diff seurat_select_integration_features.xml @ 0:699c0ca328f2 draft default tip

planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/seurat_select_integration_features.xml	Sat Mar 02 10:40:57 2024 +0000
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+<tool id="seurat_select_integration_features" name="Seurat select integration features" profile="18.01" version="@SEURAT_VERSION@+galaxy0">
+    <description>from a list of studies</description>
+    <macros>
+        <import>seurat_macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="version" />
+    <command detect_errors="exit_code"><![CDATA[
+    @INPUT_OBJS_PREAMBLE@
+    seurat-select-integration-features.R
+    @INPUT_OBJECTS@
+
+    --nfeatures '$nfeatures'
+
+
+    #if $assay_list
+    --assay-list '$assay_list'
+    #end if
+
+    $verbose
+
+
+    #if $fvf_nfeatures
+    --fvf-nfeatures '$fvf_nfeatures'
+    #end if
+
+
+    --file-out '$file_out'
+
+
+    ]]></command>
+    <inputs>
+        <expand macro="input_object_params" multiple="True"  />
+        <param label="Number of features" optional='true' value='2000' name="nfeatures" argument="--nfeatures" type="integer"   help="Number of features to return"/>
+        <param label="Assay-list" optional='true' name="assay_list" argument="--assay-list" type="text"   help="Name or vector of assay names (one for each object) from which to pull the variable features."/>
+        <param label="Verbose" optional='true' value='true' name="verbose" argument="--do-not-verbose" type="boolean"  truevalue='' falsevalue='--do-not-verbose' checked='true' help="Print messages"/>
+        <param label="Fvf nfeatures" optional='true' value='2000' name="fvf_nfeatures" argument="--fvf-nfeatures" type="integer"   help="nfeatures for FindVariableFeatures. Used if VariableFeatures have not been set for any object in input."/>
+
+    </inputs>
+    <outputs>
+        <data label="${tool.name} on ${on_string}: Rdata file with features" name="file_out" format='rdata' />
+    </outputs>
+    <tests>
+      <!-- MANUAL TESTS -->
+      <test>
+        <param name="rds_seurat_file" ftype="rdata" value="ifnb_ctrl_norm_fvg.rds,ifnb_stim_norm_fvg.rds"/>
+        <output name="file_out" ftype="rdata" >
+          <assert_contents>
+            <has_size value="9506" delta="950"/>
+          </assert_contents>
+        </output>
+      </test>
+      <!-- END MANUAL TESTS -->
+    </tests>
+<help>
+<!-- MANUAL HELP -->
+<![CDATA[
+.. class:: infomark
+
+**What it does**
+
+@SEURAT_INTRO@
+
+This tool aims to facilitate the first steps of the Seurat 4.0.4 https://satijalab.org/seurat/articles/integration_introduction.html
+tutorial, to select features for integration of different datasets. This features can be used then with the integration tool.
+
+All options are documented in-line.
+
+-----
+
+**Inputs**
+
+* A set of Seurat objects (can be given in other formats as well) to integrate. These objects should be at least normalised and have the find variable genes/features method applied.
+* All other inputs are optional (see above).
+
+-----
+
+**Outputs**
+
+* A Seurat (or other format depending on selection) with the integrated object.
+
+@VERSION_HISTORY@
+]]>
+<!-- END MANUAL HELP -->
+</help>
+    <expand macro="citations" />
+</tool>