| Previous changeset 14:c6611adc8f4a (2023-10-13) |
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Commit message:
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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modified:
scanpy-integrate-combat.xml scanpy_macros2.xml |
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removed:
scanpy_macros.xml |
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| diff -r c6611adc8f4a -r 3c47bc560688 scanpy-integrate-combat.xml --- a/scanpy-integrate-combat.xml Fri Oct 13 14:07:56 2023 +0000 +++ b/scanpy-integrate-combat.xml Tue Feb 27 16:43:23 2024 +0000 |
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| @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="utf-8"?> -<tool id="scanpy_integrate_combat" name="Scanpy ComBat" version="@TOOL_VERSION@+galaxy93" profile="@PROFILE@"> +<tool id="scanpy_integrate_combat" name="Scanpy ComBat" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> <description>adjust expression for variables that might introduce batch effect</description> <macros> <import>scanpy_macros2.xml</import> @@ -8,7 +8,7 @@ <command detect_errors="exit_code"><![CDATA[ #if $batch_key ln -s '${input_obj_file}' input.h5 && - PYTHONIOENCODING=utf-8 scanpy-integrate combat + PYTHONIOENCODING=utf-8 scanpy-cli integrate combat --batch-key '${batch_key}' #if $batch_layer --batch-layer '${batch_layer}' @@ -58,13 +58,17 @@ <param name="input_format" value="anndata"/> <param name="output_format" value="anndata"/> <param name="batch_key" value="louvain"/> - <output name="output_h5" file="combat.h5" ftype="h5" compare="sim_size"/> + <output name="output_h5" ftype="h5"> + <assert_contents> + <has_h5_keys keys="layers/combat"/> + </assert_contents> + </output> </test> <test> <param name="input_obj_file" value="find_cluster.h5"/> <param name="input_format" value="anndata"/> <param name="output_format" value="anndata"/> - <output name="output_h5" file="combat_copy.h5" ftype="h5" compare="sim_size"/> + <output name="output_h5" file="combat_copy.h5" ftype="h5" compare="sim_size" delta_frac="0.1"/> </test> </tests> |
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| diff -r c6611adc8f4a -r 3c47bc560688 scanpy_macros.xml --- a/scanpy_macros.xml Fri Oct 13 14:07:56 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,109 +0,0 @@ -<macros> - <token name="@TOOL_VERSION@">1.3.2</token> - <token name="@HELP@">More information can be found at https://scanpy.readthedocs.io</token> - <token name="@PLOT_OPTS@"> -#if $do_plotting.plot - -P output.png - --projectio $do_plotting.projection - --components $do_plotting.components - #if $do_plotting.color_by - --color-by $do_plotting.color_by - #end if - #if $do_plotting.groups - --group $do_plotting.groups - #end if - #if $do_plotting.use_raw - --use-raw - #end if - #if $do_plotting.palette - --palette $do_plotting.palette - #end if - #if $do_plotting.edges - --edges - #end if - #if $do_plotting.arrows - --arrows - #end if - #if not $do_plotting.sort_order - --no-sort-order - #end if - #if $do_plotting.frameoff - --frameoff - #end if -#end if - </token> - <xml name="requirements"> - <requirements> - <requirement type="package" version="0.0.5">scanpy-scripts</requirement> - <yield/> - </requirements> - </xml> - <token name="@EXPORT_MTX_OPTS@"> - ${export_mtx} - </token> - <token name="@VERSION_HISTORY@"><![CDATA[ -**Version history** - -1.3.2+galaxy1: Normalise-data and filter-genes: Exposes ability to output 10x files. - -1.3.2+galaxy0: Initial contribution. Ni Huang and Pablo Moreno, Expression Atlas team https://www.ebi.ac.uk/gxa/home at -EMBL-EBI https://www.ebi.ac.uk/ and Teichmann Lab at Wellcome Sanger Institute. - ]]></token> - <xml name="citations"> - <citations> - <citation type="doi">10.1186/s13059-017-1382-0</citation> - <citation type="bibtex"> - @misc{githubscanpy-scripts, - author = {Ni Huang, EBI Gene Expression Team}, - year = {2018}, - title = {Scanpy-scripts: command line interface for Scanpy}, - publisher = {GitHub}, - journal = {GitHub repository}, - url = {https://github.com/ebi-gene-expression-group/scanpy-scripts}, - }</citation> - <yield /> - </citations> - </xml> - <xml name="input_object_params"> - <param name="input_obj_file" argument="--input-object-file" type="data" format="h5" label="Input object in hdf5 format"/> - <param name="input_format" argument="--input-format" type="select" label="Format of input object"> - <option value="anndata" selected="true">AnnData format hdf5</option> - <option value="loom">Loom format hdf5, current support is incomplete</option> - </param> - </xml> - <xml name="output_object_params"> - <param name="output_format" argument="--output-format" type="select" label="Format of output object"> - <option value="anndata" selected="true">AnnData format hdf5</option> - <option value="loom">Loom format hdf5, current support is defective</option> - </param> - </xml> - <xml name="output_plot_params"> - <param name="color_by" argument="--color-by" type="text" value="n_genes" label="Color by attributes, comma separated strings"/> - <param name="groups" argument="--groups" type="text" optional="ture" label="Restrict plotting to named groups, comma separated strings"/> - <param name="projection" argument="--projection" type="select" label="Plot projection"> - <option value="2d" selected="true">2D</option> - <option value="3d">3D</option> - </param> - <param name="components" argument="--components" type="text" value="1,2" label="Components to plot, comma separated integers"/> - <param name="palette" argument="--palette" type="text" optional="true" label="Palette"/> - <param name="use_raw" argument="--use-raw" type="boolean" checked="false" label="Use raw attributes if present"/> - <param name="edges" argument="--edges" type="boolean" checked="false" label="Show edges"/> - <param name="arrows" argument="--arrows" type="boolean" checked="false" label="Show arrows"/> - <param name="sort_order" argument="--no-sort-order" type="boolean" checked="true" label="Element with high color-by value plot on top"/> - <param name="frameoff" argument="--frameoff" type="boolean" checked="false" label="Omit frame"/> - </xml> - <xml name="export_mtx_params"> - <param name="export_mtx" argument="--export-mtx" type="boolean" truevalue="--export-mtx ./" falsevalue="" checked="false" label="Save normalised data to 10x format" help="If enabled, it will generate in addition to the main output in Loom or AnnData an export in 10x format of the normalised data."/> - </xml> - <xml name="export_mtx_outputs"> - <data name="matrix_10x" format="txt" from_work_dir="matrix.mtx" label="${tool.name} on ${on_string}: 10x matrix"> - <filter>export_mtx</filter> - </data> - <data name="genes_10x" format="tsv" from_work_dir="genes.tsv" label="${tool.name} on ${on_string}: 10x genes"> - <filter>export_mtx</filter> - </data> - <data name="barcodes_10x" format="tsv" from_work_dir="barcodes.tsv" label="${tool.name} on ${on_string}: 10x barcodes"> - <filter>export_mtx</filter> - </data> - </xml> -</macros> |
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| diff -r c6611adc8f4a -r 3c47bc560688 scanpy_macros2.xml --- a/scanpy_macros2.xml Fri Oct 13 14:07:56 2023 +0000 +++ b/scanpy_macros2.xml Tue Feb 27 16:43:23 2024 +0000 |
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| @@ -1,9 +1,11 @@ <macros> - <token name="@TOOL_VERSION@">1.8.1</token> + <token name="@TOOL_VERSION@">1.9.3</token> <token name="@HELP@">More information can be found at https://scanpy.readthedocs.io</token> - <token name="@PROFILE@">18.01</token> + <token name="@PROFILE@">20.09</token> <token name="@VERSION_HISTORY@"><![CDATA[ **Version history** +1.9.301+galaxy0: Moves to Scanpy 1.9.3 + 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, adds additional handler on Scrubblet for workflows convenience, enables Scanpy tools to avoid outputing AnnData/matrix files when not required. @@ -69,14 +71,18 @@ <xml name="requirements"> <requirements> - <requirement type="package" version="1.1.6">scanpy-scripts</requirement> + <requirement type="package" version="1.9.301">scanpy-scripts</requirement> <yield/> + <!-- use this format when you want to test against provisional conda artifacts + <container type="docker">quay.io/biocontainers/scanpy-scripts:1.9.301 pyhdfd78af_0</container> + --> </requirements> </xml> <xml name="citations"> <citations> <yield /> + <citation type="doi">10.1038/s41592-021-01102-w</citation> <citation type="doi">10.1186/s13059-017-1382-0</citation> <citation type="bibtex"> @misc{githubscanpy-scripts, @@ -88,7 +94,6 @@ url = {https://github.com/ebi-gene-expression-group/scanpy-scripts}, }</citation> <citation type="doi">10.1101/2020.04.08.032698</citation> - <citation type="doi">10.1038/s41592-021-01102-w</citation> </citations> </xml> |