Mercurial > repos > ebi-gxa > scanpy_run_pca

comparison scanpy_macros2.xml @ 26:4428dba93375 draft default tip

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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 ee197a80b2d591c393e1662854bc119b2ecab11e-dirty
author ebi-gxa
date Tue, 27 Feb 2024 16:43:36 +0000
parents f0eecf608220
children
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25:f0eecf608220 26:4428dba93375
1 <macros> 1 <macros>
2 <token name="@TOOL_VERSION@">1.8.1</token> 2 <token name="@TOOL_VERSION@">1.9.3</token>
3 <token name="@HELP@">More information can be found at https://scanpy.readthedocs.io</token> 3 <token name="@HELP@">More information can be found at https://scanpy.readthedocs.io</token>
4 <token name="@PROFILE@">18.01</token> 4 <token name="@PROFILE@">20.09</token>
5 <token name="@VERSION_HISTORY@"><![CDATA[ 5 <token name="@VERSION_HISTORY@"><![CDATA[
6 **Version history** 6 **Version history**
7 1.9.301+galaxy0: Moves to Scanpy 1.9.3
8
7 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, 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,
8 adds additional handler on Scrubblet for workflows convenience, enables Scanpy tools to avoid outputing AnnData/matrix files when not required. 10 adds additional handler on Scrubblet for workflows convenience, enables Scanpy tools to avoid outputing AnnData/matrix files when not required.
9 11
10 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. 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.
11 13
67 </token> 69 </token>
68 <token name="@EXPORT_MTX_OPTS@">${export_mtx}</token> 70 <token name="@EXPORT_MTX_OPTS@">${export_mtx}</token>
69 71
70 <xml name="requirements"> 72 <xml name="requirements">
71 <requirements> 73 <requirements>
72 <requirement type="package" version="1.1.6">scanpy-scripts</requirement> 74 <requirement type="package" version="1.9.301">scanpy-scripts</requirement>
73 <yield/> 75 <yield/>
76 <!-- use this format when you want to test against provisional conda artifacts
77 <container type="docker">quay.io/biocontainers/scanpy-scripts:1.9.301 pyhdfd78af_0</container>
78 -->
74 </requirements> 79 </requirements>
75 </xml> 80 </xml>
76 81
77 <xml name="citations"> 82 <xml name="citations">
78 <citations> 83 <citations>
79 <yield /> 84 <yield />
85 <citation type="doi">10.1038/s41592-021-01102-w</citation>
80 <citation type="doi">10.1186/s13059-017-1382-0</citation> 86 <citation type="doi">10.1186/s13059-017-1382-0</citation>
81 <citation type="bibtex"> 87 <citation type="bibtex">
82 @misc{githubscanpy-scripts, 88 @misc{githubscanpy-scripts,
83 author = {Ni Huang, EBI Gene Expression Team}, 89 author = {Ni Huang, EBI Gene Expression Team},
84 year = {2018}, 90 year = {2018},
86 publisher = {GitHub}, 92 publisher = {GitHub},
87 journal = {GitHub repository}, 93 journal = {GitHub repository},
88 url = {https://github.com/ebi-gene-expression-group/scanpy-scripts}, 94 url = {https://github.com/ebi-gene-expression-group/scanpy-scripts},
89 }</citation> 95 }</citation>
90 <citation type="doi">10.1101/2020.04.08.032698</citation> 96 <citation type="doi">10.1101/2020.04.08.032698</citation>
91 <citation type="doi">10.1038/s41592-021-01102-w</citation>
92 </citations> 97 </citations>
93 </xml> 98 </xml>
94 99
95 <xml name="input_object_params"> 100 <xml name="input_object_params">
96 <param name="input_obj_file" argument="input-object-file" type="data" format="h5,h5ad" label="Input object in AnnData/Loom format"/> 101 <param name="input_obj_file" argument="input-object-file" type="data" format="h5,h5ad" label="Input object in AnnData/Loom format"/>