diff seurat_find_markers.xml @ 0:fde95fe95f15 draft

planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/seurat_find_markers.xml	Wed Apr 03 11:17:29 2019 -0400
@@ -0,0 +1,116 @@
+<tool id="seurat_find_markers" name="Seurat FindMarkers" version="2.3.1+galaxy1">
+    <description>find markers (differentially expressed genes)</description>
+    <macros>
+        <import>seurat_macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="version" />
+    <command detect_errors="exit_code"><![CDATA[
+seurat-find-markers.R
+
+--input-object-file '$input'
+--output-text-file output.txt
+
+#if $genes_use:
+  --genes-use '$genes_use'
+#end if
+
+#if str($logfc_threshold):
+  --logfc-threshold '$logfc_threshold'
+#end if
+
+#if str($adv.min_pct):
+  --min-pct '$adv.min_pct'
+#end if
+
+#if str($adv.min_diff_pct):
+  --min-diff-pct '$adv.min_diff_pct'
+#end if
+
+#if $adv.only_pos:
+  --only-pos '$adv.only_pos'
+#end if
+
+--test-use '$adv.test_use'
+
+#if str($max_cells_per_ident):
+  --max-cells-per-ident '$max_cells_per_ident'
+#end if
+
+#if str($min_cells_per_gene):
+  --min-cells-gene '$min_cells_per_gene'
+#end if
+
+#if str($min_cells_group):
+  --min-cells-group '$min_cells_group'
+#end if
+
+
+]]></command>
+
+    <inputs>
+        <param name="input" type="data" format="rdata" label="RDS object" />
+        <expand macro="genes-use-input"/>
+        <param name="logfc_threshold" label="LogFC logfc_threshold" optional="true" argument="--logfc-threshold" type="float" help="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="max_cells_per_ident" label="Max cells per ident" optional="true" argument="--max-cells-per-ident" type="integer" help="Down sample each identity class to a max number. Default is no downsampling. Not activated by default (set to Inf)."/>
+        <param name="min_cells_per_gene" label="Min cells per gene" optional="true" argument="--min-cells-gene" type="integer" help="Minimum number of cells expressing the gene in at least one of the two groups, currently only used for poisson and negative binomial tests."/>
+        <param name="min_cells_group" label="Min cells in one of the groups" optional="true" argument="--min-cells-group" type="integer"/>
+        <section name="adv" title="Advanced Options">
+            <param name="min_pct" type="float" label="Min Pct" optional="true" help="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="min_diff_pct" type="float" label="Min diff Pct" optional="true" help="Only test genes that show a minimum difference in the fraction of detection between the two groups. Set to -Inf by default."/>
+            <param name="only_pos" type="boolean" label="Only positive markers" truevalue="TRUE" falsevalue="" help="Only return positive markers (FALSE by default)."/>
+            <param name="test_use" type="select" label="Test to use" help="">
+              <option value="wilcox" selected="true">Wilcoxon</option>
+              <option value="bimod">Bi-modal</option>
+              <option value="roc">ROC</option>
+              <option value="t">t-Test</option>
+              <option value="tobit">tobit</option>
+              <option value="poisson">Poisson</option>
+              <option value="negbinom">Negative binomia</option>
+              <option value="MAST">MAST</option>
+              <option value="DESeq2">DESeq2</option>
+            </param>
+        </section>
+    </inputs>
+
+    <outputs>
+        <data name="output" format="txt" from_work_dir="output.txt" label="${tool.name} on ${on_string}: Text file"/>
+    </outputs>
+
+    <tests>
+        <test>
+            <param name="input" ftype="rdata" value="out_runtsne.rds"/>
+            <output name="output" ftype="txt" value="out_findmark.txt"/>
+        </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.
+
+This tool finds markers (differentially expressed genes) for each of the identity classes in a dataset. It outputs a text file containing a ranked list of putative markers, and associated statistics (p-values, ROC score, etc.)
+
+-----
+
+**Inputs**
+
+    * RDS object
+
+-----
+
+**Outputs**
+
+    * Text file
+
+.. _Seurat: https://www.nature.com/articles/nbt.4096
+.. _Satija Lab: https://satijalab.org/seurat/
+
+@VERSION_HISTORY@
+]]></help>
+      <expand macro="citations" />
+</tool>