Mercurial > repos > ebi-gxa > anndata_ops
annotate anndata_operations.xml @ 12:f1a1cf7c0153 draft
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 62f47287c7e8449c59a1f1f454852ddc669b1b1e-dirty"
| author | ebi-gxa |
|---|---|
| date | Mon, 07 Sep 2020 13:59:52 +0000 |
| parents | f0a29f4b9be9 |
| children | a4ad76e3dc4a |
| rev | line source |
|---|---|
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086d850271a2
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
ebi-gxa
parents:
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1 <?xml version="1.0" encoding="utf-8"?> |
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f0a29f4b9be9
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit e2ec0706fd62528e5198e3c050d91ab0ee6cd4da"
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2 <tool id="anndata_ops" name="AnnData Operations" version="0.0.3+galaxy1" profile="@PROFILE@"> |
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086d850271a2
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
ebi-gxa
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3 <description>modifies metadata and flags genes</description> |
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086d850271a2
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
ebi-gxa
parents:
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4 <macros> |
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086d850271a2
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
ebi-gxa
parents:
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changeset
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5 <import>scanpy_macros2.xml</import> |
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086d850271a2
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
ebi-gxa
parents:
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changeset
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6 </macros> |
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086d850271a2
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
ebi-gxa
parents:
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7 <expand macro="requirements"/> |
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086d850271a2
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
ebi-gxa
parents:
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8 <command detect_errors="exit_code"><![CDATA[ |
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086d850271a2
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
ebi-gxa
parents:
diff
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9 ln -s '${input_obj_file}' input.h5 && |
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9
b8eb50bd397c
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
ebi-gxa
parents:
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10 |
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b8eb50bd397c
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
ebi-gxa
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11 #if $copy_o.default: |
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b8eb50bd397c
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
ebi-gxa
parents:
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12 #for $i, $os in enumerate($copy_o.obs_sources): |
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b8eb50bd397c
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
ebi-gxa
parents:
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13 ln -s '${os}' obs_source_${i}.h5 && |
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b8eb50bd397c
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
ebi-gxa
parents:
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14 #end for |
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b8eb50bd397c
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
ebi-gxa
parents:
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15 #end if |
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b8eb50bd397c
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
ebi-gxa
parents:
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16 |
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b8eb50bd397c
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
ebi-gxa
parents:
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17 #if $copy_e.default: |
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b8eb50bd397c
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
ebi-gxa
parents:
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18 #for $i, $es in enumerate($copy_e.embedding_sources): |
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b8eb50bd397c
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
ebi-gxa
parents:
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19 ln -s '${es}' embedding_source_${i}.h5 && |
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b8eb50bd397c
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
ebi-gxa
parents:
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20 #end for |
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b8eb50bd397c
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
ebi-gxa
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21 #end if |
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54f1212d26ac
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 6806d147bfbb52c61d2a15281b69144fad87250a"
ebi-gxa
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22 |
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54f1212d26ac
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 6806d147bfbb52c61d2a15281b69144fad87250a"
ebi-gxa
parents:
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23 #if $copy_u.default: |
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54f1212d26ac
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 6806d147bfbb52c61d2a15281b69144fad87250a"
ebi-gxa
parents:
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24 #for $i, $us in enumerate($copy_u.uns_sources): |
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54f1212d26ac
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 6806d147bfbb52c61d2a15281b69144fad87250a"
ebi-gxa
parents:
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25 ln -s '${us}' uns_source_${i}.h5 && |
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54f1212d26ac
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 6806d147bfbb52c61d2a15281b69144fad87250a"
ebi-gxa
parents:
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26 #end for |
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54f1212d26ac
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 6806d147bfbb52c61d2a15281b69144fad87250a"
ebi-gxa
parents:
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27 #end if |
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086d850271a2
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
ebi-gxa
parents:
diff
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28 python $operations |
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086d850271a2
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
ebi-gxa
parents:
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29 ]]></command> |
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086d850271a2
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
ebi-gxa
parents:
diff
changeset
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30 <configfiles> |
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086d850271a2
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
ebi-gxa
parents:
diff
changeset
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31 <configfile name="operations"> |
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086d850271a2
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
ebi-gxa
parents:
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32 import scanpy as sc |
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b8eb50bd397c
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
ebi-gxa
parents:
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33 import anndata |
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b8eb50bd397c
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
ebi-gxa
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34 from numpy import all |
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0
086d850271a2
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
ebi-gxa
parents:
diff
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35 import logging |
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086d850271a2
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
ebi-gxa
parents:
diff
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36 |
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086d850271a2
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
ebi-gxa
parents:
diff
changeset
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37 adata = sc.read('input.h5') |
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086d850271a2
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
ebi-gxa
parents:
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38 |
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11
f0a29f4b9be9
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit e2ec0706fd62528e5198e3c050d91ab0ee6cd4da"
ebi-gxa
parents:
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39 #if $copy_adata_to_raw: |
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f0a29f4b9be9
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit e2ec0706fd62528e5198e3c050d91ab0ee6cd4da"
ebi-gxa
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40 adata.raw = adata |
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f0a29f4b9be9
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit e2ec0706fd62528e5198e3c050d91ab0ee6cd4da"
ebi-gxa
parents:
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41 #end if |
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f0a29f4b9be9
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit e2ec0706fd62528e5198e3c050d91ab0ee6cd4da"
ebi-gxa
parents:
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42 |
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0
086d850271a2
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
ebi-gxa
parents:
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43 gene_name = '${gene_symbols_field}' |
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086d850271a2
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
ebi-gxa
parents:
diff
changeset
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44 qc_vars = list() |
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086d850271a2
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
ebi-gxa
parents:
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45 |
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086d850271a2
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
ebi-gxa
parents:
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46 #for $i, $s in enumerate($modifications) |
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086d850271a2
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
ebi-gxa
parents:
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47 adata.obs['${s.to_obs}'] = adata.obs['${s.from_obs}'] |
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54f1212d26ac
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 6806d147bfbb52c61d2a15281b69144fad87250a"
ebi-gxa
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48 #if not $s.keep_original: |
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54f1212d26ac
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 6806d147bfbb52c61d2a15281b69144fad87250a"
ebi-gxa
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49 del adata.obs['${s.from_obs}'] |
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54f1212d26ac
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 6806d147bfbb52c61d2a15281b69144fad87250a"
ebi-gxa
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50 #end if |
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0
086d850271a2
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
ebi-gxa
parents:
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51 #end for |
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086d850271a2
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
ebi-gxa
parents:
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52 |
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086d850271a2
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
ebi-gxa
parents:
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53 gene_names = getattr(adata.var, gene_name) |
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086d850271a2
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
ebi-gxa
parents:
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54 |
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086d850271a2
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
ebi-gxa
parents:
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55 #for $i, $flag in enumerate($gene_flags) |
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086d850271a2
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
ebi-gxa
parents:
diff
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56 k_cat = gene_names.str.startswith('${flag.startswith}') |
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086d850271a2
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
ebi-gxa
parents:
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57 if k_cat.sum() > 0: |
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086d850271a2
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
ebi-gxa
parents:
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58 adata.var['${flag.flag}'] = k_cat |
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086d850271a2
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
ebi-gxa
parents:
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59 qc_vars.append('${flag.flag}') |
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086d850271a2
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
ebi-gxa
parents:
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60 else: |
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086d850271a2
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
ebi-gxa
parents:
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61 logging.warning('No genes starting with {} found, skip calculating expression of {} genes'.format('${flag.startswith}', '${flag.flag}')) |
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086d850271a2
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
ebi-gxa
parents:
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62 #end for |
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086d850271a2
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
ebi-gxa
parents:
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63 |
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b8eb50bd397c
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
ebi-gxa
parents:
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64 #if $copy_o.default and len($copy_o.obs_keys) > 0: |
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b8eb50bd397c
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
ebi-gxa
parents:
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65 #for $i, $obs_s in enumerate($copy_o.obs_sources): |
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b8eb50bd397c
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
ebi-gxa
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66 ad_s = sc.read('obs_source_${i}.h5') |
|
b8eb50bd397c
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
ebi-gxa
parents:
4
diff
changeset
|
67 if adata.n_obs == ad_s.n_obs and all(adata.obs_names == ad_s.obs_names): |
|
b8eb50bd397c
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
ebi-gxa
parents:
4
diff
changeset
|
68 #for $j, $o_key in enumerate($copy_o.obs_keys): |
|
b8eb50bd397c
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
ebi-gxa
parents:
4
diff
changeset
|
69 keys_to_copy = (k for k in ad_s.obs.keys() if "${o_key.contains}" in k) |
|
b8eb50bd397c
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
ebi-gxa
parents:
4
diff
changeset
|
70 for k_to_copy in keys_to_copy: |
|
b8eb50bd397c
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
ebi-gxa
parents:
4
diff
changeset
|
71 adata.obs[[k_to_copy+"_${i}"]] = ad_s.obs[[k_to_copy]] |
|
b8eb50bd397c
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
ebi-gxa
parents:
4
diff
changeset
|
72 if k_to_copy in ad_s.uns.keys(): |
|
b8eb50bd397c
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
ebi-gxa
parents:
4
diff
changeset
|
73 adata.uns[k_to_copy+"_${i}"] = ad_s.uns[k_to_copy] |
|
b8eb50bd397c
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
ebi-gxa
parents:
4
diff
changeset
|
74 #end for |
|
b8eb50bd397c
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
ebi-gxa
parents:
4
diff
changeset
|
75 else: |
|
b8eb50bd397c
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
ebi-gxa
parents:
4
diff
changeset
|
76 logging.warning("Observation source ${i} AnnData file is not compatible to be merged to main AnnData file, different cell names.") |
|
b8eb50bd397c
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
ebi-gxa
parents:
4
diff
changeset
|
77 #end for |
|
b8eb50bd397c
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
ebi-gxa
parents:
4
diff
changeset
|
78 #end if |
|
b8eb50bd397c
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
ebi-gxa
parents:
4
diff
changeset
|
79 |
|
b8eb50bd397c
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
ebi-gxa
parents:
4
diff
changeset
|
80 |
|
b8eb50bd397c
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
ebi-gxa
parents:
4
diff
changeset
|
81 #if $copy_e.default and len($copy_e.embedding_keys) > 0: |
|
b8eb50bd397c
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
ebi-gxa
parents:
4
diff
changeset
|
82 #for $i, $obs_s in enumerate($copy_e.embedding_sources): |
|
b8eb50bd397c
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
ebi-gxa
parents:
4
diff
changeset
|
83 ad_s = sc.read('embedding_source_${i}.h5') |
|
b8eb50bd397c
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
ebi-gxa
parents:
4
diff
changeset
|
84 if adata.n_obs == ad_s.n_obs and all(adata.obs_names == ad_s.obs_names): |
|
b8eb50bd397c
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
ebi-gxa
parents:
4
diff
changeset
|
85 #for $j, $e_key in enumerate($copy_e.embedding_keys): |
|
b8eb50bd397c
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
ebi-gxa
parents:
4
diff
changeset
|
86 keys_to_copy = (k for k in ad_s.obsm.keys() if "${e_key.contains}" in k) |
|
b8eb50bd397c
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
ebi-gxa
parents:
4
diff
changeset
|
87 for k_to_copy in keys_to_copy: |
|
b8eb50bd397c
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
ebi-gxa
parents:
4
diff
changeset
|
88 adata.obsm[k_to_copy+"_${i}"] = ad_s.obsm[k_to_copy] |
|
b8eb50bd397c
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
ebi-gxa
parents:
4
diff
changeset
|
89 #end for |
|
b8eb50bd397c
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
ebi-gxa
parents:
4
diff
changeset
|
90 else: |
|
b8eb50bd397c
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
ebi-gxa
parents:
4
diff
changeset
|
91 logging.warning("Embedding source ${i} AnnData file is not compatible to be merged to main AnnData file, different cell names.") |
|
b8eb50bd397c
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
ebi-gxa
parents:
4
diff
changeset
|
92 #end for |
|
b8eb50bd397c
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
ebi-gxa
parents:
4
diff
changeset
|
93 #end if |
|
b8eb50bd397c
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
ebi-gxa
parents:
4
diff
changeset
|
94 |
|
10
54f1212d26ac
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 6806d147bfbb52c61d2a15281b69144fad87250a"
ebi-gxa
parents:
9
diff
changeset
|
95 #if $copy_u.default and len($copy_u.uns_keys) > 0: |
|
54f1212d26ac
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 6806d147bfbb52c61d2a15281b69144fad87250a"
ebi-gxa
parents:
9
diff
changeset
|
96 #for $i, $uns_s in enumerate($copy_u.uns_sources): |
|
54f1212d26ac
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 6806d147bfbb52c61d2a15281b69144fad87250a"
ebi-gxa
parents:
9
diff
changeset
|
97 ad_s = sc.read('uns_source_${i}.h5') |
|
54f1212d26ac
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 6806d147bfbb52c61d2a15281b69144fad87250a"
ebi-gxa
parents:
9
diff
changeset
|
98 if adata.n_obs == ad_s.n_obs and all(adata.obs_names == ad_s.obs_names): |
|
54f1212d26ac
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 6806d147bfbb52c61d2a15281b69144fad87250a"
ebi-gxa
parents:
9
diff
changeset
|
99 #for $j, $u_key in enumerate($copy_u.uns_keys): |
|
54f1212d26ac
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 6806d147bfbb52c61d2a15281b69144fad87250a"
ebi-gxa
parents:
9
diff
changeset
|
100 keys_to_copy = (k for k in ad_s.uns.keys() if "${u_key.contains}" in k) |
|
54f1212d26ac
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 6806d147bfbb52c61d2a15281b69144fad87250a"
ebi-gxa
parents:
9
diff
changeset
|
101 for k_to_copy in keys_to_copy: |
|
54f1212d26ac
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 6806d147bfbb52c61d2a15281b69144fad87250a"
ebi-gxa
parents:
9
diff
changeset
|
102 adata.uns[k_to_copy+"_${i}"] = ad_s.uns[k_to_copy] |
|
54f1212d26ac
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 6806d147bfbb52c61d2a15281b69144fad87250a"
ebi-gxa
parents:
9
diff
changeset
|
103 #end for |
|
54f1212d26ac
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 6806d147bfbb52c61d2a15281b69144fad87250a"
ebi-gxa
parents:
9
diff
changeset
|
104 else: |
|
54f1212d26ac
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 6806d147bfbb52c61d2a15281b69144fad87250a"
ebi-gxa
parents:
9
diff
changeset
|
105 logging.warning("Uns source ${i} AnnData file is not compatible to be merged to main AnnData file, different cell names.") |
|
54f1212d26ac
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 6806d147bfbb52c61d2a15281b69144fad87250a"
ebi-gxa
parents:
9
diff
changeset
|
106 #end for |
|
54f1212d26ac
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 6806d147bfbb52c61d2a15281b69144fad87250a"
ebi-gxa
parents:
9
diff
changeset
|
107 #end if |
|
54f1212d26ac
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 6806d147bfbb52c61d2a15281b69144fad87250a"
ebi-gxa
parents:
9
diff
changeset
|
108 |
|
9
b8eb50bd397c
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
ebi-gxa
parents:
4
diff
changeset
|
109 #if $sanitize_varm: |
|
b8eb50bd397c
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
ebi-gxa
parents:
4
diff
changeset
|
110 if hasattr(adata, 'raw') and hasattr(adata.raw, 'X') and hasattr(adata.raw, 'var'): |
|
b8eb50bd397c
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
ebi-gxa
parents:
4
diff
changeset
|
111 new_ad = anndata.AnnData(X=adata.raw.X, obs=adata.obs, var=adata.raw.var) |
|
b8eb50bd397c
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
ebi-gxa
parents:
4
diff
changeset
|
112 adata.raw = new_ad |
|
b8eb50bd397c
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
ebi-gxa
parents:
4
diff
changeset
|
113 #end if |
|
0
086d850271a2
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
ebi-gxa
parents:
diff
changeset
|
114 |
|
086d850271a2
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
ebi-gxa
parents:
diff
changeset
|
115 if len(qc_vars) > 0: |
|
086d850271a2
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
ebi-gxa
parents:
diff
changeset
|
116 pct_top = [${top_genes}] |
|
086d850271a2
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
ebi-gxa
parents:
diff
changeset
|
117 sc.pp.calculate_qc_metrics(adata, qc_vars=qc_vars, percent_top=pct_top, inplace=True) |
|
086d850271a2
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
ebi-gxa
parents:
diff
changeset
|
118 |
|
086d850271a2
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
ebi-gxa
parents:
diff
changeset
|
119 if 'n_genes' not in adata.obs.columns: |
|
086d850271a2
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
ebi-gxa
parents:
diff
changeset
|
120 sc.pp.filter_cells(adata, min_genes=0) |
|
086d850271a2
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
ebi-gxa
parents:
diff
changeset
|
121 if 'n_counts' not in adata.obs.columns: |
|
086d850271a2
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
ebi-gxa
parents:
diff
changeset
|
122 sc.pp.filter_cells(adata, min_counts=0) |
|
086d850271a2
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
ebi-gxa
parents:
diff
changeset
|
123 if 'n_cells' not in adata.var.columns: |
|
086d850271a2
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
ebi-gxa
parents:
diff
changeset
|
124 sc.pp.filter_genes(adata, min_cells=0) |
|
086d850271a2
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
ebi-gxa
parents:
diff
changeset
|
125 if 'n_counts' not in adata.var.columns: |
|
086d850271a2
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
ebi-gxa
parents:
diff
changeset
|
126 sc.pp.filter_genes(adata, min_counts=0) |
|
086d850271a2
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
ebi-gxa
parents:
diff
changeset
|
127 |
|
086d850271a2
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
ebi-gxa
parents:
diff
changeset
|
128 adata.write('output.h5', compression='gzip') |
|
086d850271a2
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
ebi-gxa
parents:
diff
changeset
|
129 </configfile> |
|
086d850271a2
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
ebi-gxa
parents:
diff
changeset
|
130 </configfiles> |
|
086d850271a2
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
ebi-gxa
parents:
diff
changeset
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131 |
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086d850271a2
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
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132 <inputs> |
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ba18139e7400
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 400799f99ee36ad12b990b1ccabf4be16a26c003
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133 <param name="input_obj_file" argument="input-object-file" type="data" format="h5,h5ad" label="Input object in hdf5 AnnData format"/> |
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ba18139e7400
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 400799f99ee36ad12b990b1ccabf4be16a26c003
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134 <expand macro="output_object_params_no_loom"/> |
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f0a29f4b9be9
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit e2ec0706fd62528e5198e3c050d91ab0ee6cd4da"
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135 <param name="copy_adata_to_raw" type="boolean" label="Copy AnnData to .raw" help="If activated, it will do 'adata.raw = adata'" checked="false"/> |
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0
086d850271a2
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
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136 <repeat name="modifications" title="Change field names in AnnData observations" min="0"> |
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086d850271a2
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
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137 <param name="from_obs" type="text" label="Original name" help="Name in observations that you want to change"> |
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086d850271a2
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
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138 <sanitizer> |
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086d850271a2
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
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139 <valid initial="string.printable"/> |
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086d850271a2
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
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140 </sanitizer> |
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086d850271a2
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
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141 </param> |
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086d850271a2
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
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142 <param name="to_obs" type="text" label="New name" help="New name in observations that you want to change"/> |
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54f1212d26ac
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 6806d147bfbb52c61d2a15281b69144fad87250a"
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143 <param name="keep_original" type="boolean" label="Keep original" help="If activated, it will also keep the original column" checked="false"/> |
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086d850271a2
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
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144 </repeat> |
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086d850271a2
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
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145 <param name="gene_symbols_field" value='index' type="text" label="Gene symbols field in AnnData" help="Field inside var.params where the gene symbols are, normally 'index' or 'gene_symbols'"/> |
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086d850271a2
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
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146 <repeat name="gene_flags" title="Flag genes that start with these names"> |
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086d850271a2
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
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147 <param name="startswith" type="text" label="Starts with" help="Text that you expect the genes to be flagged to start with, such as 'MT-' for mito genes"/> |
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086d850271a2
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
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148 <param name="flag" type="text" label="Var name" help="Name of the column in var.names where this boolean flag is stored, for example 'mito' for mitochondrial genes."/> |
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086d850271a2
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
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149 </repeat> |
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086d850271a2
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
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150 <param name="top_genes" label="Number of top genes" value='50' help="to calculate percentage of the flagged genes in that number of top genes. Used by sc.pp.calculate_qc_metrics (integer)." type="integer"/> |
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b8eb50bd397c
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
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151 <conditional name="copy_o"> |
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b8eb50bd397c
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
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152 <param name="default" type="boolean" checked="false" label="Copy observations (such as clusters)"/> |
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b8eb50bd397c
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
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153 <when value="true"> |
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54f1212d26ac
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 6806d147bfbb52c61d2a15281b69144fad87250a"
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154 <repeat name="obs_keys" title="Keys from obs to copy" help="will copy all obs keys in the given AnnData object to the main AnnData object. Make sure to use AnnData objects that are compatible in terms of genes, cells and expression data. You can use this to copy clusters. Uns elements with the same name will be also transferred." min="1"> |
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9
b8eb50bd397c
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
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155 <param name="contains" type="text" label="Key contains" help="Keys to be copied need to contain the text set here."/> |
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b8eb50bd397c
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
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156 </repeat> |
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b8eb50bd397c
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
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157 <param name="obs_sources" type="data" label="AnnData objects with obs to copy" help="Extracts obs (such as clusters) from these AnnData objects and merges them into the main input. Make sure to use AnnData objects that are compatible in terms of genes, cells and expression data." format="h5,h5ad" multiple="true"/> |
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b8eb50bd397c
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
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158 <!-- <param name="check_o" type="boolean" label="Check compatibility" help="checks if the provided AnnData objects are compatible (same genes and cells) for merging." checked="true"/> --> |
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b8eb50bd397c
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
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159 </when> |
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b8eb50bd397c
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
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160 <when value="false"/> |
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b8eb50bd397c
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
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161 </conditional> |
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b8eb50bd397c
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
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162 <conditional name="copy_e"> |
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b8eb50bd397c
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
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163 <param name="default" type="boolean" checked="false" label="Copy embeddings (such as UMAP, tSNE)"/> |
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b8eb50bd397c
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
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164 <when value="true"> |
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b8eb50bd397c
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
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165 <repeat name="embedding_keys" title="Keys from embeddings to copy" help="will copy all embedding keys in the given AnnData object to the main AnnData object. Make sure to use AnnData objects that are compatible in terms of genes, cells and expression data. You can use this to copy tSNE, UMAP, etc." min="1"> |
|
b8eb50bd397c
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
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166 <param name="contains" type="text" label="Key contains" help="Keys to be copied need to contain the text set here."/> |
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b8eb50bd397c
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
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167 </repeat> |
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b8eb50bd397c
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
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168 <param name="embedding_sources" type="data" label="AnnData objects with embeddings to copy" help="Extracts embeddings (tSNE, UMAP) from these AnnData objects and merges them into the main input. Make sure to use AnnData objects that are compatible in terms of genes, cells and expression data." format="h5,h5ad" multiple="true"/> |
|
b8eb50bd397c
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
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169 <!-- <param name="check_e" type="boolean" label="Check compatibility" help="checks if the provided AnnData objects are compatible (same genes and cells) for merging." checked="true"/> --> |
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b8eb50bd397c
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
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170 </when> |
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b8eb50bd397c
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
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171 <when value="false"/> |
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b8eb50bd397c
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
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172 </conditional> |
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10
54f1212d26ac
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 6806d147bfbb52c61d2a15281b69144fad87250a"
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173 <conditional name="copy_u"> |
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54f1212d26ac
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 6806d147bfbb52c61d2a15281b69144fad87250a"
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174 <param name="default" type="boolean" checked="false" label="Copy uns"/> |
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54f1212d26ac
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 6806d147bfbb52c61d2a15281b69144fad87250a"
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175 <when value="true"> |
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54f1212d26ac
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 6806d147bfbb52c61d2a15281b69144fad87250a"
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176 <repeat name="uns_keys" title="Keys from uns to copy" help="will copy all uns keys in the given AnnData object to the main AnnData object. Make sure to use AnnData objects that are compatible in terms of genes, cells and expression data. You can use this to copy rank_genes_groups for instance." min="1"> |
|
54f1212d26ac
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 6806d147bfbb52c61d2a15281b69144fad87250a"
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177 <param name="contains" type="text" label="Key contains" help="Keys to be copied need to contain the text set here."/> |
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54f1212d26ac
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 6806d147bfbb52c61d2a15281b69144fad87250a"
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178 </repeat> |
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54f1212d26ac
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 6806d147bfbb52c61d2a15281b69144fad87250a"
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179 <param name="uns_sources" type="data" label="AnnData objects with uns to copy" help="Extracts uns (such as ranked_genes_groups) from these AnnData objects and merges them into the main input. Make sure to use AnnData objects that are compatible in terms of genes, cells and expression data." format="h5,h5ad" multiple="true"/> |
|
54f1212d26ac
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 6806d147bfbb52c61d2a15281b69144fad87250a"
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180 </when> |
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54f1212d26ac
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 6806d147bfbb52c61d2a15281b69144fad87250a"
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181 </conditional> |
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9
b8eb50bd397c
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
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182 <param name="sanitize_varm" type="boolean" checked="false" label="Sanitise any null raw.varm objects if any" help="This might be relevant for interfacing with newer versions of AnnData, that might complain if .raw includes a varm null object."/> |
|
0
086d850271a2
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
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183 </inputs> |
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086d850271a2
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
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184 |
|
086d850271a2
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
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185 <outputs> |
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2
ba18139e7400
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 400799f99ee36ad12b990b1ccabf4be16a26c003
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0
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186 <expand macro="output_data_obj_no_loom" description="metadata changes on"/> |
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0
086d850271a2
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
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187 </outputs> |
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086d850271a2
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
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188 |
|
086d850271a2
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
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189 <tests> |
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086d850271a2
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
ebi-gxa
parents:
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190 <test> |
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086d850271a2
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
ebi-gxa
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191 <param name="input_obj_file" value="find_cluster.h5"/> |
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086d850271a2
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
ebi-gxa
parents:
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192 <param name="input_format" value="anndata"/> |
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planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
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193 <param name="color_by" value="louvain"/> |
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194 <output name="output_h5ad" file="anndata_ops.h5" ftype="h5ad" compare="sim_size"/> |
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planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
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195 </test> |
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planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
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196 </tests> |
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197 |
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198 <help><![CDATA[ |
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199 ============================= |
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200 Operations on AnnData objects |
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201 ============================= |
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202 |
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203 Performs the following operations: |
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planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
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204 |
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205 * Change observation fields, mostly for downstreaming processes convenience. Multiple fields can be changed as one. |
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planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
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206 * Flag genes that start with a certain text: useful for flagging mitochondrial, spikes or other groups of genes. |
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planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
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207 * For the flags created, calculates qc metrics (pct_<flag>_counts). |
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planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
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208 * Calculates `n_genes`, `n_counts` for cells and `n_cells`, `n_counts` for genes. |
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planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
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209 * For top <N> genes specified, calculate qc metrics (pct_counts_in_top_<N>_genes). |
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210 * Copy from a set of compatible AnnData objects (same cells and genes): |
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211 * Observations, such as clustering results. |
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212 * Embeddings, such as tSNE or UMAPs. |
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213 * Unstructure annotations, like gene markers. |
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214 |
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215 This functionality will probably be added in the future to a larger package. |
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planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
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216 ]]></help> |
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planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
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217 <expand macro="citations"/> |
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218 </tool> |