| Next changeset 1:0869b0264af1 (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-macros.xml monocle3-preprocess.xml |
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| diff -r 000000000000 -r 384b9bcf2807 monocle3-macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/monocle3-macros.xml Mon Sep 16 09:50:29 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> |
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| diff -r 000000000000 -r 384b9bcf2807 monocle3-preprocess.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/monocle3-preprocess.xml Mon Sep 16 09:50:29 2019 -0400 |
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| @@ -0,0 +1,84 @@ +<?xml version="1.0" encoding="utf-8"?> +<tool id="monocle3_preprocess" name="Monocle3 preprocess" version="@TOOL_VERSION@+galaxy0"> + <description>a Monocle3 object to an initially dimensionally reduced space</description> + <macros> + <import>monocle3-macros.xml</import> + </macros> + <expand macro="requirements"/> + <command detect_errors="exit_code"><![CDATA[ +LANG=en_US.UTF-8 monocle3 preprocess + --method '${method}' +#if $num_dim + --num-dim '${num_dim}' +#end if + --norm-method '${norm_method}' +#if $use_genes + --use-genes '${use_genes}' +#end if +#if $residual_model_formula_str + --residual-model-formula-str '~${residual_model_formula_str}' +#end if +#if $pseudo_count + --pseudo-count '${pseudo_count}' +#end if +#if $no_scaling + --no-scaling +#end if + + @INPUT_OPTS@ + @OUTPUT_OPTS@ + + @VERBOSE@ +]]></command> + + <inputs> + <expand macro="input_object_params"/> + <expand macro="output_object_params"/> + <param name="method" argument="--method" type="select" label="Initial dimensionality reduction to perform."> + <option value="PCA" selected="true">PCA</option> + <option value="LSI">LSI</option> + </param> + <param name="num_dim" argument="--num-dim" optional="true" type="integer" value="50" label="The dimensionality of the reduced space."/> + <param name="norm_method" argument="--norm-method" type="select" label="Determines how to transform expression values prior to reducing dimensionality."> + <option value="log" selected="true">Size factor correction and log transformation</option> + <option value="size_only">Size factor correction only</option> + </param> + <param name="use_genes" argument="--use-genes" type="text" optional="true" label="Manually subset the gene pool to these genes for dimensionality reduction."/> + <param name="residual_model_formula_str" argument="--residual-model-formula-str" type="text" optional="true" label="A string model formula specifying effects to subtract from the data (excluding the leading ~)."/> + <param name="pseudo_count" argument="--pseudo-count" optional="true" type="float" value="1" label="Amount to increase expression values before dimensionality reduction."/> + <param name="no_scaling" argument="--no-scaling" type="boolean" checked="false" label="When this option is NOT set, scale each gene before running trajectory reconstruction."/> + <expand macro="verbose_flag"/> + </inputs> + + <outputs> + <data name="output_rds" format="rdata" from_work_dir="output.RDS" label="${tool.name} on ${on_string}: ${output_object_format}"/> + </outputs> + + <tests> + <test> + <param name="input_object_file" value="input.RDS"/> + <param name="input_object_format" value="cds3"/> + <param name="method" value="PCA"/> + <param name="num_dim" value="50"/> + <param name="norm_method" value="log"/> + <param name="pseudo_count" value="1"/> + <param name="output_object_format" value="cds3"/> + <output name="output_rds" file="output.rds" ftype="rdata" compare="sim_size"/> + </test> + </tests> + + <help><![CDATA[ +==================================================================================== +Preprocess Monocle3 object up to initial dimensionality reduction (`preprocess_cds`) +==================================================================================== + +Preprocess a Monocle3 object with size factor scaling of the count data, optionally +log transforming, and computing an initial dimensionality reduction. This space is +used as a starting point for a number of subsequent analyses. + +@HELP@ + +@VERSION_HISTORY@ +]]></help> + <expand macro="citations"/> +</tool> |