Mercurial > repos > ebi-gxa > scmap_index_cell

changeset 2:dd2a84734b87 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 06:36:06 -0400
parents 17b3d7e04b3c
children 5593b0744de9
files scmap_index_cell.xml scmap_macros.xml
diffstat 2 files changed, 5 insertions(+), 6 deletions(-) [+]
line wrap: on
line diff
--- a/scmap_index_cell.xml	Fri Oct 25 08:44:38 2019 -0400
+++ b/scmap_index_cell.xml	Fri Apr 03 06:36:06 2020 -0400
@@ -1,11 +1,11 @@
-<tool id="scmap_index_cell" name="scmap index cells" version="@TOOL_VERSION@+galaxy0" python_template_version="3.5">
+<tool id="scmap_index_cell" name="scmap index cells" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
     <description>creates a cell index for a dataset to enable fast approximate nearest neighbour search</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-cell.R --input-object-file "preprocessed_${input_single_cell_experiment}" --number-chunks '$n_chunks' --number-clusters '$n_clusters' --output-object-file '$output_single_cell_experiment' --random-seed '$random_seed'
+        scmap-preprocess-sce.R --input-object "${input_single_cell_experiment}" --output-sce-object "${input_single_cell_experiment}.preprocessed" && scmap-index-cell.R --input-object-file "${input_single_cell_experiment}.preprocessed" --number-chunks '$n_chunks' --number-clusters '$n_clusters' --output-object-file '$output_single_cell_experiment' --random-seed '$random_seed'
     ]]></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'" />
@@ -21,7 +21,7 @@
             <param name="n_chunks" value="50" />
             <param name="n_clusters" value="9" />
             <param name="input_single_cell_experiment" value="select_features.rds" ftype="rdata"/>
-            <output name="output_single_cell_experiment" file="index_cell.rds"/>
+            <output name="output_single_cell_experiment" file="index_cell.rds" compare="sim_size"/>
         </test>
     </tests>
     <help><![CDATA[
--- a/scmap_macros.xml	Fri Oct 25 08:44:38 2019 -0400
+++ b/scmap_macros.xml	Fri Apr 03 06:36:06 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>