changeset 0:c54f0e1a3bd8 draft

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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scpred_macros.xml	Wed Apr 08 06:18:58 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>
+

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scpred_predict.xml	Wed Apr 08 06:18:58 2020 -0400
@@ -0,0 +1,35 @@
+<tool id="scpred_predict_labels" name="Scpred predict" version="@TOOL_VERSION@+galaxy0">
+    <description>Make cell type predictions using trained model.</description>
+     <macros>
+        <import>scpred_macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        scpred_predict.R --input-object "${input_object}" --pred-data "${pred_data}" --test-labels "${test_labels}" --cell-types-column "${cell_types_column}" --output-path "${output_tbl_path}" --plot-path "${plot_path}" --confusion-table "${confusion_table}"
+        ]]></command>
+    <inputs>
+        <param type="data" name="input_object" label="Input SCE object" format="rdata" help="Input SCE object in .rds format" />
+        <param type="data" name="pred_data" label="Matrix with query data" format="rdata" help="Path to the input prediction matrix in .rds format"/>
+        <param type="data" name="test_labels" format="txt" label="Test labels" help="Path to the test labels file for evalutation of model performance in text format" />
+        <param type="text" name="cell_types_column" value="cell_type2" label="Cell types column name" help="Column name of true labels in provided metadata file" />
+    </inputs>
+    <outputs>
+        <data name="output_tbl_path" format="txt" />
+        <data name="plot_path" format="txt" />
+        <data name="confusion_table" format="txt" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_object" value="scPred_trained.rds" />
+            <param name="pred_data" value="test_matrix.mtx" />
+            <param name="test_labels" value="test_metadata.txt" />
+            <output name="output_tbl_path" file="predictions_table.txt" compare="sim_size"/>
+        </test>
+    </tests>
+     <help><![CDATA[
+    @HELP@
+    
+    @VERSION_HISTORY@
+    ]]></help>
+    <expand macro="citations" />
+</tool>