--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ct_combine_tool_outputs.xml	Wed Apr 08 11:34:35 2020 -0400
@@ -0,0 +1,37 @@
+<tool id="ct_combine_tool_outputs" name="Cell types - combine tools outputs" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
+    <description>Combine predictions for single tool from multiple datasets</description>
+    <macros>
+        <import>ct_macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        mkdir -p input_dir;
+        #for $table in $input_tables:
+          cp '$table' input_dir/;
+        #end for
+
+        combine_tool_outputs.R --input-dir input_dir --top-labels-num "${top_labels_num}" --exclusions "${exclusions}" --scores "${scores}" --output-table "${output_table}" ]]></command>
+    <inputs>
+        <param type="data" name="input_tables" label="Tables with predicted labels" multiple="true" format="tsv" help="Standardised tables obtained from multiple classifiers" />
+        <param type="integer" name="top_labels_num" label="Number of top labels" value='3' help="Number of top labels to select" />
+        <param type="data" name="exclusions" label="Exclusions file" format="yml" optional="true" help="Yaml file with trivial terms and unlabelled cells" />
+        <param type="boolean" name="scores" label="scores" checked="false" help="Are scores included into the tool outpus?" />
+    </inputs>
+    <outputs>
+        <data name="output_table" format="tsv" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_tables" value="prod_outputs_scpred/E-MTAB-6386_scpred_final-labs.tsv,prod_outputs_scpred/OTHER-DATASET_scpred_final-labs.tsv" />
+            <param name="scores" value="TRUE" />
+            <param name="exclusions" value="exclusions.yml" />
+            <output name="output_table" file="combined_results.tsv" compare="sim_size" />
+        </test>
+    </tests>
+    <help><![CDATA[
+    @HELP@
+    
+    @VERSION_HISTORY@
+    ]]></help>
+    <expand macro="citations" />
+</tool>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ct_macros.xml	Wed Apr 08 11:34:35 2020 -0400
@@ -0,0 +1,35 @@
+<macros>
+    <token name="@TOOL_VERSION@">1.0.0</token>
+    <token name="@HELP@">More information can be found at https://github.com/ebi-gene-expression-group/cell-types-analysis</token>
+    <token name="@PROFILE@">18.01</token>
+    <xml name="requirements">
+      <requirements>
+        <requirement type="package" version="0.0.8">cell-types-analysis</requirement>
+            <yield/>
+      </requirements>
+    </xml>
+    <xml name="version">
+      <version_command><![CDATA[
+        conda list | grep cell-types-analysis | egrep -o [0-9]\.[0-9]\.[0-9]
+    ]]></version_command>
+    </xml>
+    <token name="@VERSION_HISTORY@"><![CDATA[
+**Version history**
+0.0.5+galaxy0: Initial 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">
+          @misc{github-cell-types-analysis.git,
+            author = {Andrey Solovyev, EBI Gene Expression Team},
+            year = {2020},
+            title = {Suite of scripts for analysis of scRNA-seq cell type classification tool outputs},
+            publisher = {GitHub},
+            journal = {GitHub repository},
+            url = {https://github.com/ebi-gene-expression-group/cell-types-analysis.git},
+          }
+        </citation>
+        <yield />
+      </citations>
+    </xml>
+</macros>
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