Mercurial > repos > ebi-gxa > scmap_index_cell

changeset 11:dd0b44bd359a 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 13:43:08 +0000
parents 7c3f9606ed0a
children d9f79a39b39d
files scmap_index_cell.xml scmap_macros.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, 7 insertions(+), 113 deletions(-) [+]
line wrap: on
line diff
--- a/scmap_index_cell.xml	Thu Aug 13 06:14:03 2020 -0400
+++ b/scmap_index_cell.xml	Fri Nov 27 13:43:08 2020 +0000
@@ -6,7 +6,7 @@
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
         scmap-preprocess-sce.R --input-object "${input_single_cell_experiment}" --output-sce-object sce_object_preprocessed.rds &&
-        scmap-index-cell.R --input-object-file sce_object_preprocessed.rds --output-object-file '$output_single_cell_experiment' --random-seed '$random_seed'
+        scmap-index-cell.R --input-object-file sce_object_preprocessed.rds --output-object-file '$output_single_cell_experiment' --random-seed '$random_seed' --remove-mat '${remove_mat}'
         #if $train_id
         --train-id '${train_id}' 
         #end if
@@ -23,6 +23,7 @@
         <param name="n_chunks" type="integer" label="Number of chunks" optional="true" value="0" help="Number of chunks into which the expr matrix is split" />
         <param name="n_clusters" type="integer" label="Number of clusters" optional="true" value="0" help="Number of clusters per group for k-means clustering" />
         <param type="text" name="train_id" label="Dataset ID" help="ID of the training dataset" />
+        <param type="boolean" name="remove_mat" checked="false" label="Remove Matrix" help="Should the expression data be removed after classifier is trained?" />
         <param name="random_seed" type="integer" label="Random seed" value='1' help="scmap-cell contains k-means step which makes it stochastic, i.e. running it multiple times will provide slightly different results. A fixed random seed ensures reproducibility." />
     </inputs>
     <outputs>
@@ -31,7 +32,8 @@
     <tests>
         <test>
             <param name="input_single_cell_experiment" value="select_features.rds" ftype="rdata"/>
-            <output name="output_single_cell_experiment" file="index_cell.rds" compare="sim_size"/>
+            <param name="remove_mat" value="true" />
+            <output name="output_single_cell_experiment" file="index_cell.rds" compare="sim_size" delta="10000000"/>
         </test>
     </tests>
     <help><![CDATA[
--- a/scmap_macros.xml	Thu Aug 13 06:14:03 2020 -0400
+++ b/scmap_macros.xml	Fri Nov 27 13:43:08 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/test-data/closest_cells.csv	Thu Aug 13 06:14:03 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	Thu Aug 13 06:14:03 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	Thu Aug 13 06:14:03 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	Thu Aug 13 06:14:03 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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