| Next changeset 1:a4ab4af54b1a (2020-06-03) |
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Commit message:
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c388aa3bb719eff471508b6f01cae8583ee7bb1d" |
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added:
monocle3-macros.xml monocle3-topmarkers.xml |
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| diff -r 000000000000 -r bc2df96ef963 monocle3-macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/monocle3-macros.xml Thu May 14 17:17:27 2020 -0400 |
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| @@ -0,0 +1,71 @@ +<macros> + <token name="@TOOL_VERSION@">0.1.4</token> + <token name="@PROFILE@">18.01</token> + <token name="@HELP@">More information can be found at https://cole-trapnell-lab.github.io/monocle3/ and https://github.com/ebi-gene-expression-group/monocle-scripts</token> + <token name="@VERSION_HISTORY@"><![CDATA[ +**Version history** +0.1.5+galaxy0: Updated to monocle3-cli 0.0.8 to add top marker genes and fix container plots for plotCells (only those two modules upgraded). + +0.1.4+galaxy0: Updated to monocle3-cli 0.0.7 to fix bug with column headers in tsv. + +0.1.3+galaxy0: Updated to monocle3-cli 0.0.5 to fix bug with tsv inputs. + +0.1.2+galaxy0: Initial version based on monocle3-cli 0.0.3 and monocle3 0.1.2 + ]]></token> + <token name="@INPUT_OPTS@"> + --input-object-format '${input_object_format}' '${input_object_file}' + </token> + <token name="@OUTPUT_OPTS@"> + --output-object-format '${output_object_format}' output.RDS +#if $introspective + --introspective +#end if + </token> + <token name="@VERBOSE@"> +#if $verbose + --verbose +#end if + </token> + + <xml name="requirements"> + <requirements> + <requirement type="package" version="0.0.7">monocle3-cli</requirement> + <yield/> + </requirements> + </xml> + + <xml name="citations"> + <citations> + <yield /> + <citation type="doi">10.1038/nmeth.4402</citation> + <citation type="bibtex"> + @misc{githubscanpy-scripts, + author = {Ni Huang, Krzysztof Polanski, EBI Gene Expression Team}, + year = {2019}, + title = {Monocle3-cli: command line interface for Monocle3}, + publisher = {GitHub}, + journal = {GitHub repository}, + url = {https://github.com/ebi-gene-expression-group/monocle-scripts}, + }</citation> + <citation type="doi">10.1101/2020.04.08.032698</citation> + </citations> + </xml> + + <xml name="input_object_params"> + <param name="input_object_file" argument="input-object-file" type="data" format="rdata" label="Input object in RDS format"/> + <param name="input_object_format" argument="--input-object-format" type="select" label="Format of input object"> + <option value="cds3" selected="true">Monocle3 object in RDS</option> + </param> + </xml> + + <xml name="output_object_params"> + <param name="output_object_format" argument="--output-object-format" type="select" label="Format of output object"> + <option value="cds3" selected="true">Monocle3 object in RDS</option> + </param> + <param name="introspective" argument="--introspective" type="boolean" checked="true" label="Print introspective information of output object"/> + </xml> + + <xml name="verbose_flag"> + <param name="verbose" argument="--verbose" type="boolean" checked="false" label="Emit verbose output"/> + </xml> +</macros> |
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| diff -r 000000000000 -r bc2df96ef963 monocle3-topmarkers.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/monocle3-topmarkers.xml Thu May 14 17:17:27 2020 -0400 |
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| @@ -0,0 +1,103 @@ +<?xml version="1.0" encoding="utf-8"?> +<tool id="monocle3_topmarkers" name="Monocle3 top markers" version="0.1.5+galaxy0" profile="@PROFILE@"> + <description>for cell groups</description> + <macros> + <import>monocle3-macros.xml</import> + </macros> + <requirements> + <requirement type="package" version="0.0.8">monocle3-cli</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + ln -s '$input_object' input.rds; + #if $ref_cells.source == 'file' and $ref_cells.file + list_of_cells=\$(cat $ref_cells.file | tr '\n' ',') + #end if + LANG=en_US.UTF-8 monocle3 topMarkers + --input-object-format cds3 + #if $filter_fraction_expression + --filter-fraction-expression '$filter_fraction_expression' + #end if + #if $top_n_markers + --top-n-markers '$top_n_markers' + #end if + #if $plot_top_markers + --plot-top-markers top_markers.pdf + #end if + #if $save_full_markers + --save-full-markers full_markers.tsv + #end if + #if $ref_cells.source == 'file' and $ref_cells.file + --reference-cells \$list_of_cells + #end if + #if $ref_cells.source == 'number' and $ref_cells.number + --reference-cells '$ref_cells.number' + #end if + #if $marker_sig_test + --marker-sig-test + #end if + #if $genes_to_test_per_group + --genes-to-test-per-group '$genes_to_test_per_group' + #end if + #if $group_cells_by + --group-cells-by '$group_cells_by' + #end if + --cores \${GALAXY_SLOTS:-1} + --introspective + + input.rds + output.tsv + ]]></command> +<inputs> + <param label="Input Object" name="input_object" type="data" format='rdata' help="Input file with monocle3 object cds3 in RDS"/> + <conditional name="ref_cells"> + <param label="Reference cells source" name="source" type="select" argument="--reference-cells" help="(Optional) Set of cells to be considered as reference for marker significance test. Accelerates the marker significance test at some cost in sensitivity."> + <option value="file">File</option> + <option value="number">Number of cells</option> + </param> + <when value="file"> + <param label="Reference cells file" name="file" optional="true" argument="--reference-cells" type="data" format='txt' help="File with cells to be used as reference cells."/> + </when> + <when value="number"> + <param label="Number of reference cells" name="number" optional="true" argument="--reference-cells" type="integer" help="Number of cells to be used as reference cells."/> + </when> + </conditional> + <param label="Filter fraction for expression" optional='true' value="0.1" name="filter_fraction_expression" argument="--filter-fraction-expression" type="float" help="Filters the markers test result by this fraction of expression"/> + <param label="Top-n-markers" optional='true' value="5" name="top_n_markers" argument="--top-n-markers" type="integer" help="The number of top marker genes to report in plots and in top markers list"/> + <param label="Number of genes to test per group" optional='true' value="25" name="genes_to_test_per_group" argument="--genes-to-test-per-group" type="integer" help="how many genes of the top ranked specific genes by Jenson-Shannon, to do the more expensive regression test on"/> + <param label="Group cell by" optional='true' value='cluster' name="group_cells_by" argument="--group-cells-by" type="text" help="Cell groups, choose from 'cluster', 'partition', or any categorical variable in `colData(cds)`"/> + <param label="Use logistic regression to asses discriminatory power" value='false' name="marker_sig_test" argument="--marker-sig-test" type="boolean" checked='false' help="whether to assess the discriminative power of each marker through logistic regression. Can be slow, consider disabling to speed up top_markers()."/> + <param label="Save full markers" value='false' name="save_full_markers" argument="--save-full-markers" type="boolean" checked='false' help="whether to generate the full markers list as well."/> + <param label="Plot top markers" value='false' name="plot_top_markers" argument="--plot-top-markers" type="boolean" checked='true' help="whether to generate the top markers plot."/> +</inputs> + +<outputs> + <data label="${tool.name} on ${on_string}: Top markers plot" name="top_markers_plot" format='pdf' from_work_dir='top_markers.pdf'> + <filter>plot_top_markers</filter> + </data> + <data label="${tool.name} on ${on_string}: Full markers" name="full_markers" from_work_dir="full_markers.tsv" format='tabular'> + <filter>save_full_markers</filter> + </data> + <data label="${tool.name} on ${on_string}: Top markers" name="top_markers_table" from_work_dir="output.tsv" format='tabular' /> +</outputs> + +<tests> + <test> + <param name="input_object_file" value="input.rds"/> + <param name="filter_fraction_expression" value="0.1"/> + <output name="top_markers_table" file="top_markers_table.tsv" ftype="tsv" compare="sim_size"/> + </test> +</tests> + +<help><![CDATA[ +========================================================== +Monocle3 top markers genes +========================================================== + +Identify the genes most specifically expressed in groups of cells. See inline help for options. + +@HELP@ + +@VERSION_HISTORY@ +]]></help> +<expand macro="citations"/> +</tool> |