25 && cp '$hd5_format.in.tenx.genes' 'mtx/genes.tsv' |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
2
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26 && cp '$hd5_format.in.tenx.barcodes' 'mtx/barcodes.tsv' |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
2
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27 #else if $hd5_format.in.tenx.use == 'v3_10x' |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
2
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28 && cp '$hd5_format.in.matrix' 'mtx/matrix.mtx' |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
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29 && gzip 'mtx/matrix.mtx' |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
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30 && cp '$hd5_format.in.tenx.features' 'mtx/features.tsv' |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
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31 && gzip 'mtx/features.tsv' |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
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32 && cp '$hd5_format.in.tenx.barcodes' 'mtx/barcodes.tsv' |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
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33 && gzip 'mtx/barcodes.tsv' |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
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34 #end if |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
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35 && |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
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36 #else if $hd5_format.in.adata_format == 'umi_tools' |
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499059586799
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 53df027ff1c3c3f580b2cc356887b0c8cce82a94"
iuc
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37 ## avoid gzipping in the inputdir |
499059586799
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 53df027ff1c3c3f580b2cc356887b0c8cce82a94"
iuc
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38 gzip -c '$hd5_format.in.input' > umi_tools_input.gz |
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b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
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39 && |
0
69e2275406fd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
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40 #end if |
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b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
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41 |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
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42 @CMD@ |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
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43 |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
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44 #if $hd5_format.in.adata_format == 'mtx' |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
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45 && rm -rf mtx |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
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46 #end if |
0
69e2275406fd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
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47 |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
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48 #else: |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
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49 python '$__tool_directory__/tsv_to_loompy.py' |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
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50 -c '${hd5_format.coldata}' |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
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51 -r '${hd5_format.rowdata}' |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
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52 -f '${hd5_format.mainmatrix}' |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
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53 #if $hd5_format.other_files: |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
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54 '${hd5_format.other_files}' |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
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55 #end if |
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69e2275406fd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
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56 #end if |
69e2275406fd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
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57 ]]></command> |
69e2275406fd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
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58 <configfiles> |
69e2275406fd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
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59 <configfile name="script_file"><![CDATA[ |
69e2275406fd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
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60 @CMD_imports@ |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
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61 #if $hd5_format.filetype == 'anndata' |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 6497f5415b57bedd849b876883574b3f0050741a"
iuc
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62 #if $hd5_format.in.adata_format == 'loom' |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
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63 adata = ad.read_loom( |
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b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
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64 '$hd5_format.in.input', |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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65 sparse=$hd5_format.in.sparse, |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
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66 cleanup=$hd5_format.in.cleanup, |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
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67 X_name='$hd5_format.in.x_name', |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
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68 obs_names='$hd5_format.in.obs_names', |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
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69 var_names='$hd5_format.in.var_names') |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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70 |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 6497f5415b57bedd849b876883574b3f0050741a"
iuc
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71 #else if $hd5_format.in.adata_format == 'tabular' |
cfc3f5a57dc6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 6497f5415b57bedd849b876883574b3f0050741a"
iuc
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72 #set delimiter=$hd5_format.in.input.metadata.delimiter |
cfc3f5a57dc6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 6497f5415b57bedd849b876883574b3f0050741a"
iuc
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73 #if $delimiter != ',' |
cfc3f5a57dc6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 6497f5415b57bedd849b876883574b3f0050741a"
iuc
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74 #set delimiter='\\t' |
cfc3f5a57dc6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 6497f5415b57bedd849b876883574b3f0050741a"
iuc
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75 #end if |
0
69e2275406fd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
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76 adata = ad.read_csv( |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
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77 '$hd5_format.in.input', |
0
69e2275406fd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
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78 delimiter='$delimiter', |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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79 first_column_names=$hd5_format.in.first_column_names) |
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80 |
7
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81 #else if $hd5_format.in.adata_format == '10x_h5' |
5
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 5744259254d4254a29cb7a6687fbbfd103301064"
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82 import scanpy as sc |
32e547223c9e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 5744259254d4254a29cb7a6687fbbfd103301064"
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83 adata = sc.read_10x_h5('$hd5_format.in.input') |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 5744259254d4254a29cb7a6687fbbfd103301064"
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84 |
7
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85 #else if $hd5_format.in.adata_format == 'mtx' |
cfc3f5a57dc6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 6497f5415b57bedd849b876883574b3f0050741a"
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86 #if $hd5_format.in.tenx.use == 'no' |
3
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87 adata = ad.read_mtx(filename='$hd5_format.in.matrix') |
7
cfc3f5a57dc6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 6497f5415b57bedd849b876883574b3f0050741a"
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88 #else |
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89 import scanpy as sc |
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90 adata = sc.read_10x_mtx( |
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91 'mtx', |
3
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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92 var_names='$hd5_format.in.tenx.var_names', |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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93 make_unique=$hd5_format.in.tenx.make_unique, |
0
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94 cache=False, |
3
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95 gex_only=$hd5_format.in.tenx.gex_only) |
7
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96 #end if |
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97 |
7
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98 #else if $hd5_format.in.adata_format == 'umi_tools' |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 53df027ff1c3c3f580b2cc356887b0c8cce82a94"
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99 adata = ad.read_umi_tools('umi_tools_input.gz') |
7
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100 #end if |
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101 adata.write('anndata.h5ad') |
3
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102 #end if |
0
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103 ]]></configfile> |
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104 </configfiles> |
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105 <inputs> |
3
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106 <conditional name="hd5_format"> |
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107 <param name="filetype" type="select" label="hd5 format to be created"> |
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108 <option value="anndata" selected="true">Anndata file</option> |
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109 <option value="loom">Loom file</option> |
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110 </param> |
3
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111 <when value="anndata"> |
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112 <conditional name="in"> |
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113 <param name="adata_format" type="select" label="Format for the annotated data matrix"> |
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114 <option value="loom">Loom</option> |
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115 <option value="tabular">Tabular, CSV, TSV</option> |
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116 <option value="10x_h5">H5 format from Cell ranger or not</option> |
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117 <option value="mtx">Matrix Market (mtx), from Cell ranger or not</option> |
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118 <option value="umi_tools">UMI tools</option> |
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119 </param> |
3
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120 <when value="loom"> |
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121 <param name="input" type="data" format="loom" label="Annotated data matrix"/> |
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122 <param name="sparse" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Is the data matrix to read sparse?"/> |
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123 <param name="cleanup" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Cleanup?"/> |
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124 <param name="x_name" type="text" value="spliced" label="X_name"/> |
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125 <param name="obs_names" type="text" value="CellID" label="obs_names"/> |
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126 <param name="var_names" type="text" value="Gene" label="var_names"/> |
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127 </when> |
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128 <when value="tabular"> |
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129 <param name="input" type="data" format="tabular,csv,tsv" label="Annotated data matrix"/> |
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130 <param name="first_column_names" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Does the first column store the row names?"/> |
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131 </when> |
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132 <when value="10x_h5" > |
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133 <param name="input" type="data" format="h5" label="Data matrix"/> |
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134 </when> |
3
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135 <when value="mtx"> |
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136 <param name="matrix" type="data" format="mtx" label="Matrix"/> |
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137 <conditional name="tenx"> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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138 <param name="use" type="select" label="Use 10x Genomics formatted mtx"> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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139 <option value="no">No</option> |
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140 <option value="legacy_10x">Output from Cell Ranger v2 or earlier versions</option> |
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141 <option value="v3_10x">Output from Cell Ranger v3 or later versions</option> |
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142 </param> |
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143 <when value="no"/> |
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144 <when value="legacy_10x"> |
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145 <param name="genes" type="data" format="tabular" label="Genes"/> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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146 <expand macro="params_10x"/> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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147 </when> |
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148 <when value="v3_10x"> |
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149 <param name="features" type="data" format="tabular" label="Features"/> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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150 <expand macro="params_10x"/> |
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151 </when> |
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152 </conditional> |
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153 </when> |
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154 <when value="umi_tools"> |
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155 <param name="input" type="data" format="tabular" label="condensed count matrix from UMI tools"/> |
0
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156 </when> |
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157 </conditional> |
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158 </when> |
3
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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159 <when value="loom"> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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160 <param name="mainmatrix" type="data" format="tabular" label="File for main layer of loom file." help="All subsequent tsv must be the same dimensions as this file. When converted back to tsv using hd5 export, this will be labeled as 'mainmatrix.tsv'"/> |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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161 <param name="other_files" type="data" format="tabular" multiple="true" optional="true" label="Add layers" help="Adds layers of same dimension to the loom file. When converted to tsv using hd5 export, these layers will retain their names."/> |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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162 <param name="coldata" type="data" format="tabular" label="Tsv of column data." help="First row is column attributes, subsequent are values."/> |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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163 <param name="rowdata" type="data" format="tabular" label="Tsv of row data." help="First row is row attributes, subsequent are values."/> |
0
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164 </when> |
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165 </conditional> |
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166 </inputs> |
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167 <outputs> |
3
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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168 <data name="anndata" format="h5ad" from_work_dir="anndata.h5ad" label="Anndata import on ${on_string}"> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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169 <filter>hd5_format['filetype'] == 'anndata'</filter> |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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170 </data> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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171 <data name="loomdata" format="loom" from_work_dir="converted.loom" label="Loom import on ${on_string}"> |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
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172 <filter>hd5_format['filetype'] == 'loom'</filter> |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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173 </data> |
0
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174 </outputs> |
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175 <tests> |
3
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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176 <test expect_num_outputs="1"> |
0
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177 <conditional name="in"> |
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178 <param name="adata_format" value="loom"/> |
7
cfc3f5a57dc6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 6497f5415b57bedd849b876883574b3f0050741a"
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179 <param name="input" ftype="loom" value="krumsiek11.loom" /> |
0
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180 <param name="sparse" value="True"/> |
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181 <param name="cleanup" value="False"/> |
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182 <param name="x_name" value="spliced"/> |
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183 <param name="obs_names" value="CellID" /> |
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184 <param name="var_names" value="Gene"/> |
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185 </conditional> |
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186 <assert_stdout> |
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187 <has_text_matching expression="ad.read_loom"/> |
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188 <has_text_matching expression="sparse=True"/> |
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189 <has_text_matching expression="cleanup=False"/> |
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190 <has_text_matching expression="X_name='spliced'"/> |
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191 <has_text_matching expression="obs_names='CellID'"/> |
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192 <has_text_matching expression="var_names='Gene'"/> |
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193 </assert_stdout> |
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194 <output name="anndata" value="import.loom.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/> |
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195 </test> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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196 <test expect_num_outputs="1"> |
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197 <conditional name="in"> |
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198 <param name="adata_format" value="tabular"/> |
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199 <param name="input" value="adata.csv"/> |
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200 <param name="first_column_names" value="true"/> |
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201 </conditional> |
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202 <assert_stdout> |
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203 <has_text_matching expression="ad.read_csv"/> |
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204 <has_text_matching expression="delimiter=','"/> |
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205 <has_text_matching expression="first_column_names=True"/> |
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206 </assert_stdout> |
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207 <output name="anndata" value="import.csv.h5ad" ftype="h5ad" compare="sim_size"/> |
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208 </test> |
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209 <test expect_num_outputs="1"> |
0
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210 <conditional name="in"> |
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211 <param name="adata_format" value="tabular"/> |
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212 <param name="input" value="adata.tsv"/> |
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213 <param name="first_column_names" value="true"/> |
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214 </conditional> |
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215 <assert_stdout> |
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216 <has_text_matching expression="ad.read_csv"/> |
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217 <has_text_matching expression="delimiter='\\t'"/> |
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218 <has_text_matching expression="first_column_names=True"/> |
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219 </assert_stdout> |
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220 <output name="anndata" value="import.tsv.h5ad" ftype="h5ad" compare="sim_size"/> |
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221 </test> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 6497f5415b57bedd849b876883574b3f0050741a"
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222 <test expect_num_outputs="1"> |
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223 <conditional name="in"> |
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224 <param name="adata_format" value="mtx"/> |
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225 <param name="matrix" value="matrix_10x_v1.2.0.mtx"/> |
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226 <conditional name="tenx"> |
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227 <param name="use" value="no"/> |
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228 </conditional> |
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229 </conditional> |
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230 <output name="anndata" value="import.mtx.no_10x.h5ad" ftype="h5ad" compare="sim_size"/> |
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231 </test> |
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232 <!--<test> |
0
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233 <conditional name="in"> |
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234 <param name="adata_format" value="mtx"/> |
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235 <param name="matrix" value="matrix_10x_v1.2.0.mtx"/> |
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236 <conditional name="tenx"> |
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237 <param name="use" value="legacy_10x"/> |
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238 <param name="genes" value="genes_10x_v1.2.0.tsv"/> |
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239 <param name="barcodes" value="barcodes_10x_v1.2.0.tsv"/> |
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240 <param name="var_names" value="gene_symbols"/> |
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241 <param name="make_unique" value="true"/> |
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242 <param name="gex_only" value="true"/> |
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243 </conditional> |
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244 </conditional> |
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245 <output name="anndata" value="import.mtx.legacy_10x.h5ad" ftype="h5ad" compare="sim_size"/> |
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246 </test> |
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247 <test> |
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248 <conditional name="in"> |
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249 <param name="adata_format" value="mtx"/> |
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250 <param name="matrix" value="matrix_10x_v3.0.0.mtx"/> |
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251 <conditional name="tenx"> |
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252 <param name="use" value="v3_10x"/> |
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253 <param name="features" value="features_10x_v3.0.0.tsv"/> |
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254 <param name="barcodes" value="barcodes_10x_v3.0.0.tsv"/> |
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255 <param name="var_names" value="gene_symbols"/> |
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256 <param name="make_unique" value="true"/> |
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257 <param name="gex_only" value="true"/> |
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258 </conditional> |
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259 </conditional> |
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260 <output name="anndata" value="import.mtx.v3_10x.h5ad" ftype="h5ad" compare="sim_size"/> |
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261 </test>!--> |
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262 <test expect_num_outputs="1"> |
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263 <param name="filetype" value="anndata"/> |
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264 <conditional name="in"> |
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265 <param name="adata_format" value="umi_tools"/> |
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266 <param name="input" value="umi_tools.tsv"/> |
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267 </conditional> |
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268 <output name="anndata" value="import.umi_tools.h5ad" ftype="h5ad" compare="sim_size"/> |
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269 </test> |
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270 <test expect_num_outputs="1"> |
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271 <param name="filetype" value="loom"/> |
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272 <param name="mainmatrix" value="firstlayer.tsv"/> |
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273 <param name="other_files" value="secondlayer.tsv"/> |
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274 <param name="coldata" value="cols.tsv"/> |
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275 <param name="rowdata" value="rows.tsv"/> |
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276 <output name="loomdata" value="converted.loom.test" ftype="loom" compare="sim_size"/> |
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277 </test> |
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278 <test expect_num_outputs="1"><!-- 10x h5 test --> |
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279 <conditional name="hd5_format"> |
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280 <param name="filetype" value="anndata"/> |
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281 <conditional name="in"> |
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282 <param name="adata_format" value="10x_h5"/> |
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283 <param name="input" value="dropletutils_input.h5"/> |
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284 </conditional> |
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285 </conditional> |
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286 <output name="anndata"> |
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287 <assert_contents> |
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288 <has_text text="HDF"/> |
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289 <has_text text="ENSG00000258728" /> |
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290 <has_text text="GCGAGAAAGTTGTAGA" /> |
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291 </assert_contents> |
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292 </output> |
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293 </test> |
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294 </tests> |
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295 <help><![CDATA[ |
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296 |
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297 **What it does** |
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298 |
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299 This tool creates an AnnData or loom dataset from several input types: |
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300 |
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301 - Loom (`read_loom method <https://anndata.readthedocs.io/en/latest/generated/anndata.read_loom.html>`__) |
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302 - Tabular (`read_csv method <https://anndata.readthedocs.io/en/latest/generated/anndata.read_csv.html>`__) |
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303 - Matrix Market (mtx), from Cell ranger or not (`read_mtx method <https://anndata.readthedocs.io/en/latest/generated/anndata.read_mtx.html>`__) |
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304 - UMI tools (`read_umi_tools method <https://anndata.readthedocs.io/en/latest/generated/anndata.read_umi_tools.html>`__) |
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305 |
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306 @HELP@ |
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307 ]]></help> |
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308 <expand macro="citations"/> |
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309 </tool> |