| Next changeset 1:e17c3123cdb5 (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-orderCells.xml |
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| diff -r 000000000000 -r 5520da33a868 monocle3-macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/monocle3-macros.xml Mon Sep 16 09:52:31 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 5520da33a868 monocle3-orderCells.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/monocle3-orderCells.xml Mon Sep 16 09:52:31 2019 -0400 |
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| @@ -0,0 +1,74 @@ +<?xml version="1.0" encoding="utf-8"?> +<tool id="monocle3_orderCells" name="Monocle3 orderCells" version="@TOOL_VERSION@+galaxy0"> + <description>along trajectories</description> + <macros> + <import>monocle3-macros.xml</import> + </macros> + <expand macro="requirements"/> + <command detect_errors="exit_code"><![CDATA[ +LANG=en_US.UTF-8 monocle3 orderCells + --reduction-method '${reduction_method}' +#if $root_pr_nodes + --root-pr-nodes '${root_pr_nodes}' +#end if +#if $root_cells + --root-cells '${root_cells}' +#end if +#if $cell_phenotype + --cell-phenotype '${cell_phenotype}' +#end if +#if $root_type + --root-type '${root_type}' +#end if + + @INPUT_OPTS@ + @OUTPUT_OPTS@ + + @VERBOSE@ +]]></command> + + <inputs> + <expand macro="input_object_params"/> + <expand macro="output_object_params"/> + <param name="root_pr_nodes" argument="--root-pr-nodes" type="text" optional="true" label="The starting principal points. We learn a principal graph that passes through the middle of the data points and use it to represent the developmental process. Exclusive with the root cell option."/> + <param name="root_cells" argument="--root-cells" type="text" optional="true" label="The starting cells. Each cell corresponds to a principal point and multiple cells can correspond to the same principal point. Exclusive with the root node option."/> + <param name="cell_phenotype" argument="--cell-phenotype" type="text" optional="true" label="The cell phenotype (column in pdata) used to identify root principal nodes."/> + <param name="root_type" argument="--root-type" type="text" optional="true" label="The value in the cell phenotype column used to extract root nodes."/> + <param name="reduction_method" argument="--reduction-method" type="select" label="The dimensionality reduction that was used for clustering."> + <option selected="true" value="UMAP">UMAP</option> + <option value="tSNE">tSNE</option> + <option value="PCA">PCA</option> + <option value="LSI">LSI</option> + </param> + <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="reduction_method" value="UMAP"/> + <param name="cell_phenotype" value="embryo.time.bin"/> + <param name="root_type" value="130-170"/> + <param name="output_object_format" value="cds3"/> + <output name="output_rds" file="output.rds" ftype="rdata" compare="sim_size"/> + </test> + </tests> + + <help><![CDATA[ +========================================== +Monocle3 ordering of cells (`order_cells`) +========================================== + +Order cells using the inferred graph + +@HELP@ + +@VERSION_HISTORY@ +]]></help> + <expand macro="citations"/> +</tool> |