changeset 6:14eb5128af69 draft default tip

"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit a1ad1ddd9b8e4db5bb82c3accae8311e0e488b19"

--- a/ct_get_empirical_dist.xml	Mon Jul 13 07:24:39 2020 -0400
+++ b/ct_get_empirical_dist.xml	Fri Nov 27 13:38:33 2020 +0000
@@ -1,22 +1,16 @@
-<tool id="ct_get_empirical_dist" name="Cell types - get empirical distribution" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@">
-    <description>Get empirical distribution for tool performance table</description>
+<tool id="ct_get_empirical_dist" name="Cell types - get empirical distribution" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
+    <description>for tool performance table</description>
     <macros>
         <import>ct_macros.xml</import>
     </macros>
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
 
-        get_empirical_dist.R --input-ref-file "${input_ref_file}" --label-column-ref "${label_col_ref}" --lab-cl-mapping "${lab_cl_mapping}" --num-iterations "${num_iter}" --num-cores \${GALAXY_SLOTS:-1}  --output-path "${output_list_path}" 
+        get_empirical_dist.R --input-ref-file "${input_ref_file}" --label-column-ref "${label_col_ref}" --lab-cl-mapping "${lab_cl_mapping}" --num-iterations "${num_iter}"  --parallel "TRUE" --num-cores \${GALAXY_SLOTS:-1} --tmpdir ./  --output-path "${output_list_path}" 
 
-        #if $parallel
-        --parallel "${parallel}"
-        #end if
         #if $ontology_graph
         --ontology-graph "${ontology_graph}"
         #end if 
-        #if $tmpdir
-        --tmpdir "${tmpdir}"
-        #end if
         #if $sample_labs
         --sample-labs "${sample_labs}"
         #end if
@@ -31,12 +25,12 @@
     <inputs>
         <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" optional="true" 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="text" name="label_col_ref" label="Reference label column" value="cell_type" help="Label column in reference file">
+        <expand macro="sanitize_strings" />
+        </param>
         <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="sample_labs" value='50' label="Number of labels to sample" help="Numbre of labels to sample for each permutation" />
+        <param type="integer" name="sample_labs" value='50' label="Number of labels to sample" help="Number 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>
@@ -46,10 +40,9 @@
     <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="label_col_ref" value='Sample Characteristic[cell type]' />
             <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>

--- a/ct_macros.xml	Mon Jul 13 07:24:39 2020 -0400
+++ b/ct_macros.xml	Fri Nov 27 13:38:33 2020 +0000
@@ -1,10 +1,10 @@
 <macros>
-    <token name="@TOOL_VERSION@">1.1.0</token>
+    <token name="@TOOL_VERSION@">1.1.1</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="0.1.1">cell-types-analysis</requirement>
+        <requirement type="package" version="0.1.9">cell-types-analysis</requirement>
             <yield/>
       </requirements>
     </xml>
@@ -15,6 +15,7 @@
     </xml>
     <token name="@VERSION_HISTORY@"><![CDATA[
 **Version history**
+0.1.6+galaxy0: Add removing non-alphanumeric characters from labels in metadata files
 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>
@@ -34,6 +35,17 @@
             <option value="resnik">resnik</option>
         </param>
     </xml>
+    <xml name="sanitize_strings">
+        <sanitizer invalid_char="">
+        <valid initial="string.ascii_letters,string.digits">
+            <add value="_" />
+            <add value="-" />
+            <add value="[" />
+            <add value="]" />
+            <add value=" " />
+            </valid>
+    </sanitizer>
+    </xml>
     <xml name="citations">
       <citations>
         <citation type="bibtex">