Mercurial > repos > ebi-gxa > scmap_scmap_cell

changeset 12:65b719530dd5 draft

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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit a1ad1ddd9b8e4db5bb82c3accae8311e0e488b19"
author ebi-gxa
date Fri, 27 Nov 2020 13:44:11 +0000
parents 1543a50e08c9
children 48400c291093
files scmap_macros.xml scmap_scmap_cell.xml test-data/closest_cells.csv test-data/closest_cells_clusters.csv test-data/closest_cells_clusters.rds test-data/closest_cells_similarities.csv test-data/index_cell.rds test-data/index_cluster.png test-data/index_cluster.rds test-data/project_cluster.csv test-data/project_cluster.rds test-data/select_features.png test-data/select_features.rds test-data/test_sce.rds
diffstat 14 files changed, 8 insertions(+), 117 deletions(-) [+]
line wrap: on
line diff
--- a/scmap_macros.xml	Fri Aug 14 10:44:26 2020 -0400
+++ b/scmap_macros.xml	Fri Nov 27 13:44:11 2020 +0000
@@ -1,10 +1,10 @@
 <macros>
-    <token name="@TOOL_VERSION@">1.6.2</token>
+    <token name="@TOOL_VERSION@">1.6.3</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" version="0.0.10">scmap-cli</requirement>
+        <requirement type="package" version="0.0.11">scmap-cli</requirement>
             <yield/>
       </requirements>
     </xml>
@@ -15,6 +15,7 @@
     </xml>
     <token name="@VERSION_HISTORY@"><![CDATA[
 **Version history**
+1.6.3+galaxy0: Update scmap-cli to 0.0.11
 1.6.2+galaxy0: Update scmap-cli to 0.0.10
 1.6.1+galaxy0: Update scmap-cli to 0.0.9.
 1.6.0+galaxy0: Initial contribution. Jonathan Manning, Expression Atlas team https://www.ebi.ac.uk/gxa/home at EMBL-EBI https://www.ebi.ac.uk/.
--- a/scmap_scmap_cell.xml	Fri Aug 14 10:44:26 2020 -0400
+++ b/scmap_scmap_cell.xml	Fri Nov 27 13:44:11 2020 +0000
@@ -21,7 +21,6 @@
       <param type="data" name="index_single_cell_experiment" label="Index SingleCellExperiment object" format="rdata" help="File with serialized SingleCellExperiment object as produced by 'scmap select features' and 'scmap index clusters', onto which another dataset will be projected." />
       <param type="data" name="project_single_cell_experiment" label="SingleCellExperiment object to project" format="rdata" help="File with serialized SingleCellExperiment object to project onto the index'" />
       <param name="n_nearest_neighbours" type="integer" label="Number of nearest neighbours" value='5' help="A positive integer specifying the number of nearest neighbours to find" />
-      
      <conditional name="cluster_projection">
         <param name="do_cluster_projection" type="boolean" checked="false" label="Annotate cells of the projection dataset using labels of the reference?" help="If cell cluster annotation is available for the reference datasets, in addition to finding top 10 nearest neighbours scmap-cell also allows to annotate cells of the projection dataset using labels of the reference."/>
         <when value="true" >
@@ -43,12 +42,12 @@
     <tests>
         <test>
             <param name="index_single_cell_experiment" value="index_cell.rds" ftype="rdata"/>
-            <param name="project_single_cell_experiment" value="test_sce.rds" ftype="rdata"/>
-            <param name="cluster_projection" value="true" ftype="rdata"/>
+            <param name="project_single_cell_experiment" value="test_sce_processed.rds" ftype="rdata"/>
+            <param name="cluster_projection" value="true" />
             <output name="output_single_cell_experiment" file="closest_cells_clusters.rds" compare="sim_size"/>
-            <output name="closest_cells_clusters_csv" file="closest_cells_clusters.csv" compare="sim_size" />
-            <output name="closest_cells_text_file" file="closest_cells.csv" compare="sim_size"/>
-            <output name="closest_cells_similarities_text_file" file="closest_cells_similarities.csv" compare="sim_size"/>
+            <output name="closest_cells_clusters_csv" file="closest_cells_clusters.tsv" compare="sim_size" />
+            <output name="closest_cells_text_file" file="closest_cells.tsv" compare="sim_size"/>
+            <output name="closest_cells_similarities_text_file" file="closest_cells_similarities.tsv" compare="sim_size"/>
         </test>
     </tests>
     <help><![CDATA[
--- a/test-data/closest_cells.csv	Fri Aug 14 10:44:26 2020 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
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--- a/test-data/closest_cells_clusters.csv	Fri Aug 14 10:44:26 2020 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
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Binary file test-data/closest_cells_clusters.rds has changed
--- a/test-data/closest_cells_similarities.csv	Fri Aug 14 10:44:26 2020 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
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Binary file test-data/index_cell.rds has changed
Binary file test-data/index_cluster.png has changed
Binary file test-data/index_cluster.rds has changed
--- a/test-data/project_cluster.csv	Fri Aug 14 10:44:26 2020 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,91 +0,0 @@
-,cell,scmap_cluster_labs,scmap_cluster_siml,combined_labs
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-70,Late.blastocyst..1..Cell.10.RPKM.,blast,0.956481724858848,blast
-71,Late.blastocyst..1..Cell.11.RPKM.,blast,0.956159281369748,blast
-72,Late.blastocyst..1..Cell.12.RPKM.,blast,0.96425809974187,blast
-73,Late.blastocyst..2..Cell.1.RPKM.,blast,0.954566650006314,blast
-74,Late.blastocyst..2..Cell.2.RPKM.,blast,0.859795704593317,blast
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-81,Late.blastocyst..2..Cell.9.RPKM.,blast,0.958716824617989,blast
-82,Late.blastocyst..2..Cell.10.RPKM.,blast,0.966000611704395,blast
-83,Late.blastocyst..3..Cell.1.RPKM.,blast,0.830150497819373,blast
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-88,Late.blastocyst..3..Cell.6.RPKM.,blast,0.923562228265187,blast
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-90,Late.blastocyst..3..Cell.8.RPKM.,blast,0.917408664281774,blast
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