Mercurial > repos > iuc > scanpy_filter
annotate filter.xml @ 0:6ea5a05a260a draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
author | iuc |
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date | Mon, 04 Mar 2019 10:15:02 -0500 |
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children | 6a76b60e05f5 |
rev | line source |
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0
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
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1 <tool id="scanpy_filter" name="Filter with scanpy" version="@galaxy_version@"> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
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2 <description></description> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
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3 <macros> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
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4 <import>macros.xml</import> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
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5 </macros> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
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6 <expand macro="requirements"/> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
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7 <expand macro="version_command"/> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
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8 <command detect_errors="exit_code"><![CDATA[ |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
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changeset
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9 @CMD@ |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
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10 ]]></command> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
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11 <configfiles> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
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changeset
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12 <configfile name="script_file"><![CDATA[ |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
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13 @CMD_imports@ |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
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14 @CMD_read_inputs@ |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
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15 |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
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changeset
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16 #if $method.method == 'pp.filter_cells' |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
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17 res = sc.pp.filter_cells( |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
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18 #if $modify_anndata.modify_anndata == 'true' |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
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19 adata, |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
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20 #else |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
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21 adata.X, |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
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22 #end if |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
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23 #if $method.filter.filter == 'min_counts' |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
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24 min_counts=$method.filter.min_counts, |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
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25 #elif $method.filter.filter == 'max_counts' |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
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26 max_counts=$method.filter.max_counts, |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
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27 #elif $method.filter.filter == 'min_genes' |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
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28 min_genes=$method.filter.min_genes, |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
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29 #elif $method.filter.filter == 'max_genes' |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
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30 max_genes=$method.filter.max_genes, |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
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31 #end if |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
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32 copy=False) |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
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33 |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
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34 #if $modify_anndata.modify_anndata == 'true' |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
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35 df = adata.obs |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
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36 #else |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
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37 df = pd.DataFrame(data=dict(cell_subset=res[0], number_per_cell=res[1])) |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
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38 #end if |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
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39 |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
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40 #if $method.filter.filter == 'min_counts' or $method.filter.filter == 'max_counts' |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
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41 df.to_csv('$counts_per_cell', sep='\t') |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
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42 #elif $method.filter.filter == 'min_genes' or $method.filter.filter == 'max_genes' |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
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43 df.to_csv('$genes_per_cell', sep='\t') |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
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44 #end if |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
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45 |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
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changeset
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46 #elif $method.method == 'pp.filter_genes' |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
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47 res = sc.pp.filter_genes( |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
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48 #if $modify_anndata.modify_anndata == 'true' |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
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49 adata, |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
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changeset
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50 #else |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
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51 adata.X, |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
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52 #end if |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
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53 #if $method.filter.filter == 'min_counts' |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
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54 min_counts=$method.filter.min_counts, |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
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55 #elif $method.filter.filter == 'max_counts' |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
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56 max_counts=$method.filter.max_counts, |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
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57 #elif $method.filter.filter == 'min_cells' |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
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58 min_cells=$method.filter.min_cells, |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
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59 #elif $method.filter.filter == 'max_cells' |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
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60 max_cells=$method.filter.max_cells, |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
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61 #end if |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
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62 copy=False) |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
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63 |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
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64 #if $modify_anndata.modify_anndata == 'true' |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
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65 df = adata.var |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
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66 #else |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
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67 df = pd.DataFrame(data=dict(gene_subset=res[0], number_per_gene=res[1])) |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
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68 #end if |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
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69 |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
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70 #if $method.filter.filter == 'min_counts' or $method.filter.filter == 'max_counts' |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
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71 df.to_csv('$counts_per_gene', sep='\t') |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
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72 #elif $method.filter.filter == 'min_cells' or $method.filter.filter == 'max_cells' |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
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73 df.to_csv('$cells_per_gene', sep='\t') |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
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74 #end if |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
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75 |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
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76 #elif $method.method == 'pp.filter_genes_dispersion' |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
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77 res = sc.pp.filter_genes_dispersion( |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
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78 #if $modify_anndata.modify_anndata == 'true' |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
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79 adata, |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
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80 #else |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
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81 adata.X, |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
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82 #end if |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
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83 flavor='$method.flavor.flavor', |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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84 #if $method.flavor.flavor=='seurat' |
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85 min_mean=$method.flavor.min_mean, |
6ea5a05a260a
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86 max_mean=$method.flavor.max_mean, |
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87 min_disp=$method.flavor.min_disp, |
6ea5a05a260a
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88 #if $method.flavor.max_disp |
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89 max_disp=$method.flavor.max_disp, |
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90 #end if |
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91 #else |
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92 n_top_genes=$method.flavor.n_top_genes, |
6ea5a05a260a
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93 #end if |
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94 n_bins=$method.n_bins, |
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95 log=$method.log, |
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96 copy=False) |
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97 |
6ea5a05a260a
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98 #if $modify_anndata.modify_anndata == 'true' |
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99 adata.var.to_csv('$per_gene', sep='\t') |
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100 #else |
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101 pd.DataFrame(res).to_csv('$per_gene', sep='\t') |
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102 #end if |
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103 |
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104 #elif $method.method == 'pp.subsample' |
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105 sc.pp.subsample( |
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106 data=adata, |
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107 #if $method.type.type == 'fraction' |
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108 fraction=$method.type.fraction, |
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109 #else if $method.type.type == 'n_obs' |
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110 n_obs=$method.type.n_obs, |
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111 #end if |
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112 random_state=$method.random_state, |
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113 copy=False) |
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114 |
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115 #end if |
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116 |
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117 @CMD_anndata_write_modify_outputs@ |
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118 ]]></configfile> |
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119 </configfiles> |
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120 <inputs> |
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121 <expand macro="inputs_anndata"/> |
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122 <conditional name="method"> |
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123 <param argument="method" type="select" label="Method used for filtering"> |
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124 <option value="pp.filter_cells">Filter cell outliers based on counts and numbers of genes expressed, using `pp.filter_cells`</option> |
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125 <option value="pp.filter_genes">Filter genes based on number of cells or counts, using `pp.filter_genes`</option> |
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126 <option value="pp.filter_genes_dispersion">Extract highly variable genes, using `pp.filter_genes_dispersion`</option> |
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127 <!--<option value="pp.highly_variable_genes">, using `tl.highly_variable_genes`</option>!--> |
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128 <option value="pp.subsample">Subsample to a fraction of the number of observations, using `pp.subsample`</option> |
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129 <!--<option value="queries.gene_coordinates">, using `queries.gene_coordinates`</option>!--> |
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130 <!--<option value="queries.mitochondrial_genes">, using `queries.mitochondrial_genes`</option>!--> |
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131 </param> |
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132 <when value="pp.filter_cells"> |
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133 <conditional name="filter"> |
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134 <param argument="filter" type="select" label="Filter"> |
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135 <option value="min_counts">Minimum number of counts</option> |
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136 <option value="max_counts">Maximum number of counts</option> |
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137 <option value="min_genes">Minimum number of genes expressed</option> |
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138 <option value="max_genes">Maximum number of genes expressed</option> |
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139 </param> |
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140 <when value="min_counts"> |
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141 <param argument="min_counts" type="integer" min="0" value="" label="Minimum number of counts required for a cell to pass filtering" help=""/> |
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142 </when> |
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143 <when value="max_counts"> |
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144 <param argument="max_counts" type="integer" min="0" value="" label="Maximum number of counts required for a cell to pass filtering" help=""/> |
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145 </when> |
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146 <when value="min_genes"> |
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147 <param argument="min_genes" type="integer" min="0" value="" label="Minimum number of genes expressed required for a cell to pass filtering" help=""/> |
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148 </when> |
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149 <when value="max_genes"> |
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150 <param argument="max_genes" type="integer" min="0" value="" label="Maximum number of genes expressed required for a cell to pass filtering" help=""/> |
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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="pp.filter_genes"> |
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155 <conditional name="filter"> |
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156 <param argument="filter" type="select" label="Filter"> |
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157 <option value="min_counts">Minimum number of counts</option> |
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158 <option value="max_counts">Maximum number of counts</option> |
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159 <option value="min_cells">Minimum number of cells expressed</option> |
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160 <option value="max_cells">Maximum number of cells expressed</option> |
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161 </param> |
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162 <when value="min_counts"> |
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163 <param argument="min_counts" type="integer" min="0" value="" label="Minimum number of counts required for a gene to pass filtering" help=""/> |
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164 </when> |
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165 <when value="max_counts"> |
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166 <param argument="max_counts" type="integer" min="0" value="" label="Maximum number of counts required for a gene to pass filtering" help=""/> |
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167 </when> |
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168 <when value="min_cells"> |
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169 <param argument="min_cells" type="integer" min="0" value="" label="Minimum number of cells expressed required for a gene to pass filtering" help=""/> |
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170 </when> |
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171 <when value="max_cells"> |
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172 <param argument="max_cells" type="integer" min="0" value="" label="Maximum number of cells expressed required for a gene to pass filtering" help=""/> |
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173 </when> |
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174 </conditional> |
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175 </when> |
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176 <when value="pp.filter_genes_dispersion"> |
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177 <conditional name='flavor'> |
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178 <param argument="flavor" type="select" label="Flavor for computing normalized dispersion" help=""> |
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179 <option value="seurat">seurat: expects non-logarithmized data</option> |
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180 <option value="cell_ranger">cell_ranger: usually called for logarithmized data</option> |
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181 </param> |
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182 <when value="seurat"> |
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183 <param argument="min_mean" type="float" value="0.0125" label="Minimal mean cutoff" help=""/> |
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184 <param argument="max_mean" type="float" value="3" label="Maximal mean cutoff" help=""/> |
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185 <param argument="min_disp" type="float" value="0.5" label="Minimal normalized dispersion cutoff" help=""/> |
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186 <param argument="max_disp" type="float" value="" optional="true" label="Maximal normalized dispersion cutoff" help=""/> |
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187 </when> |
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188 <when value="cell_ranger"> |
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189 <param argument="n_top_genes" type="integer" value="" label="Number of highly-variable genes to keep" help=""/> |
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190 </when> |
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191 </conditional> |
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192 <param argument="n_bins" type="integer" value="20" label="Number of bins for binning the mean gene expression" help="Normalization is done with respect to each bin. If just a single gene falls into a bin, the normalized dispersion is artificially set to 1"/> |
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193 <expand macro="param_log"/> |
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194 </when> |
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195 <when value="pp.subsample"> |
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196 <conditional name="type"> |
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197 <param name="type" type="select" label="Type of subsampling"> |
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198 <option value="fraction">By fraction</option> |
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199 <option value="n_obs">By number of observation</option> |
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200 </param> |
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201 <when value="fraction"> |
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202 <param argument="fraction" type="float" value="" label="Subsample to this `fraction` of the number of observations" help=""/> |
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203 </when> |
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204 <when value="n_obs"> |
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205 <param argument="n_obs" type="integer" min="0" value="" label="Subsample to this number of observations" help=""/> |
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206 </when> |
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207 </conditional> |
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208 <param argument="random_state" type="integer" value="0" label="Random seed to change subsampling" help=""/> |
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209 </when> |
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210 </conditional> |
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211 <expand macro="anndata_modify_output_input"/> |
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212 </inputs> |
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213 <outputs> |
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214 <expand macro="anndata_modify_outputs"/> |
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215 <!-- for pp.filter_cells --> |
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216 <data name="counts_per_cell" format="tabular" label="${tool.name} on ${on_string}: Counts per cells after filtering"> |
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217 <filter>method['method'] == 'pp.filter_cells' and (method['filter']['filter'] == 'min_counts' or method['filter']['filter'] == 'max_counts')</filter> |
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218 </data> |
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219 <data name="genes_per_cell" format="tabular" label="${tool.name} on ${on_string}: Number of genes per cell after filtering"> |
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220 <filter>method['method'] == 'pp.filter_cells' and (method['filter']['filter'] == 'min_genes' or method['filter']['filter'] == 'max_genes')</filter> |
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221 </data> |
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222 <!-- for pp.filter_genes --> |
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223 <data name="counts_per_gene" format="tabular" label="${tool.name} on ${on_string}: Counts per genes after filtering"> |
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224 <filter>method['method'] == 'pp.filter_genes' and (method['filter']['filter'] == 'min_counts' or method['filter']['filter'] == 'max_counts')</filter> |
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225 </data> |
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226 <data name="cells_per_gene" format="tabular" label="${tool.name} on ${on_string}: Number of cells per genes after filtering"> |
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227 <filter>method['method'] == 'pp.filter_genes' and (method['filter']['filter'] == 'min_cells' or method['filter']['filter'] == 'max_cells')</filter> |
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228 </data> |
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229 <!-- for pp.filter_genes_dispersion --> |
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230 <data name="per_gene" format="tabular" label="${tool.name} on ${on_string}: Means, dispersions and normalized dispersions per gene"> |
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231 <filter>method['method'] == 'pp.filter_genes_dispersion'</filter> |
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232 </data> |
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233 </outputs> |
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234 <tests> |
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235 <test expect_num_outputs="2"> |
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236 <conditional name="input"> |
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237 <param name="format" value="h5ad" /> |
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238 <param name="adata" value="krumsiek11.h5ad" /> |
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239 </conditional> |
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240 <conditional name="method"> |
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241 <param name="method" value="pp.filter_cells"/> |
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242 <conditional name="filter"> |
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243 <param name="filter" value="min_counts"/> |
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244 <param name="min_counts" value="3"/> |
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245 </conditional> |
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246 </conditional> |
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247 <conditional name="modify_anndata"> |
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248 <param name="modify_anndata" value="true"/> |
6ea5a05a260a
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iuc
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249 <param name="anndata_output_format" value="h5ad" /> |
6ea5a05a260a
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iuc
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250 </conditional> |
6ea5a05a260a
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iuc
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251 <assert_stdout> |
6ea5a05a260a
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iuc
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252 <has_text_matching expression="sc.pp.filter_cells"/> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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253 <has_text_matching expression="min_counts=3"/> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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254 </assert_stdout> |
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255 <output name="anndata_out_h5ad" file="pp.filter_cells.krumsiek11-min_counts.h5ad" ftype="h5" compare="sim_size"/> |
6ea5a05a260a
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256 <output name="counts_per_cell"> |
6ea5a05a260a
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257 <assert_contents> |
6ea5a05a260a
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258 <has_text_matching expression="cell_type\tn_counts" /> |
6ea5a05a260a
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259 <has_text_matching expression="46\tprogenitor\t3.028" /> |
6ea5a05a260a
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260 <has_text_matching expression="85\tEry\t3.7001" /> |
6ea5a05a260a
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iuc
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261 <has_text_matching expression="150\tMk\t4.095" /> |
6ea5a05a260a
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262 <has_n_columns n="3" /> |
6ea5a05a260a
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263 </assert_contents> |
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264 </output> |
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265 </test> |
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266 <test expect_num_outputs="2"> |
6ea5a05a260a
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267 <conditional name="input"> |
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268 <param name="format" value="loom" /> |
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269 <param name="adata" value="krumsiek11.loom" /> |
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270 <param name="sparse" value="True"/> |
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271 <param name="cleanup" value="False"/> |
6ea5a05a260a
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272 <param name="x_name" value="spliced"/> |
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273 <param name="obs_names" value="CellID" /> |
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274 <param name="var_names" value="Gene"/> |
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275 </conditional> |
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276 <conditional name="method"> |
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277 <param name="method" value="pp.filter_cells"/> |
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278 <conditional name="filter"> |
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279 <param name="filter" value="min_counts"/> |
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280 <param name="min_counts" value="3"/> |
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281 </conditional> |
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282 </conditional> |
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283 <conditional name="modify_anndata"> |
6ea5a05a260a
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284 <param name="modify_anndata" value="true"/> |
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285 <param name="anndata_output_format" value="loom" /> |
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286 </conditional> |
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287 <assert_stdout> |
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288 <has_text_matching expression="sc.pp.filter_cells"/> |
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289 <has_text_matching expression="min_counts=3"/> |
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290 </assert_stdout> |
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291 <output name="anndata_out_loom" file="pp.filter_cells.krumsiek11-min_counts.loom" ftype="loom" compare="sim_size"/> |
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292 <output name="counts_per_cell"> |
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293 <assert_contents> |
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294 <has_text_matching expression="cell_type\tn_counts" /> |
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295 <has_text_matching expression="46\tprogenitor\t3.028" /> |
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296 <has_text_matching expression="85\tEry\t3.7001" /> |
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iuc
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297 <has_text_matching expression="97\tMo\t3.925" /> |
6ea5a05a260a
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298 <has_text_matching expression="150\tMk\t4.095" /> |
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299 <has_n_columns n="3" /> |
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300 </assert_contents> |
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301 </output> |
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302 </test> |
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303 <test expect_num_outputs="1"> |
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304 <conditional name="input"> |
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305 <param name="format" value="h5ad" /> |
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306 <param name="adata" value="krumsiek11.h5ad"/> |
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307 </conditional> |
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308 <conditional name="method"> |
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309 <param name="method" value="pp.filter_cells"/> |
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310 <conditional name="filter"> |
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311 <param name="filter" value="max_genes"/> |
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312 <param name="max_genes" value="100"/> |
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313 </conditional> |
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314 </conditional> |
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315 <conditional name="modify_anndata"> |
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316 <param name="modify_anndata" value="false"/> |
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317 </conditional> |
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318 <assert_stdout> |
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319 <has_text_matching expression="sc.pp.filter_cells"/> |
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320 <has_text_matching expression="adata.X"/> |
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321 <has_text_matching expression="max_genes=100"/> |
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322 </assert_stdout> |
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323 <output name="genes_per_cell" file="pp.filter_cells.number_per_cell.krumsiek11-max_genes.tabular"/> |
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324 </test> |
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325 <test expect_num_outputs="2"> |
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326 <conditional name="input"> |
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327 <param name="format" value="h5ad" /> |
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328 <param name="adata" value="krumsiek11.h5ad" /> |
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329 </conditional> |
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330 <conditional name="method"> |
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iuc
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changeset
|
331 <param name="method" value="pp.filter_genes"/> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
|
332 <conditional name="filter"> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
|
333 <param name="filter" value="min_counts"/> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
|
334 <param name="min_counts" value="3"/> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
|
335 </conditional> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
|
336 </conditional> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
|
337 <conditional name="modify_anndata"> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
|
338 <param name="modify_anndata" value="true"/> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
|
339 <param name="anndata_output_format" value="h5ad" /> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
|
340 </conditional> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
|
341 <assert_stdout> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
|
342 <has_text_matching expression="sc.pp.filter_genes"/> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
|
343 <has_text_matching expression="min_counts=3"/> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
|
344 </assert_stdout> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
|
345 <output name="anndata_out_h5ad" file="pp.filter_genes.krumsiek11-min_counts.h5ad" ftype="h5" compare="sim_size"/> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
|
346 <output name="counts_per_gene" file="pp.filter_genes.number_per_gene.krumsiek11-min_counts.tabular"/> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
|
347 </test> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
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348 <test expect_num_outputs="1"> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
|
349 <conditional name="input"> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
|
350 <param name="format" value="h5ad" /> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
|
351 <param name="adata" value="pbmc68k_reduced.h5ad"/> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
|
352 </conditional> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
|
353 <conditional name="method"> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
|
354 <param name="method" value="pp.filter_genes"/> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
|
355 <conditional name="filter"> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
|
356 <param name="filter" value="max_cells"/> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
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changeset
|
357 <param name="max_cells" value="500"/> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
|
358 </conditional> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
|
359 </conditional> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
|
360 <conditional name="modify_anndata"> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
|
361 <param name="modify_anndata" value="false"/> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
|
362 </conditional> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
|
363 <assert_stdout> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
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364 <has_text_matching expression="sc.pp.filter_genes"/> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
|
365 <has_text_matching expression="adata.X"/> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
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changeset
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366 <has_text_matching expression="max_cells=500"/> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
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changeset
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367 </assert_stdout> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
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changeset
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368 <output name="cells_per_gene" file="pp.filter_genes.number_per_gene.pbmc68k_reduced-max_cells.tabular"/> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
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changeset
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369 </test> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
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370 <test expect_num_outputs="2"> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
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371 <conditional name="input"> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
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changeset
|
372 <param name="format" value="h5ad" /> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
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changeset
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373 <param name="adata" value="krumsiek11.h5ad" /> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
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changeset
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374 </conditional> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
|
375 <conditional name="method"> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
|
376 <param name="method" value="pp.filter_genes_dispersion"/> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
|
377 <conditional name="flavor"> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
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changeset
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378 <param name="flavor" value="seurat"/> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
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changeset
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379 <param name="min_mean" value="0.0125"/> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
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changeset
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380 <param name="max_mean" value="3"/> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
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changeset
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381 <param name="min_disp" value="0.5"/> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
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changeset
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382 </conditional> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
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changeset
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383 <param name="n_bins" value="20" /> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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changeset
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384 <param name="log" value="true"/> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
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changeset
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385 </conditional> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
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386 <conditional name="modify_anndata"> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
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changeset
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387 <param name="modify_anndata" value="true"/> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
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changeset
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388 <param name="anndata_output_format" value="h5ad" /> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
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changeset
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389 </conditional> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
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changeset
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390 <assert_stdout> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
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changeset
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391 <has_text_matching expression="sc.pp.filter_genes_dispersion"/> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
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changeset
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392 <has_text_matching expression="flavor='seurat'"/> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
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changeset
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393 <has_text_matching expression="min_mean=0.0125"/> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
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changeset
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394 <has_text_matching expression="max_mean=3.0"/> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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changeset
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395 <has_text_matching expression="min_disp=0.5"/> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
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changeset
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396 <has_text_matching expression="n_bins=20"/> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
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changeset
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397 <has_text_matching expression="log=True"/> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
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changeset
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398 </assert_stdout> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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changeset
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399 <output name="anndata_out_h5ad" file="pp.filter_genes_dispersion.krumsiek11-seurat.h5ad" ftype="h5" compare="sim_size"/> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
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400 <output name="per_gene" file="pp.filter_genes_dispersion.per_gene.krumsiek11-seurat.tabular"/> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
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401 </test> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
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402 <test expect_num_outputs="1"> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
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403 <conditional name="input"> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
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404 <param name="format" value="h5ad" /> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
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405 <param name="adata" value="krumsiek11.h5ad" /> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
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406 </conditional> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
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407 <conditional name="method"> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
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408 <param name="method" value="pp.filter_genes_dispersion"/> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
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409 <conditional name="flavor"> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
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410 <param name="flavor" value="cell_ranger"/> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
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changeset
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411 <param name="n_top_genes" value="2"/> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
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412 </conditional> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
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413 <param name="n_bins" value="20"/> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
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changeset
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414 <param name="log" value="true"/> |
6ea5a05a260a
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iuc
parents:
diff
changeset
|
415 </conditional> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
|
416 <conditional name="modify_anndata"> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
|
417 <param name="modify_anndata" value="false"/> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
|
418 </conditional> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
|
419 <assert_stdout> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
|
420 <has_text_matching expression="sc.pp.filter_genes_dispersion"/> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
|
421 <has_text_matching expression="flavor='cell_ranger'"/> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
|
422 <has_text_matching expression="n_top_genes=2"/> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
|
423 <has_text_matching expression="n_bins=20"/> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
|
424 <has_text_matching expression="og=True"/> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
|
425 </assert_stdout> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
|
426 <output name="per_gene" file="pp.filter_genes_dispersion.per_gene.krumsiek11-cell_ranger.tabular"/> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
|
427 </test> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
|
428 <test expect_num_outputs="1"> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
|
429 <conditional name="input"> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
|
430 <param name="format" value="h5ad" /> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
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changeset
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431 <param name="adata" value="krumsiek11.h5ad" /> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
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432 </conditional> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
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433 <conditional name="method"> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
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changeset
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434 <param name="method" value="pp.subsample"/> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
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changeset
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435 <conditional name="type"> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
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changeset
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436 <param name="type" value="fraction" /> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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changeset
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437 <param name="fraction" value="0.5"/> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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changeset
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438 </conditional> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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changeset
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439 <param name="random_state" value="0"/> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
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440 </conditional> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
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changeset
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441 <conditional name="modify_anndata"> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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changeset
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442 <param name="modify_anndata" value="true"/> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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443 <param name="anndata_output_format" value="h5ad" /> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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444 </conditional> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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445 <assert_stdout> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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446 <has_text_matching expression="sc.pp.subsample"/> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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447 <has_text_matching expression="fraction=0.5"/> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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448 <has_text_matching expression="random_state=0"/> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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449 </assert_stdout> |
6ea5a05a260a
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iuc
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450 <output name="anndata_out_h5ad" file="pp.subsample.krumsiek11_fraction.h5ad" ftype="h5" compare="sim_size"/> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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451 </test> |
6ea5a05a260a
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iuc
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452 <test expect_num_outputs="1"> |
6ea5a05a260a
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iuc
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453 <conditional name="input"> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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454 <param name="format" value="h5ad" /> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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455 <param name="adata" value="krumsiek11.h5ad" /> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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456 </conditional> |
6ea5a05a260a
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iuc
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457 <conditional name="method"> |
6ea5a05a260a
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iuc
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458 <param name="method" value="pp.subsample"/> |
6ea5a05a260a
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iuc
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459 <conditional name="type"> |
6ea5a05a260a
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iuc
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460 <param name="type" value="n_obs" /> |
6ea5a05a260a
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iuc
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461 <param name="n_obs" value="10"/> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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462 </conditional> |
6ea5a05a260a
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iuc
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463 <param name="random_state" value="0"/> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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464 </conditional> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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changeset
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465 <conditional name="modify_anndata"> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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466 <param name="modify_anndata" value="true"/> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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467 <param name="anndata_output_format" value="h5ad" /> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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468 </conditional> |
6ea5a05a260a
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iuc
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469 <assert_stdout> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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470 <has_text_matching expression="sc.pp.subsample"/> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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471 <has_text_matching expression="n_obs=10"/> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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472 <has_text_matching expression="random_state=0"/> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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473 </assert_stdout> |
6ea5a05a260a
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iuc
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474 <output name="anndata_out_h5ad" file="pp.subsample.krumsiek11_n_obs.h5ad" ftype="h5" compare="sim_size"/> |
6ea5a05a260a
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iuc
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475 </test> |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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476 </tests> |
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iuc
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477 <help><![CDATA[ |
6ea5a05a260a
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478 |
6ea5a05a260a
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479 Filter cells outliers based on counts and numbers of genes expressed (`pp.filter_cells`) |
6ea5a05a260a
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480 ======================================================================================== |
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481 |
6ea5a05a260a
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482 For instance, only keep cells with at least `min_counts` counts or |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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483 `min_genes` genes expressed. This is to filter measurement outliers, i.e., |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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484 "unreliable" observations. |
6ea5a05a260a
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iuc
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485 |
6ea5a05a260a
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486 Only provide one of the optional parameters `min_counts`, `min_genes`, |
6ea5a05a260a
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487 `max_counts`, `max_genes` per call. |
6ea5a05a260a
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488 |
6ea5a05a260a
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iuc
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489 More details on the `scanpy documentation |
6ea5a05a260a
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490 <https://scanpy.readthedocs.io/en/latest/api/scanpy.api.pp.filter_cells.html#scanpy.api.pp.filter_cells>`__ |
6ea5a05a260a
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iuc
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491 |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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changeset
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492 Return |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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493 ------ |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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changeset
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494 |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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495 number_per_cell : Number per cell (either `n_counts` or `n_genes` per cell) |
6ea5a05a260a
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iuc
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496 |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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changeset
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497 |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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498 Filter genes based on number of cells or counts (`pp.filter_genes`) |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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499 =================================================================== |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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500 |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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501 Keep genes that have at least `min_counts` counts or are expressed in at |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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502 least `min_cells` cells or have at most `max_counts` counts or are expressed |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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503 in at most `max_cells` cells. |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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504 |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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505 Only provide one of the optional parameters `min_counts`, `min_cells`, |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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506 `max_counts`, `max_cells` per call. |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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507 |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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508 More details on the `scanpy documentation |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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509 <https://scanpy.readthedocs.io/en/latest/api/scanpy.api.pp.filter_genes.html#scanpy.api.pp.filter_genes>`__ |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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510 |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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511 Return |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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512 ------ |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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513 |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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514 number_per_gene : Number per genes (either `n_counts` or `n_genes` per cell) |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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515 |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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516 |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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517 Extract highly variable genes (`pp.filter_genes_dispersion`) |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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518 ============================================================ |
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519 |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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520 If trying out parameters, pass the data matrix instead of AnnData. |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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521 |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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522 Depending on `flavor`, this reproduces the R-implementations of Seurat and Cell Ranger. |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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523 |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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524 The normalized dispersion is obtained by scaling with the mean and standard |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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525 deviation of the dispersions for genes falling into a given bin for mean |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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526 expression of genes. This means that for each bin of mean expression, highly |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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527 variable genes are selected. |
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528 |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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529 Use `flavor='cell_ranger'` with care and in the same way as in `pp.recipe_zheng17`. |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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530 |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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531 More details on the `scanpy documentation |
6ea5a05a260a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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532 <https://scanpy.readthedocs.io/en/latest/api/scanpy.api.pp.filter_genes_dispersion.html#scanpy.api.pp.filter_genes_dispersion>`__ |
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533 |
6ea5a05a260a
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534 Returns |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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535 ------- |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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536 - The annotated matrix filtered, with the annotations |
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537 - A table with the means, dispersions, and normalized dispersions per gene, logarithmized when `log` is `True`. |
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538 |
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539 |
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540 Subsample to a fraction of the number of observations (`pp.subsample`) |
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541 ====================================================================== |
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542 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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543 More details on the `scanpy documentation |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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544 <https://scanpy.readthedocs.io/en/latest/api/scanpy.api.pp.subsample.html#scanpy.api.pp.subsample>`__ |
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545 |
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546 |
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547 ]]></help> |
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548 <expand macro="citations"/> |
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549 </tool> |