Mercurial > repos > ebi-gxa > anndata_ops

annotate anndata_operations.xml @ 1:339d205356c6 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 1d069e25584e436d7628694cb8853a15f1f85604
author ebi-gxa
date Wed, 20 Nov 2019 05:15:30 -0500
parents 086d850271a2
children ba18139e7400
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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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2 <tool id="anndata_ops" name="AnnData Operations" version="0.0.1+galaxy0">
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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"/>
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8 <command detect_errors="exit_code"><![CDATA[
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9 ln -s '${input_obj_file}' input.h5 &&
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10 python $operations
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11 ]]></command>
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12 <configfiles>
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13 <configfile name="operations">
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14 import scanpy as sc
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15 import logging
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17 adata = sc.read('input.h5')
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19 gene_name = '${gene_symbols_field}'
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20 qc_vars = list()
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22 #for $i, $s in enumerate($modifications)
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23 adata.obs['${s.to_obs}'] = adata.obs['${s.from_obs}']
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24 #end for
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26 gene_names = getattr(adata.var, gene_name)
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28 #for $i, $flag in enumerate($gene_flags)
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29 k_cat = gene_names.str.startswith('${flag.startswith}')
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30 if k_cat.sum() > 0:
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31 adata.var['${flag.flag}'] = k_cat
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32 qc_vars.append('${flag.flag}')
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33 else:
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34 logging.warning('No genes starting with {} found, skip calculating expression of {} genes'.format('${flag.startswith}', '${flag.flag}'))
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35 #end for
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38 if len(qc_vars) > 0:
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39 pct_top = [${top_genes}]
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40 sc.pp.calculate_qc_metrics(adata, qc_vars=qc_vars, percent_top=pct_top, inplace=True)
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41
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42 if 'n_genes' not in adata.obs.columns:
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43 sc.pp.filter_cells(adata, min_genes=0)
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44 if 'n_counts' not in adata.obs.columns:
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45 sc.pp.filter_cells(adata, min_counts=0)
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46 if 'n_cells' not in adata.var.columns:
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47 sc.pp.filter_genes(adata, min_cells=0)
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48 if 'n_counts' not in adata.var.columns:
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49 sc.pp.filter_genes(adata, min_counts=0)
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50
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51 adata.write('output.h5', compression='gzip')
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52 </configfile>
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53 </configfiles>
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54
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55 <inputs>
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56 <param name="input_obj_file" argument="input-object-file" type="data" format="h5" label="Input object in hdf5 AnnData format"/>
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57 <repeat name="modifications" title="Change field names in AnnData observations" min="0">
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58 <param name="from_obs" type="text" label="Original name" help="Name in observations that you want to change">
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59 <sanitizer>
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60 <valid initial="string.printable"/>
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61 </sanitizer>
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62 </param>
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63 <param name="to_obs" type="text" label="New name" help="New name in observations that you want to change"/>
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64 </repeat>
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65 <param name="gene_symbols_field" value='index' type="text" label="Gene symbols field in AnnData" help="Field inside var.params where the gene symbols are, normally 'index' or 'gene_symbols'"/>
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66 <repeat name="gene_flags" title="Flag genes that start with these names">
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67 <param name="startswith" type="text" label="Starts with" help="Text that you expect the genes to be flagged to start with, such as 'MT-' for mito genes"/>
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68 <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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69 </repeat>
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70 <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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71 </inputs>
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72
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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73 <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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74 <data name="output" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: anndata with metadata changes."/>
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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75 </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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76
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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77 <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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78 <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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79 <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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80 <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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81 <param name="color_by" value="louvain"/>
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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82 <output name="output" file="output.h5" ftype="h5" compare="sim_size"/>
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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83 </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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84 </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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85
086d850271a2 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
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86 <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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87 =============================
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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88 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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89 =============================
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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90
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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91 Performs the following operations:
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92
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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93 * Change observation fields, mostly for downstreaming processes convenience. Multiple fields can be changed as one.
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94 * 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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95 * For the flags created, calculates qc metrics (pct_<flag>_counts).
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96 * Calculates `n_genes`, `n_counts` for cells and `n_cells`, `n_counts` for genes.
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97 * For top <N> genes specified, calculate qc metrics (pct_counts_in_top_<N>_genes).
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98
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99 This functionality will probably be added in the future to a larger package.
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100 ]]></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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101 <expand macro="citations"/>
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102 </tool>