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annotate scanpy-integrate-mnn.xml @ 13:e9788746e0f6 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 162313dc6ba68efc5003b1bd9b71a40aec87d826-dirty
author ebi-gxa
date Fri, 13 Oct 2023 14:08:05 +0000
parents 3ba9371733a2
children ff6decc0f432
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873449082a29 "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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1 <?xml version="1.0" encoding="utf-8"?>
13
e9788746e0f6 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 162313dc6ba68efc5003b1bd9b71a40aec87d826-dirty
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2 <tool id="scanpy_integrate_mnn" name="Scanpy MNN" version="@TOOL_VERSION@+galaxy93" profile="@PROFILE@">
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3 <description>correct batch effects by matching mutual nearest neighbors</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 #if $batch_key
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10 ln -s '${input_obj_file}' input.h5 &&
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11 PYTHONIOENCODING=utf-8 scanpy-integrate mnn
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12 --batch-key '${batch_key}'
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13 #if $batch_layer
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14 --batch-layer '${batch_layer}'
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15 #end if
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16 #if $key_added
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17 --key-added '${key_added}'
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18 #end if
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19 #if $var_subset
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20 #set var_subsets = ' '.join(["--var-subset '{name}' '{values}'".format(**$v) for $v in $var_subset])
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21 ${var_subsets}
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22 #if $settings.default == "false"
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23 #if $settings.n_neighbors
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24 --n-neighbors '${settings.n_neighbors}'
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25 #end if
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26 #if $settings.sigma
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27 --sigma '${settings.sigma}'
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28 #end if
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29 #if not $settings.cos_norm_in
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30 ${settings.cos_norm_in}
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31 #end if
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32 #if $settings.svd_dim
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33 --svd-dim '${settings.svd_dim}'
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34 #end if
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35 #if not $settings.var_adj
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36 ${settings.var_adj}
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37 #end if
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38 #if $settings.compute_angle
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39 ${settings.compute_angle}
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40 #end if
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41 #if $settings.svd_mode
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42 --svd-mode '${settings.svd_mode}'
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43 #end if
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44 #end if
6
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45 @SAVE_MATRIX_OPTS@
0
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46 #end if
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47 @INPUT_OPTS@
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48 @OUTPUT_OPTS@
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49 #else
1
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50 echo "No batch variables passed, simply passing original input as output unchanged." && cp '${input_obj_file}' output.h5
0
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51 #end if
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52 ]]></command>
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53
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54 <inputs>
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55 <expand macro="input_object_params"/>
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56 <expand macro="output_object_params"/>
6
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57 <expand macro="save_matrix_params"/>
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58 <param name="batch_key" type="text" argument="--batch-key" label="The name of the column in adata.obs that differentiates among experiments/batches.">
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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="batch_layer" type="text" argument="--batch-layer" label="Layer to batch correct. By default corrects the contents of .X.">
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64 <sanitizer>
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65 <valid initial="string.printable"/>
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66 </sanitizer>
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67 </param>
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68 <param name="key_added" argument="--key-added" type="text" optional="true" label="Key under which to add the computed results." help="By default a new layer will be created called 'mnn', 'mnn_{layer}' or 'mnn_{layer}_{key_added}' where those parameters were specified. A value of 'X' causes batch-corrected values to overwrite the original content of .X."/>
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69 <repeat name="var_subset" title="The subset of vars (list of str) to be used when performing MNN correction" min="0">
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70 <param name="name" type="text" value="" label="Name of the categorical variable to filter on" help="e.g. 'highly_variable'"/>
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71 <param name="values" type="text" value="" label="Category or comma-separated list of categories" help="e.g. 'True'"/>
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72 </repeat>
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73 <conditional name="settings">
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74 <param name="default" type="boolean" checked="true" label="Use programme defaults"/>
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75 <when value="true"/>
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76 <when value="false">
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77 <param name="n_neighbors" argument="--n-neighbors" type="integer" value="20" label="Number of mutual nearest neighbors."/>
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78 <param name="sigma" argument="--sigma" type="float" value="1.0" label="Sigma" help="The bandwidth of the Gaussian smoothing kernel used to compute the correction vectors." />
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79 <param name="cos_norm_in" argument="--no-cos-norm-in" type="boolean" truevalue="" falsevalue="--no-cos-norm-in" checked="True"
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80 label="Perform cosine normalization prior to computing corrected expression values?" />
873449082a29 "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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81 <param name="svd_dim" argument="--svd-dim" type="integer" optional="true" label="Number of dimensions to use for summarizing biological substructure within each batch." help="If not set, biological components will not be removed from the correction vectors."/>
873449082a29 "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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82 <param name="var_adj" argument="--no-var-adj" type="boolean" truevalue="" falsevalue="--no-var-adj" checked="True"
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83 label="Adjust variance of the correction vectors?" help="Note this step takes most computing time." />
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84 <param name="compute_angle" argument="--compute-angle" type="boolean" truevalue="--compute-angle" falsevalue="" checked="False"
873449082a29 "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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85 label="Compute the angle between each cell’s correction vector and the biological subspace of the reference batch?" />
873449082a29 "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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86 <param name="svd_mode" argument="--svd-mode" type="select" label="SVD mode" help="'svd' computes SVD using a non-randomized SVD-via-ID algorithm, while 'rsvd' uses a randomized version. 'irlb' performs truncated SVD by implicitly restarted Lanczos bidiagonalization (forked from https://github.com/airysen/irlbpy)." >
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87 <option value="rsvd" selected="true">rsvd</option>
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88 <option value="svd">svd</option>
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89 <option value="irlb">irlb</option>
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90 </param>
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91 </when>
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92 </conditional>
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93 </inputs>
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94
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95 <outputs>
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96 <expand macro="output_data_obj" description="Batch-corrected for ${batch_key}"/>
873449082a29 "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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97 </outputs>
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98
5
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99 <!--<tests>
0
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100 <test>
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101 <param name="input_obj_file" value="find_cluster.h5"/>
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102 <param name="input_format" value="anndata"/>
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103 <param name="output_format" value="anndata"/>
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104 <param name="batch_key" value="louvain"/>
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105 <output name="output_h5" file="mnn.h5" ftype="h5" compare="sim_size"/>
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106 </test>
1
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107 <test>
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108 <param name="input_obj_file" value="find_cluster.h5"/>
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109 <param name="input_format" value="anndata"/>
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110 <param name="output_format" value="anndata"/>
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111 <output name="output_h5" file="mnn_copy.h5" ftype="h5" compare="sim_size"/>
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112 </test>
5
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113 </tests>-->
0
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114
873449082a29 "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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115 <help><![CDATA[
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116 .. class:: infomark
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117
873449082a29 "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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118 **What it does**
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119
873449082a29 "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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120 Corrects for batch effects by fitting linear models, gains statistical power via an EB framework where information is borrowed across genes.
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121
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122 @HELP@
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123
873449082a29 "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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124 @VERSION_HISTORY@
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125 ]]></help>
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126 <expand macro="citations"/>
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127 </tool>