| Next changeset 1:a34f243f55a4 (2020-01-29) |
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Commit message:
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114" |
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added:
monocle3-create.xml monocle3-macros.xml |
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| diff -r 000000000000 -r 75340a5e5fb0 monocle3-create.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/monocle3-create.xml Mon Sep 16 09:52:55 2019 -0400 |
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| @@ -0,0 +1,82 @@ +<?xml version="1.0" encoding="utf-8"?> +<tool id="monocle3_create" name="Monocle3 create" version="@TOOL_VERSION@+galaxy0"> + <description>a Monocle3 object from input data</description> + <macros> + <import>monocle3-macros.xml</import> + </macros> + <expand macro="requirements"/> + <command detect_errors="exit_code"><![CDATA[ +ln -s '${expression_matrix}' expression_matrix.'${expression_matrix_format}' && +#if $cell_metadata +ln -s '${cell_metadata}' cell_metadata.'${cell_metadata_format}' && +#end if +#if $gene_annotation +ln -s '${gene_annotation}' gene_annotation.'${gene_annotation_format}' && +#end if +LANG=en_US.UTF-8 monocle3 create + --expression-matrix expression_matrix.'${expression_matrix_format}' +#if $cell_metadata + --cell-metadata cell_metadata.'${cell_metadata_format}' +#end if +#if $gene_annotation + --gene-annotation gene_annotation.'${gene_annotation_format}' +#end if + @OUTPUT_OPTS@ + @VERBOSE@ +]]></command> + + <inputs> + <param name="expression_matrix" argument="--expression-matrix" type="data" format="tsv,csv,rdata" label="Expression matrix, genes as rows, cells as columns. Required input. Provide as TSV, CSV or RDS."/> + <param name="expression_matrix_format" type="select" label="Format of expression matrix"> + <option value="rds" selected="true">RDS</option> + <option value="tsv">TSV</option> + <option value="csv">CSV</option> + </param> + <param name="cell_metadata" argument="--cell-metadata" optional="true" type="data" format="tsv,csv,rdata" label="Per-cell annotation, optional. Row names must match the column names of the expression matrix. Provide as TSV, CSV or RDS."/> + <param name="cell_metadata_format" type="select" label="Format of cell metadata"> + <option value="rds" selected="true">RDS</option> + <option value="tsv">TSV</option> + <option value="csv">CSV</option> + </param> + <param name="gene_annotation" argument="--gene-annotation" optional="true" type="data" format="tsv,csv,rdata" label="Per-gene annotation, optional. Row names must match the row names of the expression matrix. Provide as TSV, CSV or RDS."/> + <param name="gene_annotation_format" type="select" label="Format of gene annotation"> + <option value="rds" selected="true">RDS</option> + <option value="tsv">TSV</option> + <option value="csv">CSV</option> + </param> + <expand macro="output_object_params"/> + <expand macro="verbose_flag"/> + </inputs> + + <outputs> + <data name="output_rds" format="rdata" from_work_dir="output.RDS" label="${tool.name} on ${on_string}: ${output_object_format}"/> + </outputs> + + <tests> + <test> + <param name="expression_matrix" value="expression.RDS"/> + <param name="cell_metadata" value="cells.RDS"/> + <param name="gene_annotation" value="genes.RDS"/> + <param name="output_object_format" value="cds3"/> + <output name="output_rds" file="output.rds" ftype="rdata" compare="sim_size"/> + </test> + </tests> + + <help><![CDATA[ +=========================================================================== +Create Monocle3 object from input expression/metadata (`new_cell_data_set`) +=========================================================================== + +Create a Monocle3 cds3 object from input expression data and optional metadata. +The expression matrix, with genes as rows and cells as columns, is the only mandatory +input. The cell metadata (with row names matching the column names of the expression +matrix) and gene annotation (with row names matching the row names of the expression +matrix) are optional. These files can be provided as RDS objects, or CSV/TSV. Select the +format of your input files in the corresponding drop-downs. + +@HELP@ + +@VERSION_HISTORY@ +]]></help> + <expand macro="citations"/> +</tool> |
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| diff -r 000000000000 -r 75340a5e5fb0 monocle3-macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/monocle3-macros.xml Mon Sep 16 09:52:55 2019 -0400 |
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| @@ -0,0 +1,64 @@ +<macros> + <token name="@TOOL_VERSION@">0.1.2</token> + <token name="@HELP@">More information can be found at https://cole-trapnell-lab.github.io/monocle3/ and https://github.com/ebi-gene-expression-group/monocle-scripts</token> + <token name="@VERSION_HISTORY@"><![CDATA[ +**Version history** + +0.1.2+galaxy0: Initial version based on monocle3-cli 0.0.3 and monocle3 0.1.2 + ]]></token> + <token name="@INPUT_OPTS@"> + --input-object-format '${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="0.0.3">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> + </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> |