Mercurial > repos > ebi-gxa > anndata_ops
annotate anndata_operations.xml @ 23:31e5e6d606ef draft
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 85dcbc74a856bd55865bd372601de39af72dfd29-dirty"
| author | ebi-gxa |
|---|---|
| date | Tue, 28 Sep 2021 17:43:02 +0000 |
| parents | fe75d2414dc0 |
| children | 825dfd66e3fb |
| rev | line source |
|---|---|
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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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1 <?xml version="1.0" encoding="utf-8"?> |
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23
31e5e6d606ef
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 85dcbc74a856bd55865bd372601de39af72dfd29-dirty"
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2 <tool id="anndata_ops" name="AnnData Operations" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> |
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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
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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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changeset
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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:
diff
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:
diff
changeset
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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
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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
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10 |
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53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
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11 #if $copy_r.default: |
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53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
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12 ln -s '${copy_r.r_source}' r_source.h5 && |
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53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
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13 #end if |
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53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
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14 |
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53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
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15 #if $copy_x.default: |
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53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
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16 #for $i, $xs in enumerate($copy_x.xlayers): |
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53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
parents:
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17 ln -s '${xs.x_source}' x_source_${i}.h5 && |
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53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
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18 #end for |
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53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
parents:
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19 #end if |
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53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
parents:
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20 |
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53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
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21 #if $copy_l.default: |
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53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
parents:
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22 #for $i, $ls in enumerate($copy_l.layer_sources): |
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53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
parents:
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23 ln -s '${ls}' layer_source_${i}.h5 && |
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53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
parents:
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24 #end for |
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53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
parents:
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25 #end if |
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53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
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26 |
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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
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27 #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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28 #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:
4
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29 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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30 #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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31 #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
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32 |
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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 #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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34 #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
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35 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
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36 #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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37 #end if |
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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"
ebi-gxa
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38 |
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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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39 #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
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40 #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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41 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
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42 #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
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43 #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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44 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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45 ]]></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:
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46 <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
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47 <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
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48 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
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49 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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50 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:
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51 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:
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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
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53 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
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54 |
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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
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55 #if $copy_adata_to_raw: |
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f0a29f4b9be9
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit e2ec0706fd62528e5198e3c050d91ab0ee6cd4da"
ebi-gxa
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56 adata.raw = adata |
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f0a29f4b9be9
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit e2ec0706fd62528e5198e3c050d91ab0ee6cd4da"
ebi-gxa
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57 #end if |
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f0a29f4b9be9
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit e2ec0706fd62528e5198e3c050d91ab0ee6cd4da"
ebi-gxa
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58 |
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0
086d850271a2
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
ebi-gxa
parents:
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59 gene_name = '${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
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60 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:
diff
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61 |
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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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62 #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:
diff
changeset
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63 adata.obs['${s.to_obs}'] = adata.obs['${s.from_obs}'] |
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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"
ebi-gxa
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64 #if not $s.keep_original: |
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54f1212d26ac
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 6806d147bfbb52c61d2a15281b69144fad87250a"
ebi-gxa
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65 del adata.obs['${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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9
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66 #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:
diff
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67 #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
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68 |
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22
fe75d2414dc0
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 8853a954bd9c343b3458479582f1f21c3981fef0-dirty"
ebi-gxa
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69 #for $i, $s in enumerate($var_modifications) |
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fe75d2414dc0
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 8853a954bd9c343b3458479582f1f21c3981fef0-dirty"
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70 adata.var['${s.to_var}'] = adata.var['${s.from_var}'] |
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fe75d2414dc0
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 8853a954bd9c343b3458479582f1f21c3981fef0-dirty"
ebi-gxa
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71 #if not $s.keep_original: |
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fe75d2414dc0
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 8853a954bd9c343b3458479582f1f21c3981fef0-dirty"
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72 del adata.var['${s.from_var}'] |
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fe75d2414dc0
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 8853a954bd9c343b3458479582f1f21c3981fef0-dirty"
ebi-gxa
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73 #end if |
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fe75d2414dc0
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 8853a954bd9c343b3458479582f1f21c3981fef0-dirty"
ebi-gxa
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74 #end for |
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fe75d2414dc0
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 8853a954bd9c343b3458479582f1f21c3981fef0-dirty"
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75 |
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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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changeset
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76 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
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parents:
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77 |
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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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78 #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
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79 k_cat = gene_names.str.startswith('${flag.startswith}') |
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086d850271a2
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
ebi-gxa
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80 if k_cat.sum() > 0: |
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086d850271a2
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
ebi-gxa
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changeset
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81 adata.var['${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
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changeset
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82 qc_vars.append('${flag.flag}') |
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086d850271a2
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
ebi-gxa
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83 else: |
|
086d850271a2
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
ebi-gxa
parents:
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changeset
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84 logging.warning('No genes starting with {} found, skip calculating expression of {} genes'.format('${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:
diff
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|
85 #end for |
|
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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86 |
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19
53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
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87 #if $copy_r.default and $copy_r.r_source: |
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53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
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88 ad_s = sc.read('r_source.h5') |
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53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
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parents:
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89 if not all(adata.obs.index.isin(ad_s.obs.index)): |
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53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
parents:
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90 logging.error("Specified object for .raw must contain all .obs from main object.") |
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53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
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91 sys.exit(1) |
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53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
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92 else: |
|
53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
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93 adata.raw = ad_s[adata.obs.index] |
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53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
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94 del ad_s |
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53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
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95 #end if |
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53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
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96 |
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53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
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97 #if $copy_x.default and len($copy_x.xlayers) > 0: |
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53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
parents:
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98 #for $i, $x_s in enumerate($copy_x.xlayers): |
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53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
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18
diff
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99 ad_s = sc.read('x_source_${i}.h5') |
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53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
parents:
18
diff
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100 if adata.n_obs == ad_s.n_obs and all(adata.obs_names == ad_s.obs_names): |
|
53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
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101 #set xs=$copy_x.xlayers[$i] |
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22
fe75d2414dc0
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 8853a954bd9c343b3458479582f1f21c3981fef0-dirty"
ebi-gxa
parents:
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102 if "${xs.dest}" == '': |
|
19
53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
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diff
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103 logging.error("%sth destination layer for %sth X source not specified" % ("${i}", "${i}")) |
|
53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
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104 sys.exit(1) |
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53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
parents:
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diff
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|
105 adata.layers["${xs.dest}"] = ad_s.X |
|
53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
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106 else: |
|
53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
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107 logging.error("X source ${i} AnnData file is not compatible to be merged to main AnnData file, different cell names.") |
|
53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
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108 sys.exit(1) |
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53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
parents:
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|
109 del ad_s |
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53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
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110 #end for |
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53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
parents:
18
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111 #end if |
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53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
parents:
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112 |
|
53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
parents:
18
diff
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113 #if $copy_l.default and len($copy_l.layers) > 0: |
|
53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
parents:
18
diff
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114 #for $i, $layer_s in enumerate($copy_l.layer_sources): |
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53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
parents:
18
diff
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115 ad_s = sc.read('layer_source_${i}.h5') |
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53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
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diff
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116 if adata.n_obs == ad_s.n_obs and all(adata.obs_names == ad_s.obs_names): |
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53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
parents:
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diff
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117 #for $j, $l_key in enumerate($copy_l.layers): |
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53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
parents:
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diff
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118 layers_to_copy = (k for k in ad_s.layers.keys() if "${l_key.contains}" in k) |
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53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
parents:
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119 for l_to_copy in layers_to_copy: |
|
53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
parents:
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120 suffix='' |
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53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
parents:
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121 if l_to_copy in adata.layers: |
|
22
fe75d2414dc0
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 8853a954bd9c343b3458479582f1f21c3981fef0-dirty"
ebi-gxa
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122 suffix = "_${i}" |
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fe75d2414dc0
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 8853a954bd9c343b3458479582f1f21c3981fef0-dirty"
ebi-gxa
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123 |
|
19
53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
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124 adata.layers[l_to_copy+suffix] = ad_s.layers[l_to_copy] |
|
53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
parents:
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125 #end for |
|
53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
parents:
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126 else: |
|
53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
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127 logging.error("Layer source ${i} AnnData file is not compatible to be merged to main AnnData file, different cell names.") |
|
53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
parents:
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128 sys.exit(1) |
|
53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
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129 del ad_s |
|
53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
parents:
18
diff
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|
130 #end for |
|
53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
parents:
18
diff
changeset
|
131 #end if |
|
53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
parents:
18
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132 |
|
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
|
133 #if $copy_o.default and len($copy_o.obs_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
|
134 #for $i, $obs_s in enumerate($copy_o.obs_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
|
135 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
|
136 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
|
137 #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
|
138 keys_to_copy = (k for k in ad_s.obs.keys() if "${o_key.contains}" in k) |
|
b8eb50bd397c
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
ebi-gxa
parents:
4
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changeset
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139 for k_to_copy in keys_to_copy: |
|
15
c09d61ede252
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 044580b6bfcd36a5c1cb9e70b40045eb8f71b7e2-dirty"
ebi-gxa
parents:
14
diff
changeset
|
140 suffix='' |
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c09d61ede252
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 044580b6bfcd36a5c1cb9e70b40045eb8f71b7e2-dirty"
ebi-gxa
parents:
14
diff
changeset
|
141 if k_to_copy in adata.obs: |
|
22
fe75d2414dc0
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 8853a954bd9c343b3458479582f1f21c3981fef0-dirty"
ebi-gxa
parents:
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diff
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142 suffix = "_${i}" |
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fe75d2414dc0
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 8853a954bd9c343b3458479582f1f21c3981fef0-dirty"
ebi-gxa
parents:
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143 |
|
15
c09d61ede252
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 044580b6bfcd36a5c1cb9e70b40045eb8f71b7e2-dirty"
ebi-gxa
parents:
14
diff
changeset
|
144 adata.obs[[k_to_copy+suffix]] = ad_s.obs[[k_to_copy]] |
|
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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diff
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145 if k_to_copy in ad_s.uns.keys(): |
|
15
c09d61ede252
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 044580b6bfcd36a5c1cb9e70b40045eb8f71b7e2-dirty"
ebi-gxa
parents:
14
diff
changeset
|
146 adata.uns[k_to_copy+suffix] = ad_s.uns[k_to_copy] |
|
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
|
147 #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
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148 else: |
|
19
53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
parents:
18
diff
changeset
|
149 logging.error("Observation source ${i} AnnData file is not compatible to be merged to main AnnData file, different cell names.") |
|
53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
parents:
18
diff
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|
150 sys.exit(1) |
|
53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
parents:
18
diff
changeset
|
151 del ad_s |
|
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
|
152 #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
|
153 #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
|
154 |
|
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
|
155 |
|
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
|
156 #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
|
157 #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
|
158 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
|
159 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
|
160 #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
|
161 keys_to_copy = (k for k in ad_s.obsm.keys() if "${e_key.contains}" in k) |
|
b8eb50bd397c
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
ebi-gxa
parents:
4
diff
changeset
|
162 for k_to_copy in keys_to_copy: |
|
15
c09d61ede252
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 044580b6bfcd36a5c1cb9e70b40045eb8f71b7e2-dirty"
ebi-gxa
parents:
14
diff
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|
163 suffix = '' |
|
c09d61ede252
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 044580b6bfcd36a5c1cb9e70b40045eb8f71b7e2-dirty"
ebi-gxa
parents:
14
diff
changeset
|
164 if k_to_copy in adata.obsm: |
|
c09d61ede252
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 044580b6bfcd36a5c1cb9e70b40045eb8f71b7e2-dirty"
ebi-gxa
parents:
14
diff
changeset
|
165 suffix = "_${i}" |
|
c09d61ede252
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 044580b6bfcd36a5c1cb9e70b40045eb8f71b7e2-dirty"
ebi-gxa
parents:
14
diff
changeset
|
166 adata.obsm[k_to_copy+suffix] = ad_s.obsm[k_to_copy] |
|
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
|
167 #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
|
168 else: |
|
19
53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
parents:
18
diff
changeset
|
169 logging.error("Embedding source ${i} AnnData file is not compatible to be merged to main AnnData file, different cell names.") |
|
53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
parents:
18
diff
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|
170 sys.exit(1) |
|
53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
parents:
18
diff
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|
171 del ad_s |
|
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
|
172 #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
|
173 #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
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|
174 |
|
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
|
175 #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
|
176 #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
|
177 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
|
178 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
|
179 #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
|
180 keys_to_copy = (k for k in ad_s.uns.keys() if "${u_key.contains}" in k) |
|
54f1212d26ac
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 6806d147bfbb52c61d2a15281b69144fad87250a"
ebi-gxa
parents:
9
diff
changeset
|
181 for k_to_copy in keys_to_copy: |
|
15
c09d61ede252
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 044580b6bfcd36a5c1cb9e70b40045eb8f71b7e2-dirty"
ebi-gxa
parents:
14
diff
changeset
|
182 suffix='' |
|
c09d61ede252
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 044580b6bfcd36a5c1cb9e70b40045eb8f71b7e2-dirty"
ebi-gxa
parents:
14
diff
changeset
|
183 if k_to_copy in adata.uns: |
|
c09d61ede252
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 044580b6bfcd36a5c1cb9e70b40045eb8f71b7e2-dirty"
ebi-gxa
parents:
14
diff
changeset
|
184 suffix="_${i}" |
|
c09d61ede252
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 044580b6bfcd36a5c1cb9e70b40045eb8f71b7e2-dirty"
ebi-gxa
parents:
14
diff
changeset
|
185 adata.uns[k_to_copy+suffix] = ad_s.uns[k_to_copy] |
|
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
|
186 #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
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|
187 else: |
|
19
53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
parents:
18
diff
changeset
|
188 logging.error("Uns source ${i} AnnData file is not compatible to be merged to main AnnData file, different cell names.") |
|
53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
parents:
18
diff
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|
189 sys.exit(1) |
|
53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
parents:
18
diff
changeset
|
190 del ad_s |
|
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
|
191 #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
|
192 #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
|
193 |
|
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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194 #if $sanitize_varm: |
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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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195 if hasattr(adata, 'raw') and hasattr(adata.raw, 'X') and hasattr(adata.raw, 'var'): |
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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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196 new_ad = anndata.AnnData(X=adata.raw.X, obs=adata.obs, var=adata.raw.var) |
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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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197 adata.raw = new_ad |
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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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198 #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
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199 |
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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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200 if len(qc_vars) > 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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201 pct_top = [${top_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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202 sc.pp.calculate_qc_metrics(adata, qc_vars=qc_vars, percent_top=pct_top, inplace=True) |
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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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203 |
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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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204 if 'n_genes' not in adata.obs.columns: |
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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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205 sc.pp.filter_cells(adata, min_genes=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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206 if 'n_counts' not in adata.obs.columns: |
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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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207 sc.pp.filter_cells(adata, min_counts=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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208 if 'n_cells' not in adata.var.columns: |
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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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209 sc.pp.filter_genes(adata, min_cells=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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210 if 'n_counts' not in adata.var.columns: |
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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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211 sc.pp.filter_genes(adata, min_counts=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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212 |
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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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213 adata.write('output.h5', compression='gzip') |
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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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214 </configfile> |
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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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215 </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
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216 |
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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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217 <inputs> |
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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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218 <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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219 <expand macro="output_object_params_no_loom"/> |
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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"
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220 <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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221 <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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222 <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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223 <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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224 <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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225 </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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226 </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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227 <param name="to_obs" type="text" label="New name" help="New name in observations that you want to change"/> |
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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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228 <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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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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229 </repeat> |
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22
fe75d2414dc0
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 8853a954bd9c343b3458479582f1f21c3981fef0-dirty"
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diff
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230 <repeat name="var_modifications" title="Change field names in AnnData var" min="0"> |
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fe75d2414dc0
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 8853a954bd9c343b3458479582f1f21c3981fef0-dirty"
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diff
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231 <param name="from_var" type="text" label="Original name" help="Name in var that you want to change"> |
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fe75d2414dc0
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 8853a954bd9c343b3458479582f1f21c3981fef0-dirty"
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232 <sanitizer> |
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fe75d2414dc0
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 8853a954bd9c343b3458479582f1f21c3981fef0-dirty"
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233 <valid initial="string.printable"/> |
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fe75d2414dc0
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 8853a954bd9c343b3458479582f1f21c3981fef0-dirty"
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234 </sanitizer> |
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fe75d2414dc0
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 8853a954bd9c343b3458479582f1f21c3981fef0-dirty"
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235 </param> |
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fe75d2414dc0
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 8853a954bd9c343b3458479582f1f21c3981fef0-dirty"
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236 <param name="to_var" type="text" label="New name" help="New name in var that you want to change"/> |
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fe75d2414dc0
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 8853a954bd9c343b3458479582f1f21c3981fef0-dirty"
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237 <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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fe75d2414dc0
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 8853a954bd9c343b3458479582f1f21c3981fef0-dirty"
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238 </repeat> |
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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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239 <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
ebi-gxa
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240 <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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241 <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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242 <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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243 </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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244 <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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19
53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
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245 <conditional name="copy_r"> |
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53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
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246 <param name="default" type="boolean" checked="false" label="Copy adata.X to adata.raw"/> |
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53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
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247 <when value="true"> |
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53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
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248 <param name="r_source" type="data" label="AnnData object .X with to copy to .raw" help="Copies adata (subset to matching obs) from this AnnData object into the main input as .raw. Make sure to use an AnnData object containing all .obs in the main input." format="h5,h5ad" /> |
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53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
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249 </when> |
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53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
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250 <when value="false"/> |
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53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
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251 </conditional> |
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53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
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252 <conditional name="copy_x"> |
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53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
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253 <param name="default" type="boolean" checked="false" label="Copy .X to layers"/> |
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53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
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254 <when value="true"> |
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53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
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255 <repeat name="xlayers" title="Source objects for .X and paired destination layers in the main AnnData object" help="make sure to use AnnData objects that are compatible in terms of genes, cells and expression data." min="1"> |
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53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
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|
256 <param name="x_source" type="data" label="AnnData objects with .X to copy" help="Extracts .X from these AnnData objects and merges them into the main input as layers. Make sure to use AnnData objects that are compatible in terms of genes, cells and expression data." format="h5,h5ad" /> |
|
53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
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257 <param name="dest" type="text" label="Destination layer" /> |
|
53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
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258 </repeat> |
|
53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
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259 </when> |
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53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
parents:
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260 <when value="false"/> |
|
53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
parents:
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261 </conditional> |
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53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
parents:
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262 <conditional name="copy_l"> |
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53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
parents:
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263 <param name="default" type="boolean" checked="false" label="Copy layers"/> |
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53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
parents:
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264 <when value="true"> |
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53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
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265 <repeat name="layers" title="Layers from which matrices will be copied" help="will copy all layers 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." min="1"> |
|
53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
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266 <param name="contains" type="text" label="Key contains" help="Keys to be copied need to contain the text set here."/> |
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53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
parents:
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267 </repeat> |
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53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
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268 <param name="layer_sources" type="data" label="AnnData objects with layers to copy" help="Extracts layers 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"/> |
|
53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
parents:
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269 </when> |
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53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
parents:
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270 <when value="false"/> |
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53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
parents:
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271 </conditional> |
|
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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272 <conditional name="copy_o"> |
|
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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273 <param name="default" type="boolean" checked="false" label="Copy observations (such as clusters)"/> |
|
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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274 <when value="true"> |
|
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
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275 <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"> |
|
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
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276 <param name="contains" type="text" label="Key contains" help="Keys to be copied need to contain the text set here."/> |
|
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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277 </repeat> |
|
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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278 <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"/> |
|
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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279 <!-- <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"/> --> |
|
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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280 </when> |
|
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
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281 <when value="false"/> |
|
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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282 </conditional> |
|
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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283 <conditional name="copy_e"> |
|
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
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|
284 <param name="default" type="boolean" checked="false" label="Copy embeddings (such as UMAP, tSNE)"/> |
|
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
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285 <when value="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"
ebi-gxa
parents:
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changeset
|
286 <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"
ebi-gxa
parents:
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diff
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|
287 <param name="contains" type="text" label="Key contains" help="Keys to be copied need to contain the text set here."/> |
|
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
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288 </repeat> |
|
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
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|
289 <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"
ebi-gxa
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4
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290 <!-- <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"/> --> |
|
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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291 </when> |
|
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
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292 <when value="false"/> |
|
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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293 </conditional> |
|
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
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294 <conditional name="copy_u"> |
|
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
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295 <param name="default" type="boolean" checked="false" label="Copy uns"/> |
|
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
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296 <when value="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"
ebi-gxa
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297 <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"
ebi-gxa
parents:
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298 <param name="contains" type="text" label="Key contains" help="Keys to be copied need to contain the text set here."/> |
|
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
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299 </repeat> |
|
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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300 <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"
ebi-gxa
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301 </when> |
|
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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302 </conditional> |
|
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
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303 <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
ebi-gxa
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304 </inputs> |
|
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
|
305 |
|
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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306 <outputs> |
|
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
ebi-gxa
parents:
0
diff
changeset
|
307 <expand macro="output_data_obj_no_loom" description="metadata changes on"/> |
|
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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308 </outputs> |
|
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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309 |
|
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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310 <tests> |
|
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
|
311 <test> |
|
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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|
312 <param name="input_obj_file" value="find_cluster.h5"/> |
|
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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313 <param name="input_format" value="anndata"/> |
|
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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314 <param name="color_by" value="louvain"/> |
|
12
f1a1cf7c0153
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 62f47287c7e8449c59a1f1f454852ddc669b1b1e-dirty"
ebi-gxa
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diff
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|
315 <output name="output_h5ad" file="anndata_ops.h5" ftype="h5ad" compare="sim_size"/> |
|
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
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316 </test> |
|
19
53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
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|
317 <test> |
|
22
fe75d2414dc0
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 8853a954bd9c343b3458479582f1f21c3981fef0-dirty"
ebi-gxa
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318 <param name="input_obj_file" value="anndata_ops.h5"/> |
|
fe75d2414dc0
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 8853a954bd9c343b3458479582f1f21c3981fef0-dirty"
ebi-gxa
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|
319 <param name="from_var" value = "gene_symbols" /> |
|
fe75d2414dc0
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 8853a954bd9c343b3458479582f1f21c3981fef0-dirty"
ebi-gxa
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changeset
|
320 <param name="to_var" value = "hello_all" /> |
|
fe75d2414dc0
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 8853a954bd9c343b3458479582f1f21c3981fef0-dirty"
ebi-gxa
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|
321 <output name="output_h5ad" ftype="h5ad"> |
|
fe75d2414dc0
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 8853a954bd9c343b3458479582f1f21c3981fef0-dirty"
ebi-gxa
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|
322 <assert_contents> |
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fe75d2414dc0
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 8853a954bd9c343b3458479582f1f21c3981fef0-dirty"
ebi-gxa
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|
323 <has_h5_keys keys="var/hello_all" /> |
|
fe75d2414dc0
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 8853a954bd9c343b3458479582f1f21c3981fef0-dirty"
ebi-gxa
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|
324 </assert_contents> |
|
fe75d2414dc0
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 8853a954bd9c343b3458479582f1f21c3981fef0-dirty"
ebi-gxa
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|
325 </output> |
|
fe75d2414dc0
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 8853a954bd9c343b3458479582f1f21c3981fef0-dirty"
ebi-gxa
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326 </test> |
|
fe75d2414dc0
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 8853a954bd9c343b3458479582f1f21c3981fef0-dirty"
ebi-gxa
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327 <test> |
|
19
53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
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328 <param name="input_obj_file" value="find_cluster.h5"/> |
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53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
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329 <param name="input_format" value="anndata"/> |
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53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
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330 <conditional name="copy_r"> |
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53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
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|
331 <param name="default" value="true"/> |
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53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
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332 <param name="r_source" value="read_10x.h5"/> |
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53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
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|
333 </conditional> |
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53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
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|
334 <output name="output_h5ad" file="anndata_ops_raw.h5" ftype="h5ad" compare="sim_size"> |
|
53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
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|
335 <assert_contents> |
|
53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
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336 <has_h5_keys keys="raw/X" /> |
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53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
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337 </assert_contents> |
|
53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
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|
338 </output> |
|
53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
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339 </test> |
|
53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
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340 <test> |
|
53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
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341 <param name="input_obj_file" value="normalise_data.h5"/> |
|
53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
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|
342 <param name="input_format" value="anndata"/> |
|
53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
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|
343 <conditional name="copy_x"> |
|
53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
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344 <param name="default" value="true"/> |
|
53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
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|
345 <repeat name="xlayers"> |
|
53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
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346 <param name="x_source" value='filter_genes.h5'/> |
|
53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
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|
347 <param name="dest" value='filtered'/> |
|
53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
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|
348 </repeat> |
|
53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
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349 </conditional> |
|
53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
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|
350 <output name="output_h5ad" file="anndata_ops_xlayer.h5" ftype="h5ad" compare="sim_size"> |
|
53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
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|
351 <assert_contents> |
|
53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
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|
352 <has_h5_keys keys="layers/filtered" /> |
|
53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
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|
353 </assert_contents> |
|
53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
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|
354 </output> |
|
53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
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|
355 </test> |
|
53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
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|
356 <test> |
|
53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
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|
357 <param name="input_obj_file" value="find_cluster.h5"/> |
|
53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
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|
358 <param name="input_format" value="anndata"/> |
|
53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
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|
359 <conditional name="copy_l"> |
|
53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
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|
360 <param name="default" value="true"/> |
|
53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
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|
361 <repeat name="layers"> |
|
53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
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|
362 <param name="contains" value='filtered'/> |
|
53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
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|
363 </repeat> |
|
53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
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|
364 <param name="layer_sources" value='anndata_ops_xlayer.h5'/> |
|
53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
parents:
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|
365 </conditional> |
|
53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
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|
366 <output name="output_h5ad" file="anndata_ops_layer.h5" ftype="h5ad" compare="sim_size"> |
|
53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
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|
367 <assert_contents> |
|
53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
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|
368 <has_h5_keys keys="layers/filtered" /> |
|
53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
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|
369 </assert_contents> |
|
53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
parents:
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|
370 </output> |
|
53a251c6d991
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
ebi-gxa
parents:
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|
371 </test> |
|
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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changeset
|
372 </tests> |
|
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
|
373 |
|
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
|
374 <help><![CDATA[ |
|
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
|
375 ============================= |
|
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
|
376 Operations on AnnData objects |
|
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
|
377 ============================= |
|
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
|
378 |
|
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
|
379 Performs the following operations: |
|
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
|
380 |
|
22
fe75d2414dc0
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 8853a954bd9c343b3458479582f1f21c3981fef0-dirty"
ebi-gxa
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|
381 * Change observation/var fields, mostly for downstreaming processes convenience. Multiple fields can be changed as one. |
|
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
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382 * Flag genes that start with a certain text: useful for flagging mitochondrial, spikes or other groups of 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
ebi-gxa
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383 * For the flags created, calculates qc metrics (pct_<flag>_counts). |
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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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384 * Calculates `n_genes`, `n_counts` for cells and `n_cells`, `n_counts` for 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
ebi-gxa
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385 * For top <N> genes specified, calculate qc metrics (pct_counts_in_top_<N>_genes). |
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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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386 * Copy from a set of compatible AnnData objects (same cells and genes): |
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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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387 * Observations, such as clustering results. |
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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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388 * Embeddings, such as tSNE or UMAPs. |
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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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389 * Unstructure annotations, like gene markers. |
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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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390 |
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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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391 This functionality will probably be added in the future to a larger package. |
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a4ad76e3dc4a
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 2db9e8cecb8d373874318e53ec2d4d7a64dd1b24-dirty"
ebi-gxa
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392 |
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a4ad76e3dc4a
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 2db9e8cecb8d373874318e53ec2d4d7a64dd1b24-dirty"
ebi-gxa
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393 History |
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a4ad76e3dc4a
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 2db9e8cecb8d373874318e53ec2d4d7a64dd1b24-dirty"
ebi-gxa
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394 ------- |
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a4ad76e3dc4a
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 2db9e8cecb8d373874318e53ec2d4d7a64dd1b24-dirty"
ebi-gxa
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395 |
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a4ad76e3dc4a
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 2db9e8cecb8d373874318e53ec2d4d7a64dd1b24-dirty"
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396 1.6.0+galaxy0: Moves to Scanpy Scripts 0.3.0 (Scanpy 1.6.0), versioning switched to track Scanpy as other tools. |
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a4ad76e3dc4a
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 2db9e8cecb8d373874318e53ec2d4d7a64dd1b24-dirty"
ebi-gxa
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397 |
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a4ad76e3dc4a
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 2db9e8cecb8d373874318e53ec2d4d7a64dd1b24-dirty"
ebi-gxa
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398 0.0.3+galaxy0: Adds ability to merge AnnData objects (Scanpy 1.4.3). |
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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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399 ]]></help> |
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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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400 <expand macro="citations"/> |
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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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401 </tool> |