Mercurial > repos > ebi-gxa > anndata_ops

annotate anndata_operations.xml @ 13:35ee5e3e87c1 draft

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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9028e8fa3761fd640dcace5d36bf9b7d558319f7-dirty"
author ebi-gxa
date Thu, 10 Sep 2020 08:42:48 +0000
parents f1a1cf7c0153
children a4ad76e3dc4a
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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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1 <?xml version="1.0" encoding="utf-8"?>
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f0a29f4b9be9 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit e2ec0706fd62528e5198e3c050d91ab0ee6cd4da"
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2 <tool id="anndata_ops" name="AnnData Operations" version="0.0.3+galaxy1" profile="@PROFILE@">
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086d850271a2 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
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3 <description>modifies metadata and flags genes</description>
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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4 <macros>
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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5 <import>scanpy_macros2.xml</import>
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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6 </macros>
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7 <expand macro="requirements"/>
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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8 <command detect_errors="exit_code"><![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
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9 ln -s '${input_obj_file}' input.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"
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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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11 #if $copy_o.default:
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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12 #for $i, $os in enumerate($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"
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13 ln -s '${os}' obs_source_${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"
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14 #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"
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15 #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"
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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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17 #if $copy_e.default:
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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18 #for $i, $es in enumerate($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"
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19 ln -s '${es}' embedding_source_${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"
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20 #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"
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21 #end if
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54f1212d26ac "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 6806d147bfbb52c61d2a15281b69144fad87250a"
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54f1212d26ac "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 6806d147bfbb52c61d2a15281b69144fad87250a"
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23 #if $copy_u.default:
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24 #for $i, $us in enumerate($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"
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25 ln -s '${us}' uns_source_${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"
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26 #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"
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27 #end if
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28 python $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
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29 ]]></command>
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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30 <configfiles>
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31 <configfile name="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
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32 import scanpy as sc
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b8eb50bd397c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
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33 import anndata
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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34 from numpy import all
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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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35 import logging
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36
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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37 adata = sc.read('input.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
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38
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f0a29f4b9be9 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit e2ec0706fd62528e5198e3c050d91ab0ee6cd4da"
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39 #if $copy_adata_to_raw:
f0a29f4b9be9 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit e2ec0706fd62528e5198e3c050d91ab0ee6cd4da"
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40 adata.raw = adata
f0a29f4b9be9 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit e2ec0706fd62528e5198e3c050d91ab0ee6cd4da"
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41 #end if
f0a29f4b9be9 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit e2ec0706fd62528e5198e3c050d91ab0ee6cd4da"
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42
0
086d850271a2 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
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43 gene_name = '${gene_symbols_field}'
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44 qc_vars = list()
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45
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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46 #for $i, $s in enumerate($modifications)
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47 adata.obs['${s.to_obs}'] = adata.obs['${s.from_obs}']
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48 #if not $s.keep_original:
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49 del adata.obs['${s.from_obs}']
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50 #end if
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51 #end for
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52
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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53 gene_names = getattr(adata.var, gene_name)
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54
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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55 #for $i, $flag in enumerate($gene_flags)
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56 k_cat = gene_names.str.startswith('${flag.startswith}')
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57 if k_cat.sum() > 0:
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58 adata.var['${flag.flag}'] = k_cat
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59 qc_vars.append('${flag.flag}')
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60 else:
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61 logging.warning('No genes starting with {} found, skip calculating expression of {} genes'.format('${flag.startswith}', '${flag.flag}'))
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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62 #end for
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63
9
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64 #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"
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65 #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"
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66 ad_s = sc.read('obs_source_${i}.h5')
b8eb50bd397c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
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67 if adata.n_obs == ad_s.n_obs and all(adata.obs_names == ad_s.obs_names):
b8eb50bd397c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
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68 #for $j, $o_key in enumerate($copy_o.obs_keys):
b8eb50bd397c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
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69 keys_to_copy = (k for k in ad_s.obs.keys() if "${o_key.contains}" in k)
b8eb50bd397c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
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70 for k_to_copy in keys_to_copy:
b8eb50bd397c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
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71 adata.obs[[k_to_copy+"_${i}"]] = ad_s.obs[[k_to_copy]]
b8eb50bd397c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
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diff changeset
72 if k_to_copy in ad_s.uns.keys():
b8eb50bd397c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
ebi-gxa
parents: 4
diff changeset
73 adata.uns[k_to_copy+"_${i}"] = ad_s.uns[k_to_copy]
b8eb50bd397c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
ebi-gxa
parents: 4
diff changeset
74 #end for
b8eb50bd397c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
ebi-gxa
parents: 4
diff changeset
75 else:
b8eb50bd397c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
ebi-gxa
parents: 4
diff changeset
76 logging.warning("Observation source ${i} AnnData file is not compatible to be merged to main AnnData file, different cell names.")
b8eb50bd397c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
ebi-gxa
parents: 4
diff changeset
77 #end for
b8eb50bd397c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
ebi-gxa
parents: 4
diff changeset
78 #end if
b8eb50bd397c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
ebi-gxa
parents: 4
diff changeset
79
b8eb50bd397c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
ebi-gxa
parents: 4
diff changeset
80
b8eb50bd397c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
ebi-gxa
parents: 4
diff changeset
81 #if $copy_e.default and len($copy_e.embedding_keys) > 0:
b8eb50bd397c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
ebi-gxa
parents: 4
diff changeset
82 #for $i, $obs_s in enumerate($copy_e.embedding_sources):
b8eb50bd397c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
ebi-gxa
parents: 4
diff changeset
83 ad_s = sc.read('embedding_source_${i}.h5')
b8eb50bd397c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
ebi-gxa
parents: 4
diff changeset
84 if adata.n_obs == ad_s.n_obs and all(adata.obs_names == ad_s.obs_names):
b8eb50bd397c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
ebi-gxa
parents: 4
diff changeset
85 #for $j, $e_key in enumerate($copy_e.embedding_keys):
b8eb50bd397c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
ebi-gxa
parents: 4
diff changeset
86 keys_to_copy = (k for k in ad_s.obsm.keys() if "${e_key.contains}" in k)
b8eb50bd397c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
ebi-gxa
parents: 4
diff changeset
87 for k_to_copy in keys_to_copy:
b8eb50bd397c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
ebi-gxa
parents: 4
diff changeset
88 adata.obsm[k_to_copy+"_${i}"] = ad_s.obsm[k_to_copy]
b8eb50bd397c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
ebi-gxa
parents: 4
diff changeset
89 #end for
b8eb50bd397c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
ebi-gxa
parents: 4
diff changeset
90 else:
b8eb50bd397c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
ebi-gxa
parents: 4
diff changeset
91 logging.warning("Embedding source ${i} AnnData file is not compatible to be merged to main AnnData file, different cell names.")
b8eb50bd397c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
ebi-gxa
parents: 4
diff changeset
92 #end for
b8eb50bd397c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
ebi-gxa
parents: 4
diff changeset
93 #end if
b8eb50bd397c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
ebi-gxa
parents: 4
diff changeset
94
10
54f1212d26ac "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 6806d147bfbb52c61d2a15281b69144fad87250a"
ebi-gxa
parents: 9
diff changeset
95 #if $copy_u.default and len($copy_u.uns_keys) > 0:
54f1212d26ac "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 6806d147bfbb52c61d2a15281b69144fad87250a"
ebi-gxa
parents: 9
diff changeset
96 #for $i, $uns_s in enumerate($copy_u.uns_sources):
54f1212d26ac "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 6806d147bfbb52c61d2a15281b69144fad87250a"
ebi-gxa
parents: 9
diff changeset
97 ad_s = sc.read('uns_source_${i}.h5')
54f1212d26ac "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 6806d147bfbb52c61d2a15281b69144fad87250a"
ebi-gxa
parents: 9
diff changeset
98 if adata.n_obs == ad_s.n_obs and all(adata.obs_names == ad_s.obs_names):
54f1212d26ac "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 6806d147bfbb52c61d2a15281b69144fad87250a"
ebi-gxa
parents: 9
diff changeset
99 #for $j, $u_key in enumerate($copy_u.uns_keys):
54f1212d26ac "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 6806d147bfbb52c61d2a15281b69144fad87250a"
ebi-gxa
parents: 9
diff changeset
100 keys_to_copy = (k for k in ad_s.uns.keys() if "${u_key.contains}" in k)
54f1212d26ac "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 6806d147bfbb52c61d2a15281b69144fad87250a"
ebi-gxa
parents: 9
diff changeset
101 for k_to_copy in keys_to_copy:
54f1212d26ac "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 6806d147bfbb52c61d2a15281b69144fad87250a"
ebi-gxa
parents: 9
diff changeset
102 adata.uns[k_to_copy+"_${i}"] = ad_s.uns[k_to_copy]
54f1212d26ac "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 6806d147bfbb52c61d2a15281b69144fad87250a"
ebi-gxa
parents: 9
diff changeset
103 #end for
54f1212d26ac "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 6806d147bfbb52c61d2a15281b69144fad87250a"
ebi-gxa
parents: 9
diff changeset
104 else:
54f1212d26ac "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 6806d147bfbb52c61d2a15281b69144fad87250a"
ebi-gxa
parents: 9
diff changeset
105 logging.warning("Uns source ${i} AnnData file is not compatible to be merged to main AnnData file, different cell names.")
54f1212d26ac "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 6806d147bfbb52c61d2a15281b69144fad87250a"
ebi-gxa
parents: 9
diff changeset
106 #end for
54f1212d26ac "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 6806d147bfbb52c61d2a15281b69144fad87250a"
ebi-gxa
parents: 9
diff changeset
107 #end if
54f1212d26ac "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 6806d147bfbb52c61d2a15281b69144fad87250a"
ebi-gxa
parents: 9
diff changeset
108
9
b8eb50bd397c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
ebi-gxa
parents: 4
diff changeset
109 #if $sanitize_varm:
b8eb50bd397c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
ebi-gxa
parents: 4
diff changeset
110 if hasattr(adata, 'raw') and hasattr(adata.raw, 'X') and hasattr(adata.raw, 'var'):
b8eb50bd397c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
ebi-gxa
parents: 4
diff changeset
111 new_ad = anndata.AnnData(X=adata.raw.X, obs=adata.obs, var=adata.raw.var)
b8eb50bd397c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
ebi-gxa
parents: 4
diff changeset
112 adata.raw = new_ad
b8eb50bd397c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
ebi-gxa
parents: 4
diff changeset
113 #end if
0
086d850271a2 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
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parents:
diff changeset
114
086d850271a2 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
ebi-gxa
parents:
diff changeset
115 if len(qc_vars) > 0:
086d850271a2 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
ebi-gxa
parents:
diff changeset
116 pct_top = [${top_genes}]
086d850271a2 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
ebi-gxa
parents:
diff changeset
117 sc.pp.calculate_qc_metrics(adata, qc_vars=qc_vars, percent_top=pct_top, inplace=True)
086d850271a2 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
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diff changeset
118
086d850271a2 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
ebi-gxa
parents:
diff changeset
119 if 'n_genes' not in adata.obs.columns:
086d850271a2 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
ebi-gxa
parents:
diff changeset
120 sc.pp.filter_cells(adata, min_genes=0)
086d850271a2 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
ebi-gxa
parents:
diff changeset
121 if 'n_counts' not in adata.obs.columns:
086d850271a2 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
ebi-gxa
parents:
diff changeset
122 sc.pp.filter_cells(adata, min_counts=0)
086d850271a2 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
ebi-gxa
parents:
diff changeset
123 if 'n_cells' not in adata.var.columns:
086d850271a2 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
ebi-gxa
parents:
diff changeset
124 sc.pp.filter_genes(adata, min_cells=0)
086d850271a2 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
ebi-gxa
parents:
diff changeset
125 if 'n_counts' not in adata.var.columns:
086d850271a2 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
ebi-gxa
parents:
diff changeset
126 sc.pp.filter_genes(adata, min_counts=0)
086d850271a2 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
ebi-gxa
parents:
diff changeset
127
086d850271a2 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
ebi-gxa
parents:
diff changeset
128 adata.write('output.h5', compression='gzip')
086d850271a2 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
ebi-gxa
parents:
diff changeset
129 </configfile>
086d850271a2 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
ebi-gxa
parents:
diff changeset
130 </configfiles>
086d850271a2 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
ebi-gxa
parents:
diff changeset
131
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
132 <inputs>
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
133 <param name="input_obj_file" argument="input-object-file" type="data" format="h5,h5ad" label="Input object in hdf5 AnnData format"/>
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
134 <expand macro="output_object_params_no_loom"/>
11
f0a29f4b9be9 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit e2ec0706fd62528e5198e3c050d91ab0ee6cd4da"
ebi-gxa
parents: 10
diff changeset
135 <param name="copy_adata_to_raw" type="boolean" label="Copy AnnData to .raw" help="If activated, it will do 'adata.raw = adata'" checked="false"/>
0
086d850271a2 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
ebi-gxa
parents:
diff changeset
136 <repeat name="modifications" title="Change field names in AnnData observations" min="0">
086d850271a2 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
ebi-gxa
parents:
diff changeset
137 <param name="from_obs" type="text" label="Original name" help="Name in observations that you want to change">
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
138 <sanitizer>
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
139 <valid initial="string.printable"/>
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
140 </sanitizer>
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
141 </param>
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
142 <param name="to_obs" type="text" label="New name" help="New name in observations that you want to change"/>
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
143 <param name="keep_original" type="boolean" label="Keep original" help="If activated, it will also keep the original column" checked="false"/>
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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144 </repeat>
086d850271a2 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
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145 <param name="gene_symbols_field" value='index' type="text" label="Gene symbols field in AnnData" help="Field inside var.params where the gene symbols are, normally 'index' or 'gene_symbols'"/>
086d850271a2 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
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146 <repeat name="gene_flags" title="Flag genes that start with these names">
086d850271a2 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
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147 <param name="startswith" type="text" label="Starts with" help="Text that you expect the genes to be flagged to start with, such as 'MT-' for mito genes"/>
086d850271a2 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
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148 <param name="flag" type="text" label="Var name" help="Name of the column in var.names where this boolean flag is stored, for example 'mito' for mitochondrial genes."/>
086d850271a2 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
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149 </repeat>
086d850271a2 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
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150 <param name="top_genes" label="Number of top genes" value='50' help="to calculate percentage of the flagged genes in that number of top genes. Used by sc.pp.calculate_qc_metrics (integer)." type="integer"/>
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b8eb50bd397c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
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151 <conditional name="copy_o">
b8eb50bd397c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
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152 <param name="default" type="boolean" checked="false" label="Copy observations (such as clusters)"/>
b8eb50bd397c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
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153 <when value="true">
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154 <repeat name="obs_keys" title="Keys from obs to copy" help="will copy all obs keys in the given AnnData object to the main AnnData object. Make sure to use AnnData objects that are compatible in terms of genes, cells and expression data. You can use this to copy clusters. Uns elements with the same name will be also transferred." min="1">
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b8eb50bd397c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
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155 <param name="contains" type="text" label="Key contains" help="Keys to be copied need to contain the text set here."/>
b8eb50bd397c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
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156 </repeat>
b8eb50bd397c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
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157 <param name="obs_sources" type="data" label="AnnData objects with obs to copy" help="Extracts obs (such as clusters) from these AnnData objects and merges them into the main input. Make sure to use AnnData objects that are compatible in terms of genes, cells and expression data." format="h5,h5ad" multiple="true"/>
b8eb50bd397c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
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158 <!-- <param name="check_o" type="boolean" label="Check compatibility" help="checks if the provided AnnData objects are compatible (same genes and cells) for merging." checked="true"/> -->
b8eb50bd397c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
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159 </when>
b8eb50bd397c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
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160 <when value="false"/>
b8eb50bd397c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
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161 </conditional>
b8eb50bd397c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
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162 <conditional name="copy_e">
b8eb50bd397c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
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163 <param name="default" type="boolean" checked="false" label="Copy embeddings (such as UMAP, tSNE)"/>
b8eb50bd397c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
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164 <when value="true">
b8eb50bd397c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
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165 <repeat name="embedding_keys" title="Keys from embeddings to copy" help="will copy all embedding keys in the given AnnData object to the main AnnData object. Make sure to use AnnData objects that are compatible in terms of genes, cells and expression data. You can use this to copy tSNE, UMAP, etc." min="1">
b8eb50bd397c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
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166 <param name="contains" type="text" label="Key contains" help="Keys to be copied need to contain the text set here."/>
b8eb50bd397c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
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167 </repeat>
b8eb50bd397c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
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168 <param name="embedding_sources" type="data" label="AnnData objects with embeddings to copy" help="Extracts embeddings (tSNE, UMAP) from these AnnData objects and merges them into the main input. Make sure to use AnnData objects that are compatible in terms of genes, cells and expression data." format="h5,h5ad" multiple="true"/>
b8eb50bd397c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
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169 <!-- <param name="check_e" type="boolean" label="Check compatibility" help="checks if the provided AnnData objects are compatible (same genes and cells) for merging." checked="true"/> -->
b8eb50bd397c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
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170 </when>
b8eb50bd397c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
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171 <when value="false"/>
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172 </conditional>
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173 <conditional name="copy_u">
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174 <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"
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175 <when value="true">
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176 <repeat name="uns_keys" title="Keys from uns to copy" help="will copy all uns keys in the given AnnData object to the main AnnData object. Make sure to use AnnData objects that are compatible in terms of genes, cells and expression data. You can use this to copy rank_genes_groups for instance." min="1">
54f1212d26ac "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 6806d147bfbb52c61d2a15281b69144fad87250a"
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177 <param name="contains" type="text" label="Key contains" help="Keys to be copied need to contain the text set here."/>
54f1212d26ac "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 6806d147bfbb52c61d2a15281b69144fad87250a"
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178 </repeat>
54f1212d26ac "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 6806d147bfbb52c61d2a15281b69144fad87250a"
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179 <param name="uns_sources" type="data" label="AnnData objects with uns to copy" help="Extracts uns (such as ranked_genes_groups) from these AnnData objects and merges them into the main input. Make sure to use AnnData objects that are compatible in terms of genes, cells and expression data." format="h5,h5ad" multiple="true"/>
54f1212d26ac "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 6806d147bfbb52c61d2a15281b69144fad87250a"
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180 </when>
54f1212d26ac "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 6806d147bfbb52c61d2a15281b69144fad87250a"
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181 </conditional>
9
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182 <param name="sanitize_varm" type="boolean" checked="false" label="Sanitise any null raw.varm objects if any" help="This might be relevant for interfacing with newer versions of AnnData, that might complain if .raw includes a varm null object."/>
0
086d850271a2 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
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183 </inputs>
086d850271a2 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
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184
086d850271a2 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
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185 <outputs>
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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186 <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
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187 </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
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188
086d850271a2 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
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189 <tests>
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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190 <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
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191 <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
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192 <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
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193 <param name="color_by" value="louvain"/>
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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"
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194 <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
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195 </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
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196 </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
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197
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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198 <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
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199 =============================
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 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
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201 =============================
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
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 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
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204
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 * Change observation fields, mostly for downstreaming processes convenience. Multiple fields can be changed as one.
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 * Flag genes that start with a certain text: useful for flagging mitochondrial, spikes or other groups of genes.
086d850271a2 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
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207 * For the flags created, calculates qc metrics (pct_<flag>_counts).
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 * Calculates `n_genes`, `n_counts` for cells and `n_cells`, `n_counts` for genes.
086d850271a2 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
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209 * 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"
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210 * Copy from a set of compatible AnnData objects (same cells and genes):
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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211 * Observations, such as clustering results.
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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212 * Embeddings, such as tSNE or UMAPs.
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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213 * 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
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214
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 This functionality will probably be added in the future to a larger package.
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 ]]></help>
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 <expand macro="citations"/>
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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218 </tool>