Mercurial > repos > ebi-gxa > scmap_index_cluster

changeset 2:63f1a27dce34 draft

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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 542b6e6848acedbbedb6fa2d4b44c8d476597cdd"
author ebi-gxa
date Fri, 03 Apr 2020 06:35:36 -0400
parents e6d99b0652ec
children 9b60d5972dbd
files scmap_index_cluster.xml scmap_macros.xml
diffstat 2 files changed, 5 insertions(+), 6 deletions(-) [+]
line wrap: on
line diff
--- a/scmap_index_cluster.xml	Fri Oct 25 08:45:05 2019 -0400
+++ b/scmap_index_cluster.xml	Fri Apr 03 06:35:36 2020 -0400
@@ -1,11 +1,11 @@
-<tool id="scmap_index_cluster" name="scmap index clusters" version="@TOOL_VERSION@+galaxy0" python_template_version="3.5">
+<tool id="scmap_index_cluster" name="scmap index clusters" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
     <description>calculates centroids of each cell type and merges them into a single table</description>
     <macros>
         <import>scmap_macros.xml</import>
     </macros>
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
-        scmap-preprocess-sce.R --input-object "${input_single_cell_experiment}" --output-sce-object "preprocessed_${input_single_cell_experiment}" && scmap-index-cluster.R --input-object-file "preprocessed_${input_single_cell_experiment}" --cluster-col '$cluster_col' --output-object-file '$output_single_cell_experiment' --output-plot-file '$plot'
+        scmap-preprocess-sce.R --input-object "${input_single_cell_experiment}" --output-sce-object "${input_single_cell_experiment}.preprocessed" && scmap-index-cluster.R --input-object-file "${input_single_cell_experiment}" --cluster-col '$cluster_col' --output-object-file '$output_single_cell_experiment' --output-plot-file '$plot'
     ]]></command>
     <inputs>
         <param type="data" name="input_single_cell_experiment" label="SingleCellExperiment object" format="rdata" help="File with serialized SingleCellExperiment object as produced by 'scmap select features'" />
@@ -18,7 +18,7 @@
     <tests>
         <test>
             <param name="input_single_cell_experiment" value="select_features.rds" ftype="rdata"/>
-            <output name="output_single_cell_experiment" file="index_cluster.rds"/>
+            <output name="output_single_cell_experiment" file="index_cluster.rds" compare="sim_size"/>
             <output name="plot" file="index_cluster.png"/>
         </test>
     </tests>
--- a/scmap_macros.xml	Fri Oct 25 08:45:05 2019 -0400
+++ b/scmap_macros.xml	Fri Apr 03 06:35:36 2020 -0400
@@ -1,11 +1,10 @@
 <macros>
     <token name="@TOOL_VERSION@">1.6.0</token>
     <token name="@HELP@">More information can be found at https://bioconductor.org/packages/release/bioc/html/scmap.html</token>
+    <token name="@PROFILE@">18.01</token>
     <xml name="requirements">
       <requirements>
-        <requirement type="package">openblas</requirement>
-        <requirement type="package">bioconductor-delayedarray</requirement>
-        <requirement type="package" version="0.0.4">scmap-cli</requirement>
+        <requirement type="package" version="0.0.5">scmap-cli</requirement>
             <yield/>
       </requirements>
     </xml>