Mercurial > repos > iuc > seurat
diff seurat.xml @ 1:7319f83ae734 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
| author | iuc |
|---|---|
| date | Mon, 09 Dec 2019 14:32:16 -0500 |
| parents | 8d8412d35247 |
| children | 321bdd834266 |
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--- a/seurat.xml Sun Aug 26 16:24:02 2018 -0400 +++ b/seurat.xml Mon Dec 09 14:32:16 2019 -0500 @@ -1,111 +1,111 @@ <tool id="seurat" name="Seurat" version="2.3.4"> <description>- toolkit for exploration of single-cell RNA-seq data</description> <requirements> - <requirement type="package" version="3.4.1">r-base</requirement> - <requirement type="package" version="2.3.4">r-seurat</requirement> - <requirement type="package" version="1.0.0">bioconductor-singlecellexperiment</requirement> - <requirement type="package" version="1.6.0">r-optparse</requirement> + <requirement type="package" version="3.1.0">r-seurat</requirement> + <requirement type="package" version="1.16">r-rmarkdown</requirement> </requirements> - <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: ")", SingleCellExperiment version" $(R --vanilla --slave -e "library(SingleCellExperiment); cat(sessionInfo()\$otherPkgs\$SingleCellExperiment\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", optparse version" $(R --vanilla --slave -e "library(optparse); cat(sessionInfo()\$otherPkgs\$optparse\$Version)" 2> /dev/null | grep -v -i "WARNING: ") - ]]></version_command> <command detect_errors="exit_code"><![CDATA[ - -#if $rscript: - cp '$__tool_directory__/seurat.R' '$out_rscript' && +#if "vln" in $meta.plots: + #set $vln = 'T' +#else + #set $vln = 'F' +#end if +#if "feat" in $meta.plots: + #set $feat = 'T' +#else + #set $feat = 'F' #end if - -Rscript '$__tool_directory__/seurat.R' - ---counts '$counts' ---numPCs $adv.num_PCs ---min.cells $adv.min_cells ---min.genes $adv.min_genes - -#if $adv.low_thresholds: - --low.thresholds $adv.low_thresholds +#if "PCs" in $meta.plots: + #set $PCs = 'T' +#else + #set $PCs = 'F' #end if -#if $adv.high_thresholds: - --high.thresholds $adv.high_thresholds -#end if -#if $adv.x_low_cutoff: - --x.low.cutoff $adv.x_low_cutoff +#if "tsne" in $meta.plots: + #set $tsne = 'T' +#else + #set $tsne = 'F' #end if -#if $adv.x_high_cutoff: - --x.high.cutoff $adv.x_high_cutoff -#end if -#if $adv.y_cutoff: - --y.cutoff $adv.y_cutoff +#if "heat" in $meta.plots: + #set $heatmaps = 'T' +#else + #set $heatmaps = 'F' #end if -#if $adv.cells_use: - --cells.use $adv.cells_use -#end if -#if $adv.resolution: - --resolution $adv.resolution -#end if -#if $adv.min_pct: - --min.pct $adv.min_pct -#end if -#if $adv.logfc_threshold: - --logfc.threshold $adv.logfc_threshold -#end if - -#if $rds: - --rds '$rds' -#end if - -]]></command> - +Rscript -e "library(\"rmarkdown\"); render(\"$__tool_directory__/Seurat.R\", + params = list(counts = \"${counts}\", + min_cells = \"${adv.min_cells}\", + min_genes = \"${adv.min_genes}\", + low_thresholds = \"${adv.low_thresholds}\", + high_thresholds = \"${adv.high_thresholds}\", + numPCs = \"${adv.num_PCs}\", + cells_use = \"${adv.cells_use}\", + resolution = \"${adv.resolution}\", + min_pct = \"${adv.min_pct}\", + logfc_threshold = \"${adv.logfc_threshold}\", + warn = \"${meta.warn}\", + varstate = \"${meta.varstate}\", + showcode = \"${meta.showcode}\", + vlnfeat = \"$vln\", + featplot = \"$feat\", + PCplots = \"$PCs\", + tsne = \"$tsne\", + heatmaps = \"$heatmaps\"), + intermediates_dir = \".\", + output_format = html_document(), + output_dir = \".\", + output_file = \"out.html\")" + ]]></command> <inputs> - <param name="counts" type="data" format="tabular" 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="rscript" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="False" label="Output Rscript?" help="If this option is set to Yes, the Rscript used by this tool will be provided as a text file in the output. Default: No" /> - <param name="rds" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Output Seurat RDS object?" - help="Output the Seurat RDS object, can be loaded into R. Default: No"> - </param> - <section name="adv" title="Advanced Options"> - <param argument="--num_PCs" type="integer" min="0" value="10" label="Number of PCs to use in plots" help="Uses this number of PCs in PCHEatmap, JackStrawPlot, FindClusters, RunTSNE. Default: 10" /> - <param argument="--min_cells" type="integer" min="0" value="0" label="Minimum cells" help="Include genes with detected expression in at least this many cells." /> - <param argument="--min_genes" type="integer" min="0" value="0" label="Minimum genes" help="Include cells where at least this many genes are detected." /> - <param argument="--low_thresholds" type="float" optional="True" label="Low threshold for filtering cells" /> - <param argument="--high_thresholds" type="float" optional="True" label="High threshold for filtering cells" /> - <param argument="--x_low_cutoff" type="float" optional="True" label="X-axis low cutoff for variable genes" help="Bottom cutoff on x-axis for identifying variable genes" /> - <param argument="--x_high_cutoff" type="float" optional="True" label="X-axis high cutoff for variable genes" help="Top cutoff on x-axis for identifying variable genes" /> - <param argument="--y_cutoff" type="float" optional="True" label="Y-axis cutoff for variable genes" help="Bottom cutoff on y-axis for identifying variable genes" /> - <param argument="--cells_use" type="integer" min="0" optional="True" label="Cells to use for PCHeatmap" help="Plots this number of top ‘extreme’ cells on both ends of the spectrum, which dramatically speeds plotting for large datasets" /> - <param argument="--resolution" type="float" optional="True" label="Resolution parameter" help="Value of the resolution parameter used in FindClusters, use a value above (below) 1.0 if you want to obtain a larger (smaller) number of communities." /> - <param argument="--min_pct" type="float" optional="True" label="Minimum percent cells" help="With FindMarkers only test genes that are detected in a minimum fraction of min.pct cells in either of the two populations. Meant to speed up the function by not testing genes that are very infrequently expressed. Default is 0.1" /> - <param argument="--logfc_threshold" type="float" min="0" optional="True" label="LogFC threshold" + <param name="counts" 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"/> + <section name="adv" title="Advanced Options" expanded="true"> + <param name="num_PCs" type="integer" min="0" value="10" label="Number of PCs to use in plots" help="Uses this number of PCs in PCHEatmap, JackStrawPlot, FindClusters, RunTSNE. Default: 10" /> + <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." /> + <param name="low_thresholds" type="integer" value="1" label="Low threshold for filtering cells" /> + <param name="high_thresholds" type="integer" value="20000000" label="High threshold for filtering cells" /> + <param name="cells_use" type="integer" min="1" value="500" label="Cells to use for PCHeatmap" help="Plots this number of top ‘extreme’ cells on both ends of the spectrum, which dramatically speeds plotting for large datasets" /> + <param name="resolution" type="float" value="0.6" label="Resolution parameter" help="Value of the resolution parameter used in FindClusters, use a value above (below) 1.0 if you want to obtain a larger (smaller) number of communities." /> + <param name="min_pct" type="float" value="0.1" label="Minimum percent cells" help="With FindMarkers only test genes that are detected in a minimum fraction of min.pct cells in either of the two populations. Meant to speed up the function by not testing genes that are very infrequently expressed. Default is 0.1" /> + <param name="logfc_threshold" type="float" min="0" value="0.25" label="LogFC threshold" help="With FindMarkers, limit testing to genes which show, on average, at least X-fold difference (log-scale)between the two groups of cells. Default is 0.25 Increasing logfc.threshold speeds up the function, but can miss weaker signals." /> </section> + <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?"/> + <param name="plots" type="select" optional="true" multiple="true" display="checkboxes" label="Which plots should be output?"> + <option value="vln" selected="true">Violin and Scatter plots</option> + <option value="feat" selected="true">Feature counts plots</option> + <option value="PCs" selected="true">PC plots</option> + <option value="tsne" selected="true">tSNE plots</option> + <option value="heat" selected="true">Heatmap plots</option> + </param> + </section> </inputs> - <outputs> - <data name="out_pdf" format="pdf" from_work_dir="out.pdf" label="${tool.name} on ${on_string}: Plots" /> - <data name="out_rscript" format="txt" from_work_dir="out_rscript.txt" label="${tool.name} on ${on_string}: Rscript"> - <filter>rscript</filter> - </data> - <data name="out_rds" format="rds" from_work_dir="Seurat.rds" label="${tool.name} on ${on_string}: RData file"> - <filter>rds</filter> - </data> + <data name="out_html" format="html" from_work_dir="out.html" label="${tool.name} on ${on_string}" /> </outputs> <tests> - <!-- Ensure count matrix input works --> <test> - <param name="counts" ftype="tabular" value="deng_small.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="x_low_cutoff" value="0.0125" /> - <param name="x_high_cutoff" value="3" /> - <param name="y_cutoff" value="0.5" /> - <param name="numPCs" value="10" /> - <param name="cells_use" value="500"/> - <param name="resolution" value="0.6" /> - <param name="min_pct" value="0.25" /> - <param name="logfc_threshold" value="0.25" /> - <output name="out_pdf" ftype="pdf" value="out.pdf" compare="sim_size"/> + <param name="counts" ftype="tabular" value="counts.tab.gz"/> + <section name="adv"> + <param name="numPCs" value="10" /> + <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="cells_use" value="500"/> + <param name="resolution" value="0.6" /> + <param name="min_pct" value="0.25" /> + <param name="logfc_threshold" value="0.25" /> + </section> + <section name="meta"> + <param name="showcode" value="T"/> + <param name="warn" value="F"/> + <param name="varstate" value="F"/> + <param name="plots" value="feat"/> + </section> + <output name="out_html" ftype="html" value="out.html" compare="sim_size"/> </test> </tests> <help><![CDATA[ @@ -128,7 +128,7 @@ **Outputs** - * PDF of plots + * HTML of plots Optionally you can choose to output