| Previous changeset 8:828324f3292f (2021-06-10) Next changeset 10:bb9732cfcdbe (2021-12-20) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 7681c9101062f58ac4eb296a98b1644d4ed2340a" |
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modified:
Seurat.R seurat.xml |
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removed:
test-data/out.html |
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| diff -r 828324f3292f -r c4db6ec33fec Seurat.R --- a/Seurat.R Thu Jun 10 17:19:49 2021 +0000 +++ b/Seurat.R Thu Oct 21 15:57:20 2021 +0000 |
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| @@ -115,6 +115,6 @@ #+ echo = `showcode`, warning = `warn`, include = `heatmaps` markers <- Seurat::FindAllMarkers(seuset, only.pos = TRUE, min.pct = min_pct, logfc.threshold = logfc_threshold) top10 <- dplyr::group_by(markers, cluster) -top10 <- dplyr::top_n(top10, 10, avg_logFC) +top10 <- dplyr::top_n(top10, 10, avg_log2FC) Seurat::DoHeatmap(seuset, features = top10$gene) # nolint end |
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| diff -r 828324f3292f -r c4db6ec33fec seurat.xml --- a/seurat.xml Thu Jun 10 17:19:49 2021 +0000 +++ b/seurat.xml Thu Oct 21 15:57:20 2021 +0000 |
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| @@ -1,11 +1,11 @@ <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> + <token name="@TOOL_VERSION@">4.0.5</token> </macros> <requirements> <requirement type="package" version="@TOOL_VERSION@">r-seurat</requirement> - <requirement type="package" version="2.4">r-rmarkdown</requirement> + <requirement type="package" version="2.11">r-rmarkdown</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ #if "vln" in $meta.plots: @@ -66,17 +66,17 @@ <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="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="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." /> + <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?"/> @@ -115,7 +115,13 @@ <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" /> + <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> <!-- perplexity test --> <param name="counts" ftype="tabular" value="counts.tab.gz"/> @@ -137,7 +143,13 @@ <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" /> + <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> </tests> <help><![CDATA[ |
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| diff -r 828324f3292f -r c4db6ec33fec test-data/out.html --- a/test-data/out.html Thu Jun 10 17:19:49 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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width="672" /></p>\n-<pre class="r"><code>seuset <- Seurat::ScaleData(object = seuset, vars.to.regress = "nCount_RNA")</code></pre>\n-<pre><code>## Regressing out nCount_RNA</code></pre>\n-<pre><code>## Centering and scaling data matrix</code></pre>\n-\n-\n-\n-\n-</div>\n-\n-<script>\n-\n-// add bootstrap table styles to pandoc tables\n-function bootstrapStylePandocTables() {\n- $(\'tr.header\').parent(\'thead\').parent(\'table\').addClass(\'table table-condensed\');\n-}\n-$(document).ready(function () {\n- bootstrapStylePandocTables();\n-});\n-\n-\n-</script>\n-\n-<!-- tabsets -->\n-\n-<script>\n-$(document).ready(function () {\n- window.buildTabsets("TOC");\n-});\n-\n-$(document).ready(function () {\n- $(\'.tabset-dropdown > .nav-tabs > li\').click(function () {\n- $(this).parent().toggleClass(\'nav-tabs-open\')\n- });\n-});\n-</script>\n-\n-<!-- code folding -->\n-\n-\n-<!-- dynamically load mathjax for compatibility with self-contained -->\n-<script>\n- (function () {\n- var script 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