temporarily disable paired fasta input

marcelm/cutadapt#746
bernt-matthias · Dec 11, 2023 · 4028432 · 4028432
1 parent abda5b0
commit 4028432
Show file tree

Hide file tree

Showing 2 changed files with 12 additions and 7 deletions.
diff --git a/tools/cutadapt/cutadapt.xml b/tools/cutadapt/cutadapt.xml
@@ -200,13 +200,13 @@ $read_mod_options.zero_cap
             </when>
 
             <when value="paired">
-                <param name="input_1" format="@FASTQ_TYPES@" type="data" label="FASTQ/A file #1" help="Should be of datatype &quot;fastq.gz&quot;or &quot;fasta&quot;" />
-                <param name="input_2" format="@FASTQ_TYPES@" type="data" label="FASTQ/A file #2" help="Should be of datatype &quot;fastq.gz&quot;or &quot;fasta&quot;" />
+                <param name="input_1" format="@PAIRED_FASTQ_TYPES@" type="data" label="FASTQ/A file #1" help="Should be of datatype &quot;fastq.gz&quot;or &quot;fasta&quot;" />
+                <param name="input_2" format="@PAIRED_FASTQ_TYPES@" type="data" label="FASTQ/A file #2" help="Should be of datatype &quot;fastq.gz&quot;or &quot;fasta&quot;" />
                 <expand macro="paired_end_options" />
             </when>
 
             <when value="paired_collection">
-                <param name="input_1" format="@FASTQ_TYPES@" type="data_collection" collection_type="paired" label="Paired Collection" help="Should be of datatype &quot;fastq.gz&quot; or &quot;fasta&quot;" />
+                <param name="input_1" format="@PAIRED_FASTQ_TYPES@" type="data_collection" collection_type="paired" label="Paired Collection" help="Should be of datatype &quot;fastq.gz&quot; or &quot;fasta&quot;" />
                 <expand macro="paired_end_options" />
             </when>
 
@@ -1134,8 +1134,10 @@ $read_mod_options.zero_cap
             </assert_command>
         </test>
 
-        <!-- ployA trimmining https://github.com/marcelm/cutadapt/blob/e04cc32e392e1cbe0c518b4e0637cdf03533d440/tests/test_paired.py#L768 -->
-        <test expect_num_outputs="3">
+        <!-- ployA trimmining https://github.com/marcelm/cutadapt/blob/e04cc32e392e1cbe0c518b4e0637cdf03533d440/tests/test_paired.py#L768 
+             currently disabled since paired fasta input does not work with multiprocessing https://github.com/marcelm/cutadapt/issues/746
+        -->
+        <!-- <test expect_num_outputs="3">
             <param name="type" value="paired_collection" />
             <param name="input_1">
                 <collection type="paired">
@@ -1149,9 +1151,9 @@ $read_mod_options.zero_cap
                 <element name="reverse" file="cutadapt/cut/polya.2.fasta" ftype="fasta" />
             </output_collection>
             <assert_command>
-                <has_text text="--poly-a"/>
+                <has_text text="&#45;&#45;poly-a"/>
             </assert_command>
-        </test>
+        </test> -->
 
         <!-- polyA legacy https://github.com/marcelm/cutadapt/blob/e04cc32e392e1cbe0c518b4e0637cdf03533d440/tests/test_commandline.py#L267 -->
         <test expect_num_outputs="1">

diff --git a/tools/cutadapt/macros.xml b/tools/cutadapt/macros.xml
@@ -2,6 +2,9 @@
     <token name="@TOOL_VERSION@">4.5</token>
     <token name="@VERSION_SUFFIX@">0</token>
     <token name="@FASTQ_TYPES@">fastq.bz2,fastq.gz,fastq,fasta.bz2,fasta.gz,fasta</token>
+    <!-- fasta input for paired is not possible at the moment https://github.com/marcelm/cutadapt/issues/746 
+         disabled this here and corresponding tests -->
+    <token name="@PAIRED_FASTQ_TYPES@">fastq.bz2,fastq.gz,fastq</token>
     <xml name="edam_ontology">
         <edam_topics>                                                                                  
             <edam_topic>topic_0632</edam_topic>