changeset 4:5bf2827cd314 draft

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

--- a/ct_get_empirical_dist.xml	Mon Apr 27 11:12:46 2020 -0400
+++ b/ct_get_empirical_dist.xml	Wed Jun 17 12:30:58 2020 -0400
@@ -13,10 +13,13 @@
         #if $parallel
         --parallel "${parallel}"
         #end if
+        #if $sample_labs
+        --sample-labs "${sample_labs}"
+        #end if
         #if $exclusions
         --exclusions "${exclusions}"
         #end if
-        #if $exclusions
+        #if $sem_sim_metric
         --semantic-sim-metric "${sem_sim_metric}"
         #end if
         ]]></command>
@@ -24,11 +27,13 @@
         <param type="data" name="input_ref_file" label="Input reference file" format="txt" 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="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="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="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" />
+        <param type="integer" name="sample_labs" value='50' label="Number of labels to sample" help="Numbre of labels to sample for each permutation" />
+        <param type="data" name="ontology_graph" label="Ontology graph" format="obo" optional="true" help="Ontology graph to run semantis similarity computations" />
+        <expand macro="sem_siml_options" />
     </inputs>
     <outputs>
         <data name="output_list_path" format="rdata" />

--- a/ct_macros.xml	Mon Apr 27 11:12:46 2020 -0400
+++ b/ct_macros.xml	Wed Jun 17 12:30:58 2020 -0400
@@ -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">