annotate scanpy_macros2.xml @ 14:ff6decc0f432 draft default tip

planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ee197a80b2d591c393e1662854bc119b2ecab11e-dirty
author ebi-gxa
date Tue, 27 Feb 2024 16:43:26 +0000
parents e9788746e0f6
children
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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 <macros>
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ff6decc0f432 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ee197a80b2d591c393e1662854bc119b2ecab11e-dirty
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2 <token name="@TOOL_VERSION@">1.9.3</token>
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3 <token name="@HELP@">More information can be found at https://scanpy.readthedocs.io</token>
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ff6decc0f432 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ee197a80b2d591c393e1662854bc119b2ecab11e-dirty
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4 <token name="@PROFILE@">20.09</token>
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5 <token name="@VERSION_HISTORY@"><![CDATA[
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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6 **Version history**
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ff6decc0f432 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ee197a80b2d591c393e1662854bc119b2ecab11e-dirty
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7 1.9.301+galaxy0: Moves to Scanpy 1.9.3
ff6decc0f432 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ee197a80b2d591c393e1662854bc119b2ecab11e-dirty
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8
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3ba9371733a2 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 6c9d530aa653101e9e21804393ec11f38cddf027-dirty
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9 1.8.1+galaxy9: Fixes version label to get versions sorted properly on Galaxy (equivalent to 1.8.1+3+galaxy0). In addition, adds ability to make fields unique in AnnData operations,
3ba9371733a2 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 6c9d530aa653101e9e21804393ec11f38cddf027-dirty
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10 adds additional handler on Scrubblet for workflows convenience, enables Scanpy tools to avoid outputing AnnData/matrix files when not required.
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11
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94697510d55f "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9ea121884e1aecd2ee66a0686057cb3ed904b9eb-dirty"
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12 1.8.1+3+galaxy0: Upate to scanpy-scripts 1.1.3 (running scanpy ==1.8.1), including a fix to MTX output and a bugfix for the Scrublet wrapper.
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65c9c962b133 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 85dcbc74a856bd55865bd372601de39af72dfd29-dirty"
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14 1.8.1+2+galaxy0: Upate to scanpy-scripts 1.1.2 (running scanpy ==1.8.1), including improved boolean handling for mito etc.
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65c9c962b133 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 85dcbc74a856bd55865bd372601de39af72dfd29-dirty"
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16 1.8.1+1+galaxy0: Upate to scanpy-scripts 1.1.1 build 1 (running scanpy ==1.8.1), including improved Scrublet integration with batch handling.
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4951ff9f43db "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
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18 1.8.1+galaxy0: Upate to scanpy-scripts 1.0.1 (running scanpy ==1.8.1), including Scrublet integration.
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b202e078a83f "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 858a2398f1dbbd60110867c593c237358c794615-dirty"
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20 1.7.2+galaxy0: Upate to scanpy-scripts 0.3.3 (running scanpy ==1.7.2) to incorporate fix for object output from PAGA plotting, to allow PAGA init of FDG.
b202e078a83f "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 858a2398f1dbbd60110867c593c237358c794615-dirty"
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21
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22 1.6.0+galaxy0: Update to scanpy-scripts 0.2.13 (running scanpy ==1.6.0) to incorporate new options, code simplifications, and batch integration methods. Jonathan Manning, Expression Atlas team https://www.ebi.ac.uk/gxa/home at
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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23 EMBL-EBI https://www.ebi.ac.uk/
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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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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25 1.4.3+galaxy10: Update to scanpy-scripts 0.2.10 (running scanpy ==1.4.3) to address bugfixes in run-pca.
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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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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27 1.4.3+galaxy10: Update to scanpy-scripts 0.2.9 (running scanpy ==1.4.3) to address bugfixes in find-variable-genes.
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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29 1.4.3+galaxy10: Use profile 18.01 for modules.
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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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31 1.4.3+galaxy6: Update to scanpy-scripts 0.2.8 (running scanpy ==1.4.3) and wider compatibility with other Galaxy modules. Bug fixes in filtering and plotting improvements.
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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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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33 1.4.3+galaxy0: Update to scanpy-scripts 0.2.5 (running scanpy ==1.4.3).
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35 1.4.2+galaxy0: Update to scanpy-scripts 0.2.4 (requires scanpy >=1.4.2).
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37 1.3.2+galaxy1: Normalise-data and filter-genes: Exposes ability to output 10x files.
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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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39 1.3.2+galaxy0: Initial contribution. Ni Huang and Pablo Moreno, Expression Atlas team https://www.ebi.ac.uk/gxa/home at
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40 EMBL-EBI https://www.ebi.ac.uk/ and Teichmann Lab at Wellcome Sanger Institute.
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41 ]]></token>
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42 <token name="@INPUT_OPTS@">
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43 --input-format '${input_format}' input.h5
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44 </token>
6
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45 <token name="@SAVE_MATRIX_OPTS@">
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46 #if $save_raw
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47 --save-raw
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48 #end if
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49 #if $save_layer
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50 --save-layer ${save_layer}
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51 #end if
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52 </token>
0
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53 <token name="@OUTPUT_OPTS@">
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54 #if str($output_format).startswith('anndata')
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55 --show-obj stdout --output-format anndata output.h5
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56 #else
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57 --show-obj stdout --output-format loom output.h5
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58 #end if
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59 </token>
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60 <token name="@PLOT_OPTS@">
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61 #if $fig_title
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62 --title '${fig_title}'
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63 #end if
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64 --fig-size '${fig_size}'
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65 --fig-dpi ${fig_dpi}
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66 --fig-fontsize ${fig_fontsize}
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67 ${fig_frame}
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68 ./output.png
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69 </token>
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70 <token name="@EXPORT_MTX_OPTS@">${export_mtx}</token>
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71
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72 <xml name="requirements">
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73 <requirements>
14
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74 <requirement type="package" version="1.9.301">scanpy-scripts</requirement>
0
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75 <yield/>
14
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76 <!-- use this format when you want to test against provisional conda artifacts
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77 <container type="docker">quay.io/biocontainers/scanpy-scripts:1.9.301 pyhdfd78af_0</container>
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78 -->
0
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79 </requirements>
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80 </xml>
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81
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82 <xml name="citations">
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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83 <citations>
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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84 <yield />
14
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85 <citation type="doi">10.1038/s41592-021-01102-w</citation>
0
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86 <citation type="doi">10.1186/s13059-017-1382-0</citation>
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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87 <citation type="bibtex">
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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88 @misc{githubscanpy-scripts,
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89 author = {Ni Huang, EBI Gene Expression Team},
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90 year = {2018},
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91 title = {Scanpy-scripts: command line interface for Scanpy},
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92 publisher = {GitHub},
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93 journal = {GitHub repository},
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94 url = {https://github.com/ebi-gene-expression-group/scanpy-scripts},
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95 }</citation>
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96 <citation type="doi">10.1101/2020.04.08.032698</citation>
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97 </citations>
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98 </xml>
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99
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100 <xml name="input_object_params">
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101 <param name="input_obj_file" argument="input-object-file" type="data" format="h5,h5ad" label="Input object in AnnData/Loom format"/>
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102 <param name="input_format" argument="--input-format" type="select" label="Format of input object">
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103 <option value="anndata" selected="true">AnnData format hdf5</option>
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104 <option value="loom">Loom format hdf5</option>
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105 </param>
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106 </xml>
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107
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108 <xml name="output_object_params">
12
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109 <param name="output_format" argument="--output-format" type="select" label="Format of output object" help="AnnData or Loom. Legacy 'h5' datatypes are useful for interacting with older tools. Choosing 'No packaged matrix output' is useful for cases where auxiliary files are generated (like in marker genes). Do not use when there are no other output files, as the tool will generate no output in Galaxy then.">
0
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110 <option value="anndata_h5ad" selected="true">AnnData format</option>
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111 <option value="anndata">AnnData format (h5 for older versions)</option>
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112 <option value="loom">Loom format</option>
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113 <option value="loom_legacy">Loom format (h5 for older versions)</option>
12
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114 <option value="no_matrix_output">No packaged matrix output</option>
0
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115 </param>
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116 </xml>
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117
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118 <xml name="output_object_params_no_loom">
12
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119 <param name="output_format" argument="--output-format" type="select" label="Format of output object" help="Legacy 'h5' datatypes are useful for interacting with older tools. Choosing 'No packaged matrix output' is useful for cases where auxiliary files are generated (like in marker genes). Do not use when there are no other output files, as the tool will generate no output in Galaxy then.">
0
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120 <option value="anndata_h5ad" selected="true">AnnData format</option>
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121 <option value="anndata">AnnData format (h5 for older versions)</option>
12
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122 <option value="no_matrix_output">No packaged matrix output (useful for cases where auxiliary files are generated)</option>
0
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123 </param>
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124 </xml>
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125
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126 <xml name="output_data_obj_no_loom" token_description="operation">
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127 <data name="output_h5ad" format="h5ad" from_work_dir="output.h5" label="${tool.name} on ${on_string}: @DESCRIPTION@ AnnData">
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128 <filter>output_format == 'anndata_h5ad'</filter>
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129 </data>
12
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130 <data name="output_h5" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: @DESCRIPTION@ AnnData (h5)">
0
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131 <filter>output_format == 'anndata'</filter>
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132 </data>
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133 </xml>
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134
873449082a29 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 62f47287c7e8449c59a1f1f454852ddc669b1b1e-dirty"
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135 <xml name="output_data_obj" token_description="operation">
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136 <data name="output_h5ad" format="h5ad" from_work_dir="output.h5" label="${tool.name} on ${on_string}: @DESCRIPTION@ AnnData">
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137 <filter>output_format == 'anndata_h5ad'</filter>
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138 </data>
12
3ba9371733a2 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 6c9d530aa653101e9e21804393ec11f38cddf027-dirty
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139 <data name="output_h5" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: @DESCRIPTION@ AnnData (h5)">
0
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140 <filter>output_format == 'anndata'</filter>
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141 </data>
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142 <data name="output_loom_legacy" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: @DESCRIPTION@ Loom">
873449082a29 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 62f47287c7e8449c59a1f1f454852ddc669b1b1e-dirty"
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143 <filter>output_format == 'loom_legacy'</filter>
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144 </data>
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3ba9371733a2 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 6c9d530aa653101e9e21804393ec11f38cddf027-dirty
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145 <data name="output_loom" format="loom" from_work_dir="output.h5" label="${tool.name} on ${on_string}: @DESCRIPTION@ Loom (h5)">
0
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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146 <filter>output_format == 'loom'</filter>
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147 </data>
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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148 </xml>
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149
6
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150 <xml name="save_matrix_params">
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151 <param name="save_raw" argument="--save-raw" type="boolean" truevalue="yes" falsevalue="no" checked="false"
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152 label="Save adata to adata.raw before processing?" />
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153 <param name="save_layer" argument="--save-layer" type="text" optional="true"
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154 label="Save adata.X to the specified layer before processing."/>
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155 </xml>
5bb009f95e03 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
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156
0
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157 <xml name="output_plot_params">
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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158 <param name="fig_title" argument="--title" type="text" label="Figure title"/>
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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159 <param name="fig_size" argument="--fig-size" type="text" value="4,4" label="Figure size as 'width,height', e.g, '7,7'"/>
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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160 <param name="fig_dpi" argument="--fig-dpi" type="integer" min="1" value="80" label="Figure dpi"/>
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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161 <param name="fig_fontsize" argument="--fig-fontsize" type="integer" min="0" value="10" label="Figure font size"/>
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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162 <param name="fig_frame" type="boolean" truevalue="--frameon" falsevalue="--frameoff" checked="false"
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163 label="Show plot frame"/>
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164 </xml>
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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165
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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166 <xml name="export_mtx_params">
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167 <param name="export_mtx" argument="--export-mtx" type="boolean" truevalue="--export-mtx ./" falsevalue="" checked="false" label="Save to 10x mtx format" help="If enabled, it will generate in addition to the main output in Loom or AnnData an export in 10x format."/>
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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168 </xml>
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169
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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170 <xml name="export_mtx_outputs">
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171 <data name="matrix_10x" format="txt" from_work_dir="matrix.mtx" label="${tool.name} on ${on_string}: 10x matrix">
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172 <filter>export_mtx</filter>
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173 </data>
873449082a29 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 62f47287c7e8449c59a1f1f454852ddc669b1b1e-dirty"
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174 <data name="genes_10x" format="tsv" from_work_dir="genes.tsv" label="${tool.name} on ${on_string}: 10x genes">
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175 <filter>export_mtx</filter>
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176 </data>
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177 <data name="barcodes_10x" format="tsv" from_work_dir="barcodes.tsv" label="${tool.name} on ${on_string}: 10x barcodes">
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178 <filter>export_mtx</filter>
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179 </data>
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180 </xml>
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181 </macros>