comparison seurat.xml @ 9:c4db6ec33fec draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 7681c9101062f58ac4eb296a98b1644d4ed2340a"

8:828324f3292f

<tool id="seurat" name="Seurat" version="@TOOL_VERSION@+galaxy0">
    <description>- toolkit for exploration of single-cell RNA-seq data</description>
    <macros>
        <token name="@TOOL_VERSION@">3.2.2</token>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">r-seurat</requirement>
        <requirement type="package" version="2.4">r-rmarkdown</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
#if "vln" in $meta.plots:
    #set $vln = 'T'
#else

    output_file = \"out.html\")"
    ]]></command>
    <inputs>
        <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="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="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="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="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>
    </tests>
    <help><![CDATA[
.. class:: infomark

9:c4db6ec33fec

<tool id="seurat" name="Seurat" version="@TOOL_VERSION@+galaxy0">
    <description>- toolkit for exploration of single-cell RNA-seq data</description>
    <macros>
        <token name="@TOOL_VERSION@">4.0.5</token>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">r-seurat</requirement>
        <requirement type="package" version="2.11">r-rmarkdown</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
#if "vln" in $meta.plots:
    #set $vln = 'T'
#else

    output_file = \"out.html\")"
    ]]></command>
    <inputs>
        <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" />
            <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="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 at least this percentage of cells in either of the two populations. Meant to speed up the function by not testing genes that are very infrequently expressed" />
            <param name="logfc_threshold" type="float" min="0" value="0.25" label="Log fold change 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. Increasing this parameter 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="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">
                <assert_contents>
                    <has_text text="Seurat Analysis" />
                    <has_text text="Performed using Galaxy" />
                    <has_text text="img src=&quot;data:image/png;base64" />
                </assert_contents>
            </output>
        </test>
        <test> <!-- perplexity test -->
            <param name="counts" ftype="tabular" value="counts.tab.gz"/>
            <section name="adv">
                <param name="numPCs" value="10" />

                <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">
                <assert_contents>
                    <has_text text="Seurat Analysis" />
                    <has_text text="Performed using Galaxy" />
                    <has_text text="img src=&quot;data:image/png;base64" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
.. class:: infomark