comparison seurat.xml @ 6:764f076e9d52 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit e8eeff2efea68e1e5bc697d0ff6a5808cd978db2"

5:06ed31cf52ed

<tool id="seurat" name="Seurat" version="@TOOL_VERSION@+galaxy1">
    <description>- toolkit for exploration of single-cell RNA-seq data</description>
    <macros>
        <token name="@TOOL_VERSION@">3.1.5</token>
    </macros>
    <requirements>

#if "heat" in $meta.plots:
    #set $heatmaps = 'T'
#else
    #set $heatmaps = 'F'
#end if
Rscript -e "library(\"rmarkdown\"); render(\"$__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}\",

            <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="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"/>

6:764f076e9d52

<tool id="seurat" name="Seurat" version="@TOOL_VERSION@+galaxy2">
    <description>- toolkit for exploration of single-cell RNA-seq data</description>
    <macros>
        <token name="@TOOL_VERSION@">3.1.5</token>
    </macros>
    <requirements>

#if "heat" in $meta.plots:
    #set $heatmaps = 'T'
#else
    #set $heatmaps = 'F'
#end if
#if not str($adv.perplexity):
    #set $adv_perplexity = -1
#else:
    #set $adv_perplexity = $adv.perplexity
#end if
Rscript -e "library(\"rmarkdown\"); render(\"$__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}\",
        perplexity = \"${adv_perplexity}\",
        min_pct = \"${adv.min_pct}\",
        logfc_threshold = \"${adv.logfc_threshold}\",
        warn = \"${meta.warn}\",
        varstate = \"${meta.varstate}\",
        showcode = \"${meta.showcode}\",

            <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="perplexity" type="integer" value="" optional="true" label="Perplexity parameter" help="Parameter for the tSNE dimensionality reduction" />
            <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="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" delta="20000" />
        </test>
        <test> <!-- perplexity test -->
            <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="perplexity" value="16" />
                <param name="min_pct" value="0.25" />
                <param name="logfc_threshold" value="0.25" />
            </section>
            <section name="meta">
                <param name="showcode" value="T"/>