# HG changeset patch
# User ebi-gxa
# Date 1592411314 0
# Node ID f1f40671edf2bc5816734eb9bf0351ce24e767fb
# Parent  db65c4c1cb8260013827dbc22d160347e88b9220
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 8c1bd2ab8a3f988e205677a3bb1ffda1e5694fe1"

diff -r db65c4c1cb82 -r f1f40671edf2 ct_build_cell_ontology_dict.xml
--- a/ct_build_cell_ontology_dict.xml	Mon Apr 27 15:06:12 2020 +0000
+++ b/ct_build_cell_ontology_dict.xml	Wed Jun 17 16:28:34 2020 +0000
@@ -28,7 +28,7 @@
         <param type="data" name="input_sdrfs" label="Input SDRF tables" multiple="true" format="txt" help="Input SDRF tables" />
         <param type="boolean" name="condensed_sdrf" checked="false" label="Condensed SDRF" help="Are the supplied SDRFs of condensed format?" />
         <param type="text" name="barcode_col_name" label="Barcode column name" value="id" help="Name of the barcode field in provided SDRF files" />
-        <param type="text" name="cell_label_col_name" label="Cell label column name" value="cell.type" help="Name of the cell label field name in provided SDRF files" />
+        <param type="text" name="cell_label_col_name" label="Cell label column name" value="inferred cell type" help="Name of the cell label field name in provided SDRF files" />
         <param type="text" name="cell_ontology_col_name" label="Cell ontology column name" value="cell.type.ontology" help="Name of the cell ontology terms column in SDRF files (must be identical across all files)" />
     </inputs>
     <outputs>
diff -r db65c4c1cb82 -r f1f40671edf2 ct_macros.xml
--- a/ct_macros.xml	Mon Apr 27 15:06:12 2020 +0000
+++ b/ct_macros.xml	Wed Jun 17 16:28:34 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">