| Next changeset 1:f91ddb6bc4ff (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-diffExp.xml monocle3-macros.xml |
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| diff -r 000000000000 -r c0441ea8f37a monocle3-diffExp.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/monocle3-diffExp.xml Mon Sep 16 09:50:52 2019 -0400 |
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| @@ -0,0 +1,74 @@ +<?xml version="1.0" encoding="utf-8"?> +<tool id="monocle3_diffExp" name="Monocle3 diffExp" version="@TOOL_VERSION@+galaxy0"> + <description> of genes along a trajectory</description> + <macros> + <import>monocle3-macros.xml</import> + </macros> + <expand macro="requirements"/> + <command detect_errors="exit_code"><![CDATA[ +LANG=en_US.UTF-8 monocle3 diffExp + --neighbor-graph '$(neighbor_graph)' + --reduction-method '$(reduction_method)' +#if $knn + --knn '$(knn)' +#end if + --method '$(method)' + --alternative '$(alternative)' + + @INPUT_OPTS@ + output.tsv + + @VERBOSE@ +]]></command> + + <inputs> + <expand macro="input_object_params"/> + <param name="neighbor_graph" argument="--neighbor-graph" type="select" label="What neighbor graph to use, principal graph recommended for trajectory analysis."> + <option value="knn" selected="true">KNN</option> + <option value="principal_graph">Principal graph</option> + </param> + <param name="reduction_method" argument="--reduction-method" type="select" label="The reduction method to base the analysis on."> + <option value="UMAP" selected="true">UMAP</option> + </param> + <param name="knn" argument="--knn" optional="true" type="integer" value="20" label="Number of nearest neighbors used for building the kNN graph which is passed to knn2nb function during the Moran's I (Geary's C) test procedure."/> + <param name="method" argument="--method" type="select" label="A character string specifying the method for detecting significant genes showing correlated expression along the principal graph embedded in the low dimensional space."> + <option value="Moran_I" selected="true">Moran_I</option> + </param> + <param name="alternative" argument="--alternative" type="select" label="A character string specifying the alternative hypothesis."> + <option value="greater" selected="true">greater</option> + <option value="less">less</option> + <option value="two.sided">two-sided</option> + </param> + <expand macro="verbose_flag"/> + </inputs> + + <outputs> + <data name="output_tsv" format="tsv" from_work_dir="output.tsv" label="${tool.name} on ${on_string}: tsv"/> + </outputs> + + <tests> + <test> + <param name="input_object_file" value="input.RDS"/> + <param name="input_object_format" value="cds3"/> + <param name="neighbor_graph" value="knn"/> + <param name="reduction_method" value="UMAP"/> + <param name="knn" value="20"/> + <param name="method" value="Moran_I"/> + <param name="alternative" value="greater"/> + <output name="output_tsv" file="output.tsv" ftype="tsv" compare="sim_size"/> + </test> + </tests> + + <help><![CDATA[ +======================================================================== +Monocle3 differential expression testing along trajectory (`graph_test`) +======================================================================== + +Identify differentially expressed genes along the inferred trajectory. + +@HELP@ + +@VERSION_HISTORY@ +]]></help> + <expand macro="citations"/> +</tool> |
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| diff -r 000000000000 -r c0441ea8f37a monocle3-macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/monocle3-macros.xml Mon Sep 16 09:50:52 2019 -0400 |
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| @@ -0,0 +1,64 @@ +<macros> + <token name="@TOOL_VERSION@">0.1.2</token> + <token name="@HELP@">More information can be found at https://cole-trapnell-lab.github.io/monocle3/ and https://github.com/ebi-gene-expression-group/monocle-scripts</token> + <token name="@VERSION_HISTORY@"><![CDATA[ +**Version history** + +0.1.2+galaxy0: Initial version based on monocle3-cli 0.0.3 and monocle3 0.1.2 + ]]></token> + <token name="@INPUT_OPTS@"> + --input-object-format '${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> |