# HG changeset patch
# User ebi-gxa
# Date 1586341774 14400
# Node ID 156b1e9cc26925a9f7488c92c263c6f6be1a44d9

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

diff -r 000000000000 -r 156b1e9cc269 scpred_get_std_output.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scpred_get_std_output.xml	Wed Apr 08 06:29:34 2020 -0400
@@ -0,0 +1,30 @@
+<tool id="scpred_get_std_output" name="Get output in standard format" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
+    <description>This method allows to export predicted labels in a standardised format, simplifying downstream analyses.</description>
+    <macros>
+        <import>scpred_macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[ 
+        scpred_get_std_output.R --predictions-file "${predictions_file}" --get-scores "${get_scores}" --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="boolean" checked="false" name="get_scores" label="Get scores" help="Boolean: should the prediction scores be included? default: FALSE" />
+    </inputs>
+    <outputs>
+        <data name="output_table" format="txt" />
+    </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"/>
+        </test>
+    </tests>
+     <help><![CDATA[
+    @HELP@
+    
+    @VERSION_HISTORY@
+    ]]></help>
+    <expand macro="citations" />
+</tool>
diff -r 000000000000 -r 156b1e9cc269 scpred_macros.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scpred_macros.xml	Wed Apr 08 06:29:34 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>
+