Mercurial > repos > ebi-gxa > anndata_ops

annotate anndata_operations.xml @ 10:54f1212d26ac 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 6806d147bfbb52c61d2a15281b69144fad87250a"
author ebi-gxa
date Thu, 11 Jun 2020 13:07:33 -0400
parents b8eb50bd397c
children f0a29f4b9be9
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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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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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2 <tool id="anndata_ops" name="AnnData Operations" version="0.0.3+galaxy0" 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>
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4 <macros>
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5 <import>scanpy_macros2.xml</import>
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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:
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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
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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 $operations
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29 ]]></command>
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30 <configfiles>
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31 <configfile name="operations">
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32 import scanpy as sc
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33 import anndata
b8eb50bd397c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
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34 from numpy import all
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35 import logging
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36
086d850271a2 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
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37 adata = sc.read('input.h5')
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38
086d850271a2 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
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39 gene_name = '${gene_symbols_field}'
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40 qc_vars = list()
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41
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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42 #for $i, $s in enumerate($modifications)
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43 adata.obs['${s.to_obs}'] = adata.obs['${s.from_obs}']
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44 #if not $s.keep_original:
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45 del adata.obs['${s.from_obs}']
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46 #end if
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47 #end for
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48
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49 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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51 #for $i, $flag in enumerate($gene_flags)
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52 k_cat = gene_names.str.startswith('${flag.startswith}')
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53 if k_cat.sum() > 0:
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54 adata.var['${flag.flag}'] = k_cat
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55 qc_vars.append('${flag.flag}')
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56 else:
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57 logging.warning('No genes starting with {} found, skip calculating expression of {} genes'.format('${flag.startswith}', '${flag.flag}'))
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58 #end for
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59
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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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60 #if $copy_o.default and len($copy_o.obs_keys) > 0:
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61 #for $i, $obs_s in enumerate($copy_o.obs_sources):
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62 ad_s = sc.read('obs_source_${i}.h5')
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63 if adata.n_obs == ad_s.n_obs and all(adata.obs_names == ad_s.obs_names):
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64 #for $j, $o_key in enumerate($copy_o.obs_keys):
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65 keys_to_copy = (k for k in ad_s.obs.keys() if "${o_key.contains}" in k)
b8eb50bd397c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
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66 for k_to_copy in keys_to_copy:
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67 adata.obs[[k_to_copy+"_${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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68 if k_to_copy in ad_s.uns.keys():
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69 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"
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70 #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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71 else:
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72 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"
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parents: 4
diff changeset
73 #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
74 #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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parents: 4
diff changeset
75
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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parents: 4
diff changeset
76
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 #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
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78 #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
79 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
80 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
81 #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
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82 keys_to_copy = (k for k in ad_s.obsm.keys() if "${e_key.contains}" in k)
b8eb50bd397c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
ebi-gxa
parents: 4
diff changeset
83 for k_to_copy in keys_to_copy:
b8eb50bd397c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit bcab272f6785d5967b1ec68acf5390ec3ace49fd"
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84 adata.obsm[k_to_copy+"_${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
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85 #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
86 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"
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diff changeset
87 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"
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88 #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
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89 #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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90
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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91 #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"
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92 #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
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diff changeset
93 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"
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94 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"
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95 #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"
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96 keys_to_copy = (k for k in ad_s.uns.keys() if "${u_key.contains}" in k)
54f1212d26ac "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 6806d147bfbb52c61d2a15281b69144fad87250a"
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97 for k_to_copy in keys_to_copy:
54f1212d26ac "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 6806d147bfbb52c61d2a15281b69144fad87250a"
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98 adata.uns[k_to_copy+"_${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"
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99 #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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100 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
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diff changeset
101 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"
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102 #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
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diff changeset
103 #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"
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104
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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105 #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"
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diff changeset
106 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
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diff changeset
107 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"
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diff changeset
108 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
109 #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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110
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
111 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
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diff changeset
112 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
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diff changeset
113 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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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
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115 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
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116 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
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diff changeset
117 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
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diff changeset
118 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
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parents:
diff changeset
119 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
120 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
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parents:
diff changeset
121 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
122 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
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123
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
124 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
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diff changeset
125 </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
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parents:
diff changeset
126 </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
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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
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diff changeset
128 <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
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129 <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
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diff changeset
130 <expand macro="output_object_params_no_loom"/>
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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diff changeset
131 <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
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diff changeset
132 <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
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diff changeset
133 <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
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parents:
diff changeset
134 <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
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parents:
diff changeset
135 </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
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parents:
diff changeset
136 </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
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diff changeset
137 <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"
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diff changeset
138 <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
ebi-gxa
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diff changeset
139 </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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diff changeset
140 <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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parents:
diff changeset
141 <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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diff changeset
142 <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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143 <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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144 </repeat>
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145 <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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146 <conditional name="copy_o">
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147 <param name="default" type="boolean" checked="false" label="Copy observations (such as clusters)"/>
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148 <when value="true">
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149 <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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150 <param name="contains" type="text" label="Key contains" help="Keys to be copied need to contain the text set here."/>
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151 </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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152 <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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153 <!-- <param name="check_o" type="boolean" label="Check compatibility" help="checks if the provided AnnData objects are compatible (same genes and cells) for merging." checked="true"/> -->
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154 </when>
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155 <when value="false"/>
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156 </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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157 <conditional name="copy_e">
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158 <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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159 <when value="true">
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160 <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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161 <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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162 </repeat>
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163 <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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164 <!-- <param name="check_e" type="boolean" label="Check compatibility" help="checks if the provided AnnData objects are compatible (same genes and cells) for merging." checked="true"/> -->
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165 </when>
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166 <when value="false"/>
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167 </conditional>
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168 <conditional name="copy_u">
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169 <param name="default" type="boolean" checked="false" label="Copy uns"/>
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170 <when value="true">
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171 <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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172 <param name="contains" type="text" label="Key contains" help="Keys to be copied need to contain the text set here."/>
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173 </repeat>
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174 <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"/>
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175 </when>
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176 </conditional>
9
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177 <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
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178 </inputs>
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179
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180 <outputs>
2
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181 <expand macro="output_data_obj_no_loom" description="metadata changes on"/>
0
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182 </outputs>
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183
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184 <tests>
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185 <test>
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186 <param name="input_obj_file" value="find_cluster.h5"/>
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187 <param name="input_format" value="anndata"/>
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188 <param name="color_by" value="louvain"/>
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189 <output name="output_h5ad" file="output.h5" ftype="h5" compare="sim_size"/>
0
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190 </test>
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191 </tests>
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192
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193 <help><![CDATA[
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194 =============================
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195 Operations on AnnData objects
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196 =============================
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197
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198 Performs the following operations:
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199
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200 * 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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201 * 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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202 * For the flags created, calculates qc metrics (pct_<flag>_counts).
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203 * Calculates `n_genes`, `n_counts` for cells and `n_cells`, `n_counts` for genes.
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204 * For top <N> genes specified, calculate qc metrics (pct_counts_in_top_<N>_genes).
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205 * 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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206 * Observations, such as clustering results.
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207 * Embeddings, such as tSNE or UMAPs.
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208 * Unstructure annotations, like gene markers.
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209
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210 This functionality will probably be added in the future to a larger package.
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211 ]]></help>
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212 <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
ebi-gxa
parents:
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213 </tool>