Mercurial > repos > ebi-gxa > scpred_get_std_output

changeset 7:598b1d9dd135 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"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 13:45:49 +0000
parents 9f3ce66cd91f
children
files scpred_get_std_output.xml scpred_macros.xml
diffstat 2 files changed, 10 insertions(+), 8 deletions(-) [+]
line wrap: on
line diff
--- a/scpred_get_std_output.xml	Fri Aug 14 11:08:13 2020 -0400
+++ b/scpred_get_std_output.xml	Fri Nov 27 13:45:49 2020 +0000
@@ -5,10 +5,10 @@
     </macros>
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[ 
-        scpred_get_std_output.R --predictions-file "${predictions_file}" --get-scores "${get_scores}" --classifier '${classifier}' --output-table "${output_table}" 
+        scpred_get_std_output.R --predictions-object "${predictions_object}" --get-scores "${get_scores}" --classifier '${classifier}' --output-table "${output_table}" 
         ]]></command>
     <inputs>
-        <param type="data" name="predictions_file" label="Predictions file" format="txt" help="Path to the predictions file in text format" />
+        <param type="data" name="predictions_object" label="Predictions Object" format="rdata" help="Path to the predictions file in text format" />
         <param type="data" name="classifier" label="Classifier object" format="rdata" help="Path to the classifier object used to obtain predictions" />
         <param type="boolean" checked="false" name="get_scores" label="Get scores" help="Boolean: should the prediction scores be included? default: FALSE" />
     </inputs>
@@ -17,12 +17,13 @@
     </outputs>
     <tests>
         <test>
-            <param name="predictions_file" value="predictions_table.txt" />
-            <param name="get_scores" value="TRUE" />
-            <output name="output_table" file="scpred_output_tbl.txt" compare="sim_size"/>
+            <param name="predictions_object" value="predicted_data.rds" />
+            <param name="get_scores" value="True" />
+            <param name="classifier" value="scPred_trained.rds" />
+            <output name="output_table" file="scpred_output_tbl.txt" compare="sim_size" />
         </test>
     </tests>
-     <help><![CDATA[
+    <help><![CDATA[
     @HELP@
     
     @VERSION_HISTORY@
--- a/scpred_macros.xml	Fri Aug 14 11:08:13 2020 -0400
+++ b/scpred_macros.xml	Fri Nov 27 13:45:49 2020 +0000
@@ -1,10 +1,10 @@
 <macros>
-    <token name="@TOOL_VERSION@">1.0.1</token>
+    <token name="@TOOL_VERSION@">1.0.2</token>
     <token name="@HELP@">More information can be found at https://joseah.github.io/post/introduction-to-scpred/</token>
     <token name="@PROFILE@">18.01</token>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="0.0.9">scpred-cli</requirement>
+            <requirement type="package" version="0.1.0">scpred-cli</requirement>
                 <yield/>
         </requirements>
     </xml>
@@ -15,6 +15,7 @@
     </xml>
     <token name="@VERSION_HISTORY@"><![CDATA[
         **Version history**
+        1.0.2+galaxy0: Update to a new version of r-scpred
         1.0.1+galaxy0: Update output format from csv to tsv
         1.0.0+galaxy0: Initilal contribution. Andrey Solovyev, Expression Atlas team https://www.ebi.ac.uk/gxa/home at EMBL-EBI https://www.ebi.ac.uk/.
         ]]></token>