Mercurial > repos > iuc > raceid_clustering

changeset 8:f911a64454fb draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 455bad7eca54164f95755174904842907846bb42"
author iuc
date Mon, 20 Dec 2021 10:12:47 +0000
parents c4f39bf4a068
children 0bff0ee0683a
files macros.xml raceid_clustering.xml
diffstat 2 files changed, 7 insertions(+), 6 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Thu Dec 02 16:20:43 2021 +0000
+++ b/macros.xml	Mon Dec 20 10:12:47 2021 +0000
@@ -26,7 +26,8 @@
 }
     </token>
     <token name="@TOOL_VERSION@">0.2.3</token>
-    <token name="@VERSION_SUFFIX@">1</token>
+    <token name="@VERSION_SUFFIX@">2</token>
+    <token name="@PROFILE@">21.01</token>
 
     <macro name="version_command_config" token_prog="temp" token_cheetah="temp2" token_out="2&#62; '$outlog'">
         <version_command><![CDATA[
--- a/raceid_clustering.xml	Thu Dec 02 16:20:43 2021 +0000
+++ b/raceid_clustering.xml	Mon Dec 20 10:12:47 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="raceid_clustering" name="Clustering using RaceID" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" >
+<tool id="raceid_clustering" name="Clustering using RaceID" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" >
     <description>performs clustering, outlier detection, dimensional reduction</description>
     <macros>
         <import>macros.xml</import>
@@ -8,7 +8,7 @@
     <expand macro="version_command_config" prog="cluster.R" cheetah="CLUSTER_CHEETAH" out="&#38;&#62; '$outlog'" />
 
     <inputs>
-        <param name="inputrds" type="data" format="rdata" label="Input RaceID RDS" help="Requires the RDS output from the normalisation stage" />
+        <param name="inputrds" type="data" format="rds" label="Input RaceID RDS" help="Requires the RDS output from the normalisation stage" />
         <section name="clust" title="Clustering" expanded="true" >
             <!-- CompDist -->
             <param name="metric" type="select" label="Distance Metric" >
@@ -79,7 +79,7 @@
     </inputs>
     <outputs>
         <data name="outpdf" format="pdf" label="${tool.name} on ${on_string}: PDF Report" />
-        <data name="outrdat" format="rdata" label="${tool.name} on ${on_string}: RDS" />
+        <data name="outrdat" format="rds" label="${tool.name} on ${on_string}: RDS" />
         <data name="outassignments" format="tabular" label="${tool.name} on ${on_string}: Cell-to-Cluster assignments" />
         <data name="outgenelist" format="tabular" label="${tool.name} on ${on_string}: Cluster - Genes per Cluster" />
         <data name="outlog" format="txt" label="${tool.name} on ${on_string}: Log" >
@@ -95,7 +95,7 @@
                     <has_line_matching expression=".*ENSDARG00000027310\s+8.*" />
                 </assert_contents>
             </output>
-            <output name="outrdat" value="matrix2.rdat" compare="sim_size" delta="500" />
+            <output name="outrdat" value="matrix2.rdat" compare="sim_size" delta="40000" />
             <output name="outpdf" value="matrix2.pdf" compare="sim_size" delta="100" />
             <output name="outassignments" >
                 <assert_contents>
@@ -214,7 +214,7 @@
      * The initial and final clustering (as determined using random forest)
      * For each of the most differentially expressed genes in each cluster
 
-The tool requires the RData input from the previous filtering / normalisation / confounder removal step to work.
+The tool requires the RDS input from the previous filtering / normalisation / confounder removal step to work.
 
 
 ]]>