# HG changeset patch
# User ebi-gxa
# Date 1586360094 14400
# Node ID 196cc72cebd173f709e15225651b126a769585c2

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

diff -r 000000000000 -r 196cc72cebd1 ct_get_empirical_dist.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ct_get_empirical_dist.xml	Wed Apr 08 11:34:54 2020 -0400
@@ -0,0 +1,43 @@
+<tool id="ct_get_empirical_dist" name="Cell types - get empirical distribution" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
+    <description>Get empirical distribution for tool performance table</description>
+    <macros>
+        <import>ct_macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+
+         ln -s $'${ontology_graph}' cl-basic.obo;
+
+        get_empirical_dist.R --input-ref-file "${input_ref_file}" --parallel "${parallel}" --exclusions "${exclusions}" --label-column-ref "${label_col_ref}" --lab-cl-mapping "${lab_cl_mapping}" --num-iterations "${num_iter}" --num-cores "${num_cores}" --ontology-graph cl-basic.obo --semantic-sim-metric "${sem_sim_metric}" --output-path "${output_list_path}" ]]></command>
+    <inputs>
+        <param type="data" name="input_ref_file" label="Input reference file" format="tsv" help="Text file with reference cell labels" />
+        <param type="data" name="exclusions" format="yml" label="Exclusions file" help="YML file with excluded/unlabelled terms" />
+        <param type="text" name="label_col_ref" label="Reference label column" value="cell_type" help="Label column in reference file" />
+        <param type="data" name="lab_cl_mapping" label="Label - CL term mapping" format="rdata" help="Mapping between cell labels and ontology terms" />
+        <param type="boolean" name="parallel" label="Parallel execution" checked="false" help="Should the table values be computed in parallel?" />
+        <param type="integer" name="num_iter" value='5' label="Number of iterations" help="Number of simulations to generate empirical CDF" />
+        <param type="integer" name="num_cores" value='4' label="Number of cores" help="Number of cores to run the process" />
+        <param type="data" name="ontology_graph" label="Ontology graph" format="obo" help="Ontology graph to run semantis similarity computations" />
+        <param type="text" name="sem_sim_metric" label="Semantic similarity metric" value="edge_resnik" help="Type of semantic similarity metric used" />
+    </inputs>
+    <outputs>
+        <data name="output_list_path" format="rdata" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_ref_file" value="reference_sdrf.tsv" />
+            <param name="label_col_ref" value="Sample.Characteristic.cell.type." />
+            <param name="ontology_graph" value="cl-basic.obo" />
+            <param name="exclusions" value="exclusions.yml" />
+            <param name="parallel" value="TRUE" />
+            <param name="lab_cl_mapping" value="label_cl_dict.rds" />
+            <output name="output_list_path" file="empirical_dist_list.rds" compare="sim_size" />
+        </test>
+    </tests>
+    <help><![CDATA[
+    @HELP@
+
+    @VERSION_HISTORY@
+    ]]></help>
+    <expand macro="citations" />
+</tool>
diff -r 000000000000 -r 196cc72cebd1 ct_macros.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ct_macros.xml	Wed Apr 08 11:34:54 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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