| Previous changeset 0:c608fd80ec15 (2019-04-03) Next changeset 2:af5e4efa9e66 (2019-10-25) |
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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 4846776f55931e176f7e77af7c185ec6fec7d142" |
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modified:
scanpy-find-markers.xml |
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added:
scanpy_macros2.xml |
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| diff -r c608fd80ec15 -r 71668dd2d47b scanpy-find-markers.xml --- a/scanpy-find-markers.xml Wed Apr 03 11:08:46 2019 -0400 +++ b/scanpy-find-markers.xml Mon Sep 16 08:12:48 2019 -0400 |
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| @@ -2,56 +2,59 @@ <tool id="scanpy_find_markers" name="Scanpy FindMarkers" version="@TOOL_VERSION@+galaxy1"> <description>to find differentially expressed genes between groups</description> <macros> - <import>scanpy_macros.xml</import> + <import>scanpy_macros2.xml</import> </macros> <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ ln -s '${input_obj_file}' input.h5 && -PYTHONIOENCODING=utf-8 scanpy-find-markers.py - -i input.h5 - -f '${input_format}' - -o output.h5 - -F '${output_format}' - -n '${n_genes}' - #if $output_markers - --output-text-file output.csv +PYTHONIOENCODING=utf-8 scanpy-find-markers +#if $output_markers + --save output.csv +#end if + --n-genes '${n_genes}' + --groupby '${groupby}' +#if $settings.default == "false" + --method '${settings.method}' + ${settings.use_raw} + ${settings.rankby_abs} + #if $settings.groups + --groups '${settings.groups}' #end if - #if $settings.default == "false" - -g '${settings.groupby}' - --reference '${settings.reference}' - --method '${settings.method}' - #if $settings.use_raw == "false" - --no-raw - #end if - #if $settings.rankby_abs - --rankby_abs - #end if - #if $settings.groups - --groups '${settings.groups}' - #end if + --reference '${settings.reference}' + --filter-params 'min_in_group_fraction:${settings.min_in_group_fraction},max_out_group_fraction:${settings.max_out_group_fraction},min_fold_change:${settings.min_fold_change}' #end if + @INPUT_OPTS@ + @OUTPUT_OPTS@ ]]></command> <inputs> <expand macro="input_object_params"/> <expand macro="output_object_params"/> + <param name="output_markers" type="boolean" checked="true" label="Output markers table in csv format"/> <param name="n_genes" argument="--n-genes" type="integer" value="50" label="Number of top genes to show per group/cluster"/> - <param name="output_markers" type="boolean" checked="true" label="Output markers table in csv format"/> + <param name="groupby" argument="--groupby" type="text" value="louvain" label="The sample grouping/clustering to use."/> <conditional name="settings"> <param name="default" type="boolean" checked="true" label="Use programme defaults"/> <when value="true"/> <when value="false"> - <param name="groupby" argument="--groupby" type="text" value="louvain" label="The sample grouping/clustering to use."/> - <param name="use_raw" type="boolean" checked="true" label="Use raw attribute if present"/> - <param name="reference" argument="--reference" type="text" value="rest" label="If 'rest', compare to the union of the rest of the group/cluster. If a group identifier, compare to that group"/> <param name="method" argument="--method" type="select" label="Method for testing differentially expressed genes"> <option value="t-test_overestim_var" selected="true">t-test with over-estimated variance</option> <option value="t-test">t-test</option> <option value="wilcoxon">wilcoxon test, currently broken don't use</option> <option value="logreg">logistic regression</option> </param> - <param name="rankby_abs" argument="--rankby_abs" type="boolean" checked="false" label="Rank by absolute value of the scores instead of the scores"/> + <param name="use_raw" type="boolean" truevalue="--use-raw" falsevalue="--no-raw" checked="true" + label="Use raw attribute if present"/> + <param name="rankby_abs" argument="--rankby_abs" type="boolean" truevalue="--rankby-abs" falsevalue="" checked="false" + label="Rank by absolute value of the scores instead of the scores"/> <param name="groups" argument="--groups" optional="true" type="text" label="Subset of groups/clusters to which comparisons shell be restricted."/> + <param name="reference" argument="--reference" type="text" value="rest" label="If 'rest', compare to the union of the rest of the group/cluster. If a group identifier, compare to that group"/> + <param name="min_in_group_fraction" type="float" min="0.0" max="1.0" value="0.25" label="Minimum in-group fraction" + help="Post-test filtering to only keep genes expressed in at least this fraction of cells in the test group."/> + <param name="max_out_group_fraction" type="float" min="0.0" max="1.0" value="0.5" label="Maximum out-group fraction" + help="Post-test filtering to only keep genes expressed in at most this fraction of cells in the reference group."/> + <param name="min_fold_change" type="float" value="2" label="Minimum fold change" + help="Post-test filtering to only keep genes with at least this fold change of expression relative to the reference group."/> </when> </conditional> </inputs> |
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| diff -r c608fd80ec15 -r 71668dd2d47b scanpy_macros2.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scanpy_macros2.xml Mon Sep 16 08:12:48 2019 -0400 |
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| @@ -0,0 +1,94 @@ +<macros> + <token name="@TOOL_VERSION@">1.4.2</token> + <token name="@HELP@">More information can be found at https://scanpy.readthedocs.io</token> + <token name="@VERSION_HISTORY@"><![CDATA[ +**Version history** + +1.4.2+galaxy0: Update to scanpy-scripts 0.2.4 (requires scanpy >=1.4.2). + +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> + <token name="@INPUT_OPTS@"> + --input-format '${input_format}' input.h5 + </token> + <token name="@OUTPUT_OPTS@"> + --show-obj stdout --output-format '${output_format}' output.h5 + </token> + <token name="@PLOT_OPTS@"> +#if $fig_title + --title '${fig_title}' +#end if + --fig-size '${fig_size}' + --fig-dpi ${fig_dpi} + --fig-fontsize ${fig_fontsize} + ${fig_frame} + ./output.png + </token> + <token name="@EXPORT_MTX_OPTS@">${export_mtx}</token> + + <xml name="requirements"> + <requirements> + <requirement type="package" version="0.2.4.post4">scanpy-scripts</requirement> + <yield/> + </requirements> + </xml> + + <xml name="citations"> + <citations> + <yield /> + <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> + </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</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</option> + </param> + </xml> + + <xml name="output_plot_params"> + <param name="fig_title" argument="--title" type="text" label="Figure title"/> + <param name="fig_size" argument="--fig-size" type="text" value="4,4" label="Figure size as 'width,height', e.g, '7,7'"/> + <param name="fig_dpi" argument="--fig-dpi" type="integer" min="1" value="80" label="Figure dpi"/> + <param name="fig_fontsize" argument="--fig-fontsize" type="integer" min="0" value="10" label="Figure font size"/> + <param name="fig_frame" type="boolean" truevalue="--frameon" falsevalue="--frameoff" checked="false" + label="Show plot 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 mtx 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> |