# HG changeset patch
# User ebi-gxa
# Date 1586342283 14400
# Node ID db7ecc1aaf59e0c08c698d57d1bef3aafc214e5b

"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"

diff -r 000000000000 -r db7ecc1aaf59 scpred_get_feature_space.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scpred_get_feature_space.xml	Wed Apr 08 06:38:03 2020 -0400
@@ -0,0 +1,31 @@
+<tool id='scpred_get_feature_space' name='ScPred feature space' version='@TOOL_VERSION@+galaxy0' profile="@PROFILE@">
+    <description>Get feature space for training matrix</description>
+    <macros>
+         <import>scpred_macros.xml</import>
+    </macros>
+    <expand macro='requirements' />
+    <command detect_errors='exit_code'><![CDATA[
+        scpred_get_feature_space.R  --input-object '${input_object}'  --prediction-column '${prediction_column}' --explained-var-limit '${explained_var_limit}' --output-path '${output_obj_path}' --eigenvalue-plot-path '${eigenvalue_plot_path}']]></command>
+    <inputs>
+        <param type='data' name='input_object' label='Input SCE object' format='rdata' help='Input SCE object in .rds format' />
+        <param type='text' name='prediction_column' label='Prediction column' help='Name of the metadata column that contains training labels' />
+        <param type='float' name='explained_var_limit' label='Limit of explained variance' value="0.01" help='Threshold to filter principal components based on variance explained' />
+    </inputs>
+    <outputs>
+        <data name='output_obj_path' format='rdata' />
+        <data name='eigenvalue_plot_path' format='png' />
+    </outputs>
+     <tests>
+        <test>
+            <param name="input_object" value="scPred_object.rds" />
+            <param name="prediction_column" value="cell_type2" />
+            <output name="output_obj_path" file="scPred_feat_space.rds" compare="sim_size" />
+        </test>
+    </tests>
+    <help><![CDATA[
+    @HELP@
+    
+    @VERSION_HISTORY@
+    ]]></help>
+    <expand macro='citations' />
+</tool>
\ No newline at end of file
diff -r 000000000000 -r db7ecc1aaf59 scpred_macros.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scpred_macros.xml	Wed Apr 08 06:38:03 2020 -0400
@@ -0,0 +1,46 @@
+<macros>
+    <token name="@TOOL_VERSION@">1.0.0</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="0.0.5">scpred-cli</requirement>
+                <yield/>
+        </requirements>
+    </xml>
+    <xml name="version">
+        <version_command><![CDATA[
+            echo $(R --version | grep version | grep -v GNU)",  scpred version" $(R --vanilla --slave -e "library(scpred); cat(sessionInfo()\$otherPkgs\$scpred\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
+            ]]></version_command>
+    </xml>
+    <token name="@VERSION_HISTORY@"><![CDATA[
+        **Version history**
+        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>
+    <xml name="citations">
+        <citations>
+            <citation type="bibtex">
+                @article{Alquicira-Hernandez2019,
+                author = {Alquicira-Hernandez, Jose and Sathe, Anuja and Ji, Hanlee P and Nguyen, Quan and Powell, Joseph E},
+                journal = {Genome Biology},
+                title = {{scPred: accurate supervised method for cell-type classification from single-cell RNA-seq data}},
+                url = {https://doi.org/10.1186/s13059-019-1862-5},
+                year = {2019}
+                }
+            </citation>
+            <citation type="bibtex">
+                @misc{githubscpred-cli.git,
+                author = {Andrey Solovyev, EBI Gene Expression Team},
+                year = {2019},
+                title = {scpred-cli: command line interface for ScPred tool},
+                publisher = {GitHub},
+                journal = {GitHub repository},
+                url = {https://github.com/ebi-gene-expression-group/scpred-cli.git},
+              }
+
+            </citation>
+            <yield />
+        </citations>
+    </xml>
+</macros>
+