diff raceid_clustering.xml @ 6:a4b734cd253b draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 53916f6803b93234f992f5fd4fad61d7013d82af"

--- a/raceid_clustering.xml	Wed Jan 29 17:16:36 2020 -0500
+++ b/raceid_clustering.xml	Thu Apr 15 18:58:21 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="raceid_clustering" name="Clustering using RaceID" version="@VERSION_RACEID@.@VERSION_WRAPPER@" >
+<tool id="raceid_clustering" name="Clustering using RaceID" version="@VERSION_RACEID@+galaxy@VERSION_WRAPPER@" >
     <description>performs clustering, outlier detection, dimensional reduction</description>
     <macros>
         <import>macros.xml</import>
@@ -52,17 +52,22 @@
                 <param name="rfseed" type="integer" value="12345" label="Random Seed" />
             </expand>
         </section>
-        <section name="tsne" title="tSNE and FR" expanded="true" >
+        <section name="tsne" title="tSNE, FR and UMAP" expanded="true" >
             <!-- CompTSNE -->
             <param name="perplexity" type="integer" min="0" value="30" label="Perplexity" help="Perplexity of the t-SNE map" />
             <!-- CompFR -->
-            <param name="knn" type="integer" min="0" value="10" label="KNN" help="Number of nearest neighbours used for the inference of the Fruchterman-Rheingold layout" />
+            <param name="knn" type="integer" min="1" value="10" label="KNN" help="Number of nearest neighbours used for the inference of the Fruchterman-Rheingold layout" />
+            <!-- CompUMAP -->
+            <param name="umap_nn" type="integer" min="1" value="15" label="N Neighbours" help="Number of nearest neighbours used for the UMAP connectivity" />
             <expand macro="use_defaults_no" >
                 <!-- CompTSNE -->
                 <param name="initial_cmd" type="boolean" checked="true" label="tSNE map initialised by classical multidimensional scaling" />
                 <param name="rseed_tsne" type="integer" value="15555" label="Random Seed (tSNE)" />
                 <!-- CompFR -->
                 <param name="rseed_fr" type="integer" min="0" value="15555" label="Random Seed (FR)" />
+                <!-- CompUMAP -->
+                <param name="umap_epochs" type="integer" min="1" value="200" label="Number Epochs (UMAP)" />
+                <param name="umap_min_dist" type="float" min="0" value="0.1" label="Min Dist (UMAP)" />
             </expand>
         </section>
         <section name="extra" title="Extra Parameters" expanded="false" >
@@ -84,9 +89,14 @@
     <tests>
         <test>
             <param name="inputrds" value="matrix.filter.rdat" />
-            <output name="outgenelist" value="matrix2.genelist" compare="re_match"/>
-            <output name="outrdat" value="matrix2.rdat" compare="sim_size" delta="15" />
-            <output name="outpdf" value="matrix2.pdf" compare="sim_size" delta="10" />
+            <output name="outgenelist" >
+                <assert_contents>
+                    <has_line_matching expression=".*ENSDARG00000108379\s+1.*" />
+                    <has_line_matching expression=".*ENSDARG00000027310\s+8.*" />
+                </assert_contents>
+            </output>
+            <output name="outrdat" value="matrix2.rdat" compare="sim_size" delta="500" />
+            <output name="outpdf" value="matrix2.pdf" compare="sim_size" delta="100" />
             <output name="outassignments" >
                 <assert_contents>
                     <has_line_matching expression="P1_B1_ATCCAC\s1\s1\sFALSE" />
@@ -127,7 +137,12 @@
                     <param name="rfseed_fr" value="15555" />
                 </expand>
             </section>
-            <output name="outgenelist" value="intestinal.genelist" compare="re_match"/>
+            <output name="outgenelist" >
+                <assert_contents>
+                    <has_line_matching expression=".*ENSDARG00000108379\s+1.*" />
+                    <has_line_matching expression=".*ENSDARG00000027310\s+8.*" />
+                </assert_contents>
+            </output>
             <output name="outpdf" value="intestinal.pdf" compare="sim_size" delta="50" />
         </test>
         <test>
@@ -168,7 +183,12 @@
                     <param name="rfseed_fr" value="15555" />
                 </expand>
             </section>
-            <output name="outgenelist" value="intestinal_advanced.genelist" compare="re_match"/>
+            <output name="outgenelist" >
+                <assert_contents>
+                    <has_line_matching expression=".*ENSDARG00000107138\s+1.*" />
+                    <has_line_matching expression=".*ENSDARG00000016138\s+10.*" />
+                </assert_contents>
+            </output>
             <output name="outpdf" value="intestinal_advanced.pdf" compare="sim_size" delta="150" />
         </test>
     </tests>