changeset 0:01b2e83311b2 draft

"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ct_get_tool_perf_table.xml	Wed Apr 08 15:32:34 2020 +0000
@@ -0,0 +1,54 @@
+<tool id="ct_get_tool_perf_table" name="Cell types - get tool performance table" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
+    <description>Get performance table for a list of outputs generated by various tools</description>
+    <macros>
+         <import>ct_macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        mkdir -p input_dir;
+        #for $input_file in $input_files:
+          cp '$input_file' input_dir/;
+        #end for
+
+        ln -s $'${ontology_graph}' cl-basic.obo;
+       
+        get_tool_performance_table.R --input-dir input_dir --ref-file "${ref_file}" --num-cores "${num_cores}" --exclusions "${exclusions}" --parallel "${parallel}" --ontology-graph cl-basic.obo --lab-cl-mapping "${lab_cl_mapping}" --barcode-col-ref "${barcode_col_ref}" --barcode-col-pred "${barcode_col_pred}" --label-column-ref "${label_col_ref}" --label-column-pred "${label_col_pred}" --semantic-sim-metric "${semantic_sim_metric}" --output-path "${output_path}" ]]></command>
+    <inputs>
+        <param type="data" name="input_files" label="Input tables" multiple="true" format="txt" help="Classification tables obtained from multiple classisifiers" />
+        <param type="data" name="ref_file" label="Reference metadata file" format="txt" help="Metadata file with reference labels" />
+        <param type="boolean" name="parallel" label="Parallel execution" checked="false" help="Should the table values be computed in parallel?" />
+        <param type="integer" name="num_cores" label="Number of cores" value='1' help="Number of cores used for computation" />
+        <param type="data" name="exclusions" label="Exclusions" format="yml" optional="true" help="Config file with exclusions" />
+        <param type="data" name="ontology_graph" label="Ontology graph" format="obo" help="Ontology graph to run semantis similarity computations" />
+        <param type="data" name="lab_cl_mapping" label="Label - CL term mapping" format="rdata" help="Mapping between cell labels and ontology terms" />
+        <param type="text" name="barcode_col_ref" label="Reference file barcode field" value='cell_id' help="Name of barcode field in reference metadata file" />
+        <param type="text" name="barcode_col_pred" label="Predicted file barcode field" value="cell_id" help="Name of barcode field in predictions file" />
+        <param type="text" name="label_col_ref" label="Reference label column" value="cell_type" help="Label column in reference file" />
+        <param type="text" name="label_col_pred" label="Predicted file label column" value="pred_label" help="Name of label field in predictions file" />
+        <param type="text" name="semantic_sim_metric" label="Semantic similarity metric" value="edge_resnik" help="Type of semantic similarity metric used" />
+    </inputs>
+    <outputs>
+         <data name="output_path" format="tsv" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_files" value="results_dir/garnett_output.txt,results_dir/scmap-cell_output.txt,results_dir/scmap-cluster_output.txt,results_dir/scpred_output.txt" />
+            <param name="ref_file" value="reference_sdrf.tsv" />
+            <param name="ontology_graph" value="cl-basic.obo" />
+            <param name="lab_cl_mapping" value="label_cl_dict.rds" />
+            <param name="parallel" value="TRUE" />
+            <param name="exclusions" value="exclusions.yml" />
+            <param name="barcode_col_ref" value="Assay" />
+            <param name="barcode_col_pred" value="cell_id" />
+            <param name="label_col_ref" value="Sample.Characteristic.cell.type." />
+            <param name="label_col_pred" value="predicted_label" />
+            <output name="output_path" file="tool_perf_table.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 15:32:34 2020 +0000
@@ -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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