changeset 5:1b0686be3093 draft default tip

"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 8c1bd2ab8a3f988e205677a3bb1ffda1e5694fe1"

--- a/ct_get_tool_perf_table.xml	Mon Apr 27 15:05:41 2020 +0000
+++ b/ct_get_tool_perf_table.xml	Wed Jun 17 16:28:14 2020 +0000
@@ -20,6 +20,9 @@
         #if $parallel
         --parallel "${parallel}"
         #end if
+        #if $include_sem_siml
+        --include-sem-siml "${include_sem_siml}"
+        #end if
         #if $barcode_col_ref
         --barcode-col-ref "${barcode_col_ref}"
         #end if
@@ -36,20 +39,21 @@
         --semantic-sim-metric "${semantic_sim_metric}" 
         #end if
 
-
          ]]></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="boolean" name="include_sem_siml" label="Include Semantic Similarity" checked="false" help="Should semantic similarity be included in calculation of combined score?" />
         <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="ontology_graph" label="Ontology graph" optional="true" format="obo" help="Ontology graph to run semantis similarity computations" />
+        <param type="text" name="tmpdir" label="Tmpdir for caching" optional="true" help="Temporary directory for caching" />
         <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" />
+        <expand macro="sem_siml_options" />
     </inputs>
     <outputs>
          <data name="output_path" format="txt" />

--- a/ct_macros.xml	Mon Apr 27 15:05:41 2020 +0000
+++ b/ct_macros.xml	Wed Jun 17 16:28:14 2020 +0000
@@ -1,10 +1,10 @@
 <macros>
-    <token name="@TOOL_VERSION@">1.0.0</token>
+    <token name="@TOOL_VERSION@">1.1.0</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>
+        <requirement type="package" version="0.1.1">cell-types-analysis</requirement>
             <yield/>
       </requirements>
     </xml>
@@ -18,6 +18,22 @@
 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/.
 0.0.5+galaxy1: Standardise input/output format into .txt. 
     ]]></token>
+    <xml name="sem_siml_options">
+      <param type="select" name="sem_siml_metric" label="Semantic similarity metric"  help="What semantic similarity metric should be used? NB: if include-sem-siml is set to True, make sure to use a metric that is in the [0;1] interval. See https://www.bioconductor.org/packages/release/bioc/html/Onassis.html for more detail.">
+            <option value="lin" selected="true">lin</option>
+            <option value="jaccard">jaccard</option>
+            <option value="jc_norm">jc_norm</option>
+            <option value="schlicker">schlicker</option>
+            <option value="edge_resnik">edge_resnik</option>
+            <option value="sim">sim</option>
+            <option value="edge_leachod">edge_leachod</option>
+            <option value="edge_slimani">edge_slimani</option>
+            <option value="edge_wupalmer">edge_wupalmer</option>
+            <option value="edge_rada_lca">edge_rada_lca</option>
+            <option value="edge_li">edge_li</option>
+            <option value="resnik">resnik</option>
+        </param>
+    </xml>
     <xml name="citations">
       <citations>
         <citation type="bibtex">