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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
author | iuc |
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date | Fri, 07 Jul 2023 01:43:02 +0000 |
parents | c0fd285eb553 |
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<tool id="seurat" name="Seurat" version="@TOOL_VERSION@+galaxy1"> <description>- toolkit for exploration of single-cell RNA-seq data</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ #if $function.function_select == "base": Rscript -e "library(\"rmarkdown\"); render(\"$__tool_directory__/Seurat.R\", params = list(counts = \"${function.input}\", min_cells = \"${function.min_cells}\", min_genes = \"${function.min_genes}\", low_thresholds = \"${function.low_thresholds}\", high_thresholds = \"${function.high_thresholds}\", vlnfeat = \"${function.vlnfeat}\", norm_out = \"${function.norm_file}\", #if $function.variable_continue.variable_continue == "yes": featplot = \"${function.variable_continue.featplot}\", variable_out = \"${function.variable_continue.var_file}\", #if $function.variable_continue.pca_continue.pca_continue == "yes": numPCs = \"${function.variable_continue.pca_continue.num_PCs}\", PCplots = \"${function.variable_continue.pca_continue.pc_plots}\", pca_out = \"${function.variable_continue.pca_continue.pca_file}\", #if $function.variable_continue.pca_continue.clusters_continue.clusters_continue == "yes": perplexity = \"${function.variable_continue.pca_continue.clusters_continue.perplexity}\", resolution = \"${function.variable_continue.pca_continue.clusters_continue.resolution}\", nmds = \"${function.variable_continue.pca_continue.clusters_continue.nmds}\", clusters_out = \"${function.variable_continue.pca_continue.clusters_continue.clusters_file}\", #if $function.variable_continue.pca_continue.clusters_continue.markers_continue.markers_continue == "yes": min_pct = \"${function.variable_continue.pca_continue.clusters_continue.markers_continue.min_pct}\", logfc_threshold = \"${function.variable_continue.pca_continue.clusters_continue.markers_continue.logfc_threshold}\", heatmaps = \"${function.variable_continue.pca_continue.clusters_continue.markers_continue.heatmaps}\", markers_out = \"${function.variable_continue.pca_continue.clusters_continue.markers_continue.markers_file}\", end_step="\"5"\", #else: end_step="\"4"\", #end if #else: end_step="\"3"\", #end if #else: end_step="\"2"\", #end if #else: end_step="\"1"\", #end if varstate = \"${meta.varstate}\", warn = \"${meta.warn}\", showcode = \"${meta.showcode}\"), intermediates_dir = \".\", output_format = html_document(), output_dir = \".\", output_file = \"out.html\")" #else: Rscript -e "library(\"rmarkdown\"); render(\"$__tool_directory__/citeseq_Seurat.R\", params = list(rna = \"${function.rna}\", prot = \"${function.prot}\", cite_markers = \"${function.cite_markers}\", #if $function.comparison.comparison == "yes" comparison="\"T"\", feat_comp=\"${function.comparison.feat_comp}\", #else: comparison="\"F"\", feat_comp="\""\", #end if #if $function.marker_compare.marker_compare == "yes" marker_compare="\"T"\", top_x=\"${function.marker_compare.top_x}\", #else: marker_compare="\"F"\", top_x="\""\", #end if min_cells = \"${function.min_cells}\", min_genes = \"${function.min_genes}\", low_thresholds = \"${function.low_thresholds}\", high_thresholds = \"${function.high_thresholds}\", vlnfeat = \"${function.vlnfeat}\", norm_out = \"${function.norm_file}\", featplot = \"${function.featplot}\", variable_out = \"${function.var_file}\", numPCs = \"${function.num_PCs}\", PCplots = \"${function.pc_plots}\", pca_out = \"${function.pca_file}\", perplexity = \"${function.perplexity}\", resolution = \"${function.resolution}\", nmds = \"${function.nmds}\", clusters_out = \"${function.clusters_file}\", min_pct = \"${function.min_pct}\", logfc_threshold = \"${function.logfc_threshold}\", heatmaps = \"${function.heatmaps}\", markers_out = \"${function.markers_file}\", varstate = \"${meta.varstate}\", warn = \"${meta.warn}\", showcode = \"${meta.showcode}\"), intermediates_dir = \".\", output_format = html_document(), output_dir = \".\", output_file = \"out.html\")" #end if ]]></command> <inputs> <conditional name="function"> <param name="function_select" type="select" label="Which Seurat method should be run?"> <option value="base">Base</option> <option value="cite">Cite-seq</option> </param> <when value="base"> <param name="input" type="data" format="tabular,tsv" label="Counts file" help="The should be a TAB-separated count matrix with gene identifers in the first column and a header row"/> <param name="min_cells" type="integer" min="0" value="0" label="Minimum cells" help="Include genes with detected expression in at least this many cells" /> <param name="min_genes" type="integer" min="0" value="0" label="Minimum genes" help="Include cells where at least this many genes are detected"/> <expand macro="norm"/> <conditional name="variable_continue"> <param name="variable_continue" type="select" label="Continue workflow after Normalization step?"> <option value="yes">Yes</option> <option value="no" selected="true">No</option> </param> <when value="yes"> <expand macro="variable"/> <conditional name="pca_continue"> <param name="pca_continue" type="select" label="Continue workflow after scaling step?"> <option value="yes">Yes</option> <option value="no" selected="true">No</option> </param> <when value="yes"> <expand macro="pca"/> <conditional name="clusters_continue"> <param name="clusters_continue" type="select" label="Continue workflow after PCA step?"> <option value="yes">Yes</option> <option value="no" selected="true">No</option> </param> <when value="yes"> <expand macro="clusters"/> <conditional name="markers_continue"> <param name="markers_continue" type="select" label="Continue workflow after TSNE and UMAP step?"> <option value="yes">Yes</option> <option value="no" selected="true">No</option> </param> <when value="yes"> <expand macro="markers"/> </when> <when value="no"/> </conditional> </when> <when value="no"/> </conditional> </when> <when value="no"/> </conditional> </when> <when value="no"/> </conditional> </when> <when value="cite"> <param name="rna" type="data" format="tabular,tsv" label="RNA counts file" help="The should be a TAB-separated count matrix with gene identifers in the first column and a header row"/> <param name="prot" type="data" format="tabular,tsv" label="Protein counts file" help="The should be a TAB-separated count matrix with gene identifers in the first column and a header row"/> <param name="min_cells" type="integer" min="0" value="0" label="Minimum cells" help="Include genes with detected expression in at least this many cells" /> <param name="min_genes" type="integer" min="0" value="0" label="Minimum genes" help="Include cells where at least this many genes are detected"/> <expand macro="norm"/> <expand macro="variable"/> <expand macro="pca"/> <expand macro="clusters"/> <expand macro="markers"/> <expand macro="cite-seq"/> </when> </conditional> <section name="meta" title="Output options" expanded="true"> <param name="showcode" type="boolean" truevalue="T" falsevalue="F" checked="false" label="Show code alongside outputs?"/> <param name="warn" type="boolean" truevalue="T" falsevalue="F" checked="false" label="Include warnings in the output file (Yes) or pipe to stdout (No)"/> <param name="varstate" type="boolean" truevalue="T" falsevalue="F" checked="false" label="Display variable values used in code at the beginning of output file?"/> </section> </inputs> <outputs> <data name="out_html" format="html" from_work_dir="out.html" label="${tool.name} on ${on_string}" /> <data name="norm_out" format="rdata" from_work_dir="norm_out.rds" label="${tool.name} on ${on_string}: normalization intermediate output"> <filter>@FUNCTION_BASE@</filter> <filter>function['norm_file']</filter> </data> <data name="var_out" format="rdata" from_work_dir="var_out.rds" label="${tool.name} on ${on_string}: normalization and scaling intermediate output"> <filter>@FUNCTION_BASE@</filter> <filter>@VARIABLE_CONTINUE@</filter> <filter>function['variable_continue']['var_file']</filter> </data> <data name="pca_out" format="rdata" from_work_dir="pca_out.rds" label="${tool.name} on ${on_string}: PCA embedding data"> <filter>@FUNCTION_BASE@</filter> <filter>@VARIABLE_CONTINUE@</filter> <filter>@PCA_CONTINUE@</filter> <filter>function['variable_continue']['pca_continue']['pca_file']</filter> </data> <data name="cluters_out" format="rdata" from_work_dir="tsne_out.rds" label="${tool.name} on ${on_string}: TSNE embedding data"> <filter>@FUNCTION_BASE@</filter> <filter>@VARIABLE_CONTINUE@</filter> <filter>@PCA_CONTINUE@</filter> <filter>@CLUSTERS_CONTINUE@</filter> <filter>function['variable_continue']['pca_continue']['clusters_continue']['clusters_file']</filter> </data> <data name="umap_out" format="rdata" from_work_dir="umap_out.rds" label="${tool.name} on ${on_string}: UMAP embedding data"> <filter>@FUNCTION_BASE@</filter> <filter>@VARIABLE_CONTINUE@</filter> <filter>@PCA_CONTINUE@</filter> <filter>@CLUSTERS_CONTINUE@</filter> <filter>function['variable_continue']['pca_continue']['clusters_continue']['clusters_file']</filter> </data> <data name="markers_out" format="rdata" from_work_dir="markers_out.rds" label="${tool.name} on ${on_string}: Markers data"> <filter>@FUNCTION_BASE@</filter> <filter>@VARIABLE_CONTINUE@</filter> <filter>@PCA_CONTINUE@</filter> <filter>@CLUSTERS_CONTINUE@</filter> <filter>@MARKERS_CONTINUE@</filter> <filter>function['variable_continue']['pca_continue']['clusters_continue']['markers_continue']['markers_file']</filter> </data> <data name="markers_tabular" format="tabular" from_work_dir="markers_out.tsv" label="${tool.name} on ${on_string}: Markers list"> <filter>@FUNCTION_BASE@</filter> <filter>@VARIABLE_CONTINUE@</filter> <filter>@PCA_CONTINUE@</filter> <filter>@CLUSTERS_CONTINUE@</filter> <filter>@MARKERS_CONTINUE@</filter> <filter>function['variable_continue']['pca_continue']['clusters_continue']['markers_continue']['markers_file']</filter> <actions> <action name="column_names" type="metadata" default="\\,p_val,avg_log2FC,pct.1,pct.2,p_val_adj,cluster,gene" /> <action name="column_types" type="metadata" default="str,float,float,float,float,float,int,str" /> </actions> </data> <!-- cite-seq out --> <data name="protmarkerst" format="tabular" from_work_dir="protein_out.tsv" label="${tool.name} cite-seq on ${on_string}: Protein markers"> <filter>@FUNCTION_CITE@</filter> <filter>function['cite_markers']</filter> <actions> <action name="column_names" type="metadata" default="\\,p_val,avg_log2FC,pct.1,pct.2,p_val_adj,cluster,gene" /> <action name="column_types" type="metadata" default="str,float,float,float,float,float,int,str" /> </actions> </data> <data name="rnamarkerst" format="tabular" from_work_dir="rna_out.tsv" label="${tool.name} cite-seq on ${on_string}: RNA markers"> <filter>@FUNCTION_CITE@</filter> <filter>function['cite_markers']</filter> <actions> <action name="column_names" type="metadata" default="\\,p_val,avg_log2FC,pct.1,pct.2,p_val_adj,cluster,gene" /> <action name="column_types" type="metadata" default="str,float,float,float,float,float,int,str" /> </actions> </data> <data name="cite_graps" format="pdf" from_work_dir="citeseq_out.pdf" label="${tool.name} cite-seq on ${on_string}: Citeseq graphs"> <filter>@FUNCTION_CITE@</filter> <filter>function['marker_compare']['marker_compare'] == "yes"</filter> </data> <data name="norm_cite" format="rdata" from_work_dir="norm_out.rds" label="${tool.name} cite-seq on ${on_string}: normalization intermediate output"> <filter>@FUNCTION_CITE@</filter> <filter>function['norm_file']</filter> </data> <data name="var_cite" format="rdata" from_work_dir="var_out.rds" label="${tool.name} cite-seq on ${on_string}: normalization and scaling intermediate output"> <filter>@FUNCTION_CITE@</filter> <filter>function['var_file']</filter> </data> <data name="pca_cite" format="rdata" from_work_dir="pca_out.rds" label="${tool.name} cite-seq on ${on_string}: PCA embedding data"> <filter>@FUNCTION_CITE@</filter> <filter>function['pca_file']</filter> </data> <data name="cluters_cite" format="rdata" from_work_dir="tsne_out.rds" label="${tool.name} cite-seq on ${on_string}: TSNE embedding data"> <filter>@FUNCTION_CITE@</filter> <filter>function['clusters_file']</filter> </data> <data name="umap_cite" format="rdata" from_work_dir="umap_out.rds" label="${tool.name} cite-seq on ${on_string}: UMAP embedding data"> <filter>@FUNCTION_CITE@</filter> <filter>function['clusters_file']</filter> </data> <data name="markers_cite" format="rdata" from_work_dir="markers_out.rds" label="${tool.name} cite-seq on ${on_string}: Markers data"> <filter>@FUNCTION_CITE@</filter> <filter>function['markers_file']</filter> </data> <data name="markers_cite_tabular" format="tabular" from_work_dir="markers_out.tsv" label="${tool.name} cite-seq on ${on_string}: Markers list"> <filter>@FUNCTION_CITE@</filter> <filter>function['markers_file']</filter> <actions> <action name="column_names" type="metadata" default="\\,p_val,avg_log2FC,pct.1,pct.2,p_val_adj,cluster,gene" /> <action name="column_types" type="metadata" default="str,float,float,float,float,float,int,str" /> </actions> </data> </outputs> <tests> <test expect_num_outputs="8"> <conditional name="function"> <param name="function_select" value="base"/> <param name="input" ftype="tabular" value="counts.tab.gz"/> <param name="min_cells" value="3"/> <param name="min_genes" value="200"/> <param name="low_thresholds" value="1" /> <param name="high_thresholds" value="20000000" /> <param name="vlnfeat" value="T"/> <param name="norm_file" value="T"/> <conditional name="variable_continue"> <param name="variable_continue" value="yes"/> <param name="featplot" value="T"/> <param name="var_file" value="T"/> <conditional name="pca_continue"> <param name="pca_continue" value="yes"/> <param name="numPCs" value="10" /> <param name="pc_plots" value="T"/> <param name="pca_file" value="T"/> <conditional name="clusters_continue"> <param name="clusters_continue" value="yes"/> <param name="resolution" value="0.6" /> <param name="nmds" value="T"/> <param name="clusters_file" value="T"/> <conditional name="markers_continue"> <param name="markers_continue" value="yes"/> <param name="min_pct" value="0.25" /> <param name="logfc_threshold" value="0.25" /> <param name="heatmaps" value="T"/> <param name="markers_file" value="T"/> </conditional> </conditional> </conditional> </conditional> </conditional> <section name="meta"> <param name="showcode" value="T"/> <param name="warn" value="F"/> <param name="varstate" value="F"/> </section> <output name="out_html" ftype="html"> <assert_contents> <has_text text="Seurat Analysis" /> <has_text text="Performed using Galaxy" /> <has_text text="img src="data:image/png;base64" /> </assert_contents> </output> <output name="markers_tabular" file="markers.tsv" compare="sim_size" delta="500"/> </test> <test expect_num_outputs="1"> <!-- test perplexity and output filters --> <conditional name="function"> <param name="function_select" value="base"/> <param name="input" ftype="tabular" value="counts.tab.gz"/> <param name="min_cells" value="3"/> <param name="min_genes" value="200"/> <param name="low_thresholds" value="1" /> <param name="high_thresholds" value="20000000" /> <param name="vlnfeat" value="T"/> <param name="norm_file" value="F"/> <conditional name="variable_continue"> <param name="variable_continue" value="yes"/> <param name="featplot" value="T"/> <param name="var_file" value="F"/> <conditional name="pca_continue"> <param name="pca_continue" value="yes"/> <param name="numPCs" value="10" /> <param name="pc_plots" value="T"/> <param name="pca_file" value="F"/> <conditional name="clusters_continue"> <param name="clusters_continue" value="yes"/> <param name="perplexity" value="16"/> <param name="resolution" value="0.6" /> <param name="nmds" value="T"/> <param name="clusters_file" value="F"/> <conditional name="markers_continue"> <param name="markers_continue" value="yes"/> <param name="min_pct" value="0.25" /> <param name="logfc_threshold" value="0.25" /> <param name="heatmaps" value="T"/> <param name="markers_file" value="F"/> </conditional> </conditional> </conditional> </conditional> </conditional> <section name="meta"> <param name="showcode" value="T"/> <param name="warn" value="F"/> <param name="varstate" value="F"/> </section> <output name="out_html" ftype="html"> <assert_contents> <has_text text="Seurat Analysis" /> <has_text text="Performed using Galaxy" /> <has_text text="img src="data:image/png;base64" /> </assert_contents> </output> </test> <test expect_num_outputs="4"> <conditional name="function"> <param name="function_select" value="cite"/> <param name="rna" ftype="tabular" value="rna.tab.gz"/> <param name="prot" ftype="tabular" value="adt.tab.gz"/> <param name="min_cells" value="0"/> <param name="min_genes" value="0"/> <param name="low_thresholds" value="1" /> <param name="high_thresholds" value="20000000" /> <param name="vlnfeat" value="F"/> <param name="norm_file" value="F"/> <param name="featplot" value="T"/> <param name="var_file" value="F"/> <param name="num_PCs" value="20" /> <param name="pc_plots" value="T"/> <param name="pca_file" value="F"/> <param name="resolution" value="0.6" /> <param name="nmds" value="F"/> <param name="clusters_file" value="F"/> <param name="min_pct" value="0.25" /> <param name="logfc_threshold" value="0.25" /> <param name="heatmaps" value="T"/> <param name="markers_file" value="F"/> <param name="cite_markers" value="T"/> <conditional name="comparison"> <param name="comparison" value="yes"/> <param name="feat_comp" value="CD4,CD19"/> </conditional> <conditional name="marker_compare"> <param name="marker_compare" value="yes"/> <param name="top_x" value="3"/> </conditional> </conditional> <section name="meta"> <param name="showcode" value="T"/> <param name="warn" value="F"/> <param name="varstate" value="F"/> </section> <output name="rnamarkerst" ftype="tabular" file="rna_out.tsv" compare="sim_size" delta="500" /> <output name="protmarkerst" ftype="tabular" file="protein_out.tsv" compare="sim_size" delta="500" /> </test> <test expect_num_outputs="9"> <conditional name="function"> <param name="function_select" value="cite"/> <param name="rna" ftype="tabular" value="rna.tab.gz"/> <param name="prot" ftype="tabular" value="adt.tab.gz"/> <param name="min_cells" value="0"/> <param name="min_genes" value="0"/> <param name="low_thresholds" value="1" /> <param name="high_thresholds" value="20000000" /> <param name="vlnfeat" value="F"/> <param name="norm_file" value="T"/> <param name="featplot" value="T"/> <param name="var_file" value="T"/> <param name="num_PCs" value="20" /> <param name="pc_plots" value="T"/> <param name="pca_file" value="T"/> <param name="resolution" value="0.6" /> <param name="nmds" value="T"/> <param name="clusters_file" value="T"/> <param name="min_pct" value="0.25" /> <param name="logfc_threshold" value="0.25" /> <param name="heatmaps" value="T"/> <param name="markers_file" value="T"/> <param name="cite_markers" value="F"/> <conditional name="comparison"> <param name="comparison" value="yes"/> <param name="feat_comp" value="CD4,CD19"/> </conditional> <conditional name="marker_compare"> <param name="marker_compare" value="yes"/> <param name="top_x" value="3"/> </conditional> </conditional> <section name="meta"> <param name="showcode" value="T"/> <param name="warn" value="F"/> <param name="varstate" value="F"/> </section> </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. See the `Seurat Guided Clustering tutorial`_ for more information. ----- **Inputs** * Gene count matrix in TAB-separated format or * RNA and Protein count matrices in TAB-separated formats ----- **Outputs** * HTML of plots Optionally you can choose to output * R commands used to generate plots printed alongside figures .. _Seurat: https://www.nature.com/articles/nbt.4096 .. _Satija Lab: https://satijalab.org/seurat/ .. _Seurat Guided Clustering tutorial: https://satijalab.org/seurat/pbmc3k_tutorial.html ]]></help> <citations> <citation type="doi">10.1038/nbt.4096</citation> </citations> </tool>