Mercurial > repos > ebi-gxa > ct_build_cell_ontology_dict

changeset 5:512b239a11ad draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit a1ad1ddd9b8e4db5bb82c3accae8311e0e488b19"
author ebi-gxa
date Fri, 27 Nov 2020 13:37:02 +0000
parents b51c48b16ffe
children
files ct_build_cell_ontology_dict.xml ct_macros.xml
diffstat 2 files changed, 25 insertions(+), 7 deletions(-) [+]
line wrap: on
line diff
--- a/ct_build_cell_ontology_dict.xml	Wed Jun 17 12:31:51 2020 -0400
+++ b/ct_build_cell_ontology_dict.xml	Fri Nov 27 13:37:02 2020 +0000
@@ -1,4 +1,4 @@
-<tool id="ct_build_cell_ontology_dict" name="Cell types - build cell ontology map" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
+<tool id="ct_build_cell_ontology_dict" name="Cell types - build cell ontology map" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
     <description>Create a mapping from labels to CL terms</description>
     <macros>
         <import>ct_macros.xml</import>
@@ -27,9 +27,15 @@
     <inputs>
         <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="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)" />
+        <param type="text" name="barcode_col_name" label="Barcode column name" value="id" help="Name of the barcode field in provided SDRF files">
+            <expand macro="sanitize_strings" />
+        </param>
+        <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">
+            <expand macro="sanitize_strings" />
+        </param>
+        <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)">
+            <expand macro="sanitize_strings" />
+        </param>
     </inputs>
     <outputs>
         <data name="output_dict_path" format="rdata" />
@@ -37,7 +43,7 @@
     </outputs>
     <tests>
         <test>
-            <param name="input_sdrfs" value="SDRFs/ref_condensed_sdrf.tsv,SDRFs/ref_condensed_sdrf_1.tsv" />
+            <param name="input_sdrfs" value="SDRFs/E-ENAD-27.condensed-sdrf.tsv,SDRFs/ref_condensed_sdrf.tsv,SDRFs/E-GEOD-81608.condensed-sdrf.tsv" />
             <param name="condensed_sdrf" value="TRUE" />
             <output name="output_dict_path" file="label_cl_dict.rds" compare="sim_size" />
         </test>
--- a/ct_macros.xml	Wed Jun 17 12:31:51 2020 -0400
+++ b/ct_macros.xml	Fri Nov 27 13:37:02 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">