| Next changeset 1:13a27436f8ee (2019-11-25) |
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Commit message:
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4 |
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README seurat_macros.xml seurat_run_tsne.xml |
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| diff -r 000000000000 -r 3aea769deab1 README --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README Wed Apr 03 11:19:13 2019 -0400 |
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| diff -r 000000000000 -r 3aea769deab1 seurat_macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/seurat_macros.xml Wed Apr 03 11:19:13 2019 -0400 |
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| @@ -0,0 +1,50 @@ +<?xml version="1.0"?> +<macros> + + <token name="@VERSION@">0.0.5</token> + + <xml name="requirements"> + <requirements> + <requirement type="package" version="@VERSION@">seurat-scripts</requirement> + </requirements> + </xml> + + <xml name="version"> + <version_command><![CDATA[ +echo $(R --version | grep version | grep -v GNU)", seurat version" $(R --vanilla --slave -e "library(seurat); cat(sessionInfo()\$otherPkgs\$seurat\$Version)" 2> /dev/null | grep -v -i "WARNING: ") + ]]></version_command> + </xml> + + <xml name="genes-use-input"> + <param name="genes_use" argument="--genes-use" optional="true" type="data" format="tsv, txt" label="Genes to use" help="A file with gene names to use in construction of SNN graph if building directly based on expression data rather than a dimensionally reduced representation (i.e. PCs)."/> + </xml> + <xml name="dims-use-input"> + <param name="dims_use" argument="--dims-use" min="1" optional="true" type="integer" label="PCA Dimensions to use" help="Number of PCs (dimensions) to use in construction of the SNN graph."/> + </xml> + + <token name="@VERSION_HISTORY@"><![CDATA[ +**Version history** + +0.0.1: Initial contribution. Maria Doyle, https://github.com/mblue9. + +2.3.1+galaxy0: Improved documentation and further exposition of all script's options. Pablo Moreno, Jonathan Manning and Ni Huang, Expression Atlas team https://www.ebi.ac.uk/gxa/home at +EMBL-EBI https://www.ebi.ac.uk/. Parts obtained from wrappers from Christophe Antoniewski(https://github.com/drosofff) and Lea Bellenger(https://github.com/bellenger-l). + ]]></token> + + + <xml name="citations"> + <citations> + <citation type="doi">10.1038/nbt.4096</citation> + <citation type="bibtex"> + @misc{r-seurat-scripts.git, + author = {Jonathan Manning, Pablo Moreno, EBI Gene Expression Team}, + year = {2018}, + title = {Seurat-scripts: command line interface for Seurat}, + publisher = {GitHub}, + journal = {GitHub repository}, + url = {https://github.com/ebi-gene-expression-group/r-seurat-scripts.git}, + } + </citation> + </citations> + </xml> +</macros> |
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| diff -r 000000000000 -r 3aea769deab1 seurat_run_tsne.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/seurat_run_tsne.xml Wed Apr 03 11:19:13 2019 -0400 |
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| @@ -0,0 +1,84 @@ +<tool id="seurat_run_tsne" name="Seurat RunTSNE" version="2.3.1+galaxy1"> + <description>run t-SNE dimensionality reduction</description> + <macros> + <import>seurat_macros.xml</import> + </macros> + <expand macro="requirements" /> + <expand macro="version" /> + <command detect_errors="exit_code"><![CDATA[ +seurat-run-tsne.R + +--input-object-file '$input' + +#if $genes_use: + --genes-use '$genes_use' +#end if + +#if str($adv.dims_use): + --dims-use \$(seq -s , 1 '$adv.dims_use') +#else + --dims-use 1,10 +#end if + +#if not $adv.do_fast: + --do-fast '$adv.do_fast' +#end if + +--output-object-file '$output' +--output-embeddings-file output_embed +]]></command> + + <inputs> + <param name="input" argument="--input-obj-file" type="data" format="rdata" label="Seurat RDS object" help="The RDS/Rdata result of Seurat FindClusters."/> + <expand macro="genes-use-input"/> + <section name="adv" title="Advanced Options"> + <expand macro="dims-use-input"/> + <param name="do_fast" label="Faster execution" argument="--do-fast" checked="true" type="boolean" truevalue="" falsevalue="FALSE" help="If TRUE, uses the Barnes-hut implementation, which runs faster, but is less flexible. TRUE by default."/> + </section> + </inputs> + + <outputs> + <data name="output" format="rdata" from_work_dir="*.rds" label="${tool.name} on ${on_string}: Seurat RDS"/> + <data name="output_embed" format="csv" from_work_dir="output_embed" label="${tool.name} on ${on_string}: Seurat Embeddings"/> + </outputs> + + <tests> + <test> + <param name="input" ftype="rdata" value="out_findclust.rds"/> + <output name="output" ftype="rdata" value="out_runtsne.rds" compare="sim_size"/> + </test> + </tests> + <help><![CDATA[ +.. class:: infomark + +**What it does** + +Seurat_ is a toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. +It is developed and maintained by the `Satija Lab`_ at NYGC. Seurat aims to enable users to identify and +interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse +types of single cell data. + +Run t-SNE dimensionality reduction on selected features. Has the option of +running in a reduced dimensional space (i.e. spectral tSNE, recommended), +or running based on a set of genes. For details about stored TSNE calculation +parameters, see standard output of the tool. + +----- + +**Inputs** + + * RDS object + +----- + +**Outputs** + + * Seurat RDS object + +.. _Seurat: https://www.nature.com/articles/nbt.4096 +.. _Satija Lab: https://satijalab.org/seurat/ + +@VERSION_HISTORY@ +]]></help> + <expand macro="citations" /> +</tool> |