From 424954037a50876b306f397efd8e9790f62416bd Mon Sep 17 00:00:00 2001
From: Christophe Antoniewski <drosofff@users.noreply.github.com>
Date: Fri, 13 Oct 2023 11:36:22 +0200
Subject: [PATCH] update tool concat_multi_datasets (while specifying how)
 (#636)

* bump tool version and fix dev repo url

* add `format` tag in discover_datasets

* add explicit format to inputs (fastq, fastq.gz, txt, tabular, bed)

* Suppress unused Test param collection_cat_type


* added all `expect_num_outputs` tags to "1"

* add citation tag

* fix a bit the description in the tool xml...
---
 tools/concat_multi_datasets/.shed.yml      |  2 +-
 tools/concat_multi_datasets/catWrapper.xml | 41 ++++++++++++----------
 2 files changed, 23 insertions(+), 20 deletions(-)

diff --git a/tools/concat_multi_datasets/.shed.yml b/tools/concat_multi_datasets/.shed.yml
index 179440889..07d739c2a 100644
--- a/tools/concat_multi_datasets/.shed.yml
+++ b/tools/concat_multi_datasets/.shed.yml
@@ -7,6 +7,6 @@ long_description: |
 categories:
   - Text Manipulation
 homepage_url: http://artbio.fr
-remote_repository_url: https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets
+remote_repository_url: https://github.com/ARTbio/tools-artbio/tree/main/tools/concat_multi_datasets
 toolshed:
   - toolshed
diff --git a/tools/concat_multi_datasets/catWrapper.xml b/tools/concat_multi_datasets/catWrapper.xml
index 7ffdec756..a7946b4cf 100644
--- a/tools/concat_multi_datasets/catWrapper.xml
+++ b/tools/concat_multi_datasets/catWrapper.xml
@@ -1,5 +1,5 @@
-<tool id="cat_multi_datasets" name="Concatenate multiple datasets" version="1.4.1">
-    <description>tail-to-head by specifying how</description>
+<tool id="cat_multi_datasets" name="Concatenate multiple datasets" version="1.4.2">
+    <description>tail-to-head while specifying how</description>
     <command><![CDATA[
         #if $headers == 0:
             #set $concat_command = "cat"
@@ -233,10 +233,12 @@
                 <option value="nested_collection">Nested collection</option>
             </param>
             <when value="singles">
-                <param name="inputs" type="data" label="Concatenate Datasets" multiple="True" help="All inputed datasets will be concatenated tail-to-head."/>
+                <param name="inputs" type="data" label="Concatenate Datasets" multiple="True" format="fastq,fastq.gz,txt,tabular,bed"
+                       help="All inputed datasets will be concatenated tail-to-head."/>
             </when>
             <when value="paired_collection">
-                <param name="inputs" type="data_collection" collection_type="list:paired" label="Input paired collection to concatenate"/>
+                <param name="inputs" type="data_collection" collection_type="list:paired" format="fastq,fastq.gz,txt,tabular,bed"
+                       label="Input paired collection to concatenate"/>
                 <param name="paired_cat_type" type="select" label="What type of concatenation do you wish to perform?">
                     <option value="by_strand">Concatenate all datsets of same strand (outputs a single pair of datasets)</option>
                     <option value="by_pair">Concatenate pairs of datasets (outputs an unpaired collection of datasets)</option>
@@ -262,45 +264,45 @@
             <filter>global_condition['input_type'] == 'paired_collection' and global_condition['paired_cat_type'] == 'all'</filter>
         </data>
         <collection name="paired_output" type="paired" label="Concatenation by strtand">
-            <discover_datasets pattern="(?P&lt;name&gt;.*)\.listed\.(?P&lt;ext&gt;.*)\.listed" visible="false" directory="concatenated"/>
+            <discover_datasets pattern="(?P&lt;name&gt;.*)\.listed\.(?P&lt;ext&gt;.*)\.listed" format="fastq" visible="false" directory="concatenated"/>
             <filter>global_condition['input_type'] == 'paired_collection' and global_condition['paired_cat_type'] == 'by_strand'</filter>
         </collection>
         <collection name="list_output" type="list" label="Concatenation by pairs">
-            <discover_datasets pattern="(?P&lt;identifier_0&gt;.*)\.listed\.(?P&lt;ext&gt;.*)\.listed" visible="false" directory="concatenated"/>
+            <discover_datasets pattern="(?P&lt;identifier_0&gt;.*)\.listed\.(?P&lt;ext&gt;.*)\.listed" format="fastq" visible="false" directory="concatenated"/>
             <filter>(global_condition['input_type'] == 'paired_collection' and global_condition['paired_cat_type'] == 'by_pair') or (global_condition['input_type'] == 'simple_collections') or (global_condition['input_type'] == 'nested_collection')</filter>
         </collection>
     </outputs>
     <tests>
         <!-- Single files concatenation -->
-        <test> <!-- Test 2 single files concatenation with no other option -->
+        <test expect_num_outputs="1"> <!-- Test 1 single files concatenation with no other option -->
             <param name="input_type" value="singles" />
             <param name="inputs" value="1.bed,2.bed"/>
             <param name="dataset_names" value="No" />
             <param name="headers" value="0" />
             <output name="out_file1" file="cat_wrapper_out1.bed"/>
         </test>
-        <test> <!-- Test 2 single files concatenation with dataset names activated -->
+        <test expect_num_outputs="1"> <!-- Test 2 single files concatenation with dataset names activated -->
             <param name="input_type" value="singles" />
             <param name="inputs" value="1.bed,2.bed"/>
             <param name="dataset_names" value="Yes" />
             <param name="headers" value="0" />
             <output name="out_file1" file="cat_wrapper_out2.bed"/>
         </test>
-        <test> <!-- Test 2 single files concatenation skipping 1 line -->
+        <test expect_num_outputs="1"> <!-- Test 3 single files concatenation skipping 1 line -->
             <param name="input_type" value="singles" />
             <param name="inputs" value="1.bed,2.bed"/>
             <param name="dataset_names" value="No" />
             <param name="headers" value="1" />
             <output name="out_file1" file="cat_wrapper_out3.bed"/>
         </test>
-        <test> <!-- Test gz handling with no options -->
+        <test expect_num_outputs="1"> <!-- Test 4 gz handling with no options -->
             <param name="input_type" value="singles" />
             <param name="inputs" value="1_f.fastq.gz,1_r.fastq.gz"/>
             <param name="dataset_names" value="No" />
             <param name="headers" value="0" />
             <output name="out_file1" file="1.fastq.gz" decompress="True"/>
         </test>
-        <test> <!-- Test gz handling with options -->
+        <test expect_num_outputs="1"> <!-- Test 5 gz handling with options -->
             <param name="input_type" value="singles" />
             <param name="inputs" value="1_f.fastq.gz,1_r.fastq.gz"/>
             <param name="dataset_names" value="Yes" />
@@ -308,7 +310,7 @@
             <output name="out_file1" file="1_options.fastq.gz" decompress="True"/>
         </test>
         <!-- Test paired options -->
-        <test> <!-- Test paired collection concatenation by_pair with no other option -->
+        <test expect_num_outputs="1"> <!-- Test 6 paired collection concatenation by_pair with no other option -->
             <param name="input_type" value="paired_collection" />
             <param name="paired_cat_type" value="by_pair"/>
             <param name="inputs">
@@ -341,7 +343,7 @@
                 <element name="4" file="4.fastq"/>
             </output_collection>
         </test>
-        <test> <!-- Test paired collection concatenation by_strand with no other option -->
+        <test expect_num_outputs="1"> <!-- Test 7 paired collection concatenation by_strand with no other option -->
             <param name="input_type" value="paired_collection" />
             <param name="paired_cat_type" value="by_strand"/>
             <param name="inputs">
@@ -373,9 +375,8 @@
                 <element name="reverse" file="r.fastq"/>
             </output_collection>
         </test>
-        <test> <!-- Test 2 collections concatenation -->
+        <test expect_num_outputs="1"> <!-- Test 8 - 2 collections concatenation -->
             <param name="input_type" value="simple_collections" />
-            <param name="collection_cat_type" value="two_collections"/>
             <param name="input_1">
                 <collection type="list">
                     <element name="2" value="2_f.fastq"/>
@@ -398,9 +399,8 @@
                 <element name="4" file="4.fastq"/>
             </output_collection>
         </test>
-        <test> <!-- Test 2 collections concatenation with other options-->
+        <test expect_num_outputs="1"> <!-- Test 9 - 2 collections concatenation with other options-->
             <param name="input_type" value="simple_collections" />
-            <param name="collection_cat_type" value="two_collections"/>
             <param name="input_1">
                 <collection type="list">
                     <element name="1_f.fastq.gz" value="1_f.fastq.gz"/>
@@ -417,7 +417,7 @@
                 <element name="1_f.fastq.gz_1_r.fastq.gz" file="1_options.fastq.gz" decompress="True"/>
             </output_collection>
         </test>
-        <test> <!-- Test nested collections concatenation -->
+        <test expect_num_outputs="1"> <!-- Test 10 nested collections concatenation -->
             <param name="input_type" value="nested_collection" />
             <param name="inputs">
                 <collection type="list:list">
@@ -441,7 +441,7 @@
                 <element name="3" file="3.fastq"/>
             </output_collection>
         </test>
-        <test> <!-- Test nested collections concatenation with options and gzip-->
+        <test expect_num_outputs="1"> <!-- Test 11 nested collections concatenation with options and gzip-->
             <param name="input_type" value="nested_collection" />
             <param name="inputs">
                 <collection type="list:list">
@@ -672,4 +672,7 @@ output::
 Adapted from galaxy's catWrapper.xml to allow multiple input files.
 
     </help>
+    <citations>
+        <citation type="doi">10.1186/gb-2010-11-8-r86</citation>
+    </citations>
 </tool>