changeset 0:8ec19f24fcf3 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 06:37:16 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_train_test_split.xml	Wed Apr 08 06:37:16 2020 -0400
@@ -0,0 +1,37 @@
+<tool id="scpred_traint_test_split" name="Scpred train-test split" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
+    <description>CPM normalise and partition into train/test data</description>
+    <macros>
+        <import>scpred_macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        scpred_train_test_split.R --input-sce-object "${input_sce_object}" --normalised-counts-slot "${norm_counts_slot}" --training-matrix "${training_mat}" --test-matrix "${test_mat}" --cell-types-column "${cell_types_col}" --training-labels "${training_labs}" --test-labels "${test_labs}" --training-ratio "${training_ratio}" ]]></command>
+    <inputs>
+        <param type="data" name="input_sce_object" label="SCE object containing expression data" format="rdata" help="File with serialized SingleCellExperiment object that contains expression matrix" />
+        <param type="text" name="norm_counts_slot" value="normcounts" label="Normalised counts slot" help="Slot containing normalised counts in input SCE object" />
+        <param type="text" name="cell_types_col"  label="Column name for assigned cell types" />
+        <param type="float" name="training_ratio" label="Train/test split ratio" value="0.7" help="What proportion of the data set (0 to 1) should be used for training" />
+    </inputs>
+    <outputs>
+        <data name="training_mat" format="rdata" />
+        <data name="test_mat" format="rdata" />
+        <data name="training_labs" format="txt" />
+        <data name="test_labs" format="txt" /> 
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_sce_object" value="pollen_cpm.rds" />
+            <param name="cell_types_col" value="cell_type2" />
+            <output name="training_mat" file="train_matrix.mtx" compare="sim_size"/>
+            <output name="test_mat" file="test_matrix.mtx" compare="sim_size"/>
+            <output name="training_labs" file="train_metadata.txt" compare="sim_size" />
+            <output name="test_labs" file="test_metadata.txt" compare="sim_size" />
+        </test>
+    </tests>
+    <help><![CDATA[
+    @HELP@
+    
+    @VERSION_HISTORY@
+    ]]></help>
+    <expand macro="citations" />
+</tool>