# HG changeset patch
# User iuc
# Date 1711017989 0
# Node ID 944ae523bacb894e5c91abbc940d4df1d1f11982
# Parent  64172f1c1202306f9881a882c80d01c341402c1e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1973d7e076969910f753bf31adc0cdda2fc1530f

diff -r 64172f1c1202 -r 944ae523bacb cutadapt.xml
--- a/cutadapt.xml	Thu Jan 04 18:44:12 2024 +0000
+++ b/cutadapt.xml	Thu Mar 21 10:46:29 2024 +0000
@@ -39,7 +39,7 @@
     #set read1 = re.sub('[^\w\-\s]', '_', str($library.input_1.element_identifier))
 #end if
 
-#if $input_1.is_of_type("fastq"):
+#if $input_1.is_of_type("fastq", "fastq.gz", "fastq.bz2"):
     #set ext = ".fq"
 #else
     #set ext = ".fa"
@@ -61,14 +61,15 @@
 ln -f -s '${input_1}' '$read1' &&
 
 #if $paired:
-    #if $input_2.is_of_type("fastq.gz", "fastqsanger.gz"):
-        #set ext2 = ".fq.gz"
-    #else if $input_2.is_of_type("fastq.bz2", "fastqsanger.bz2"):
-        #set ext2 = ".fq.gz"
-    #else if $input_2.is_of_type('fasta'):
+    #if $input_2.is_of_type("fastq", "fastq.gz", "fastq.bz2"):
+        #set ext2 = ".fq"
+    #else
         #set ext2 = ".fa"
-    #else:
-        #set ext2 = ".fq"
+    #end if
+    #if $input_2.ext.endswith(".gz"):
+        #set ext2=ext2+".gz"
+    #elif $input_2.ext.endswith(".bz2")
+        #set ext2=ext2+".bz2"
     #end if
     #set read2 = $read2 + $ext2
     #set out2 = "out2" + $ext2
@@ -319,17 +320,17 @@
     </inputs>
 
     <outputs>
-        <data name="out1" format="fastqsanger" metadata_source="input_1" from_work_dir="out1.*" label="${tool.name} on ${on_string}: Read 1 Output">
+        <data name="out1" format="fastqsanger" metadata_source="library|input_1" default_identifier_source="library|input_1" from_work_dir="out1.*" label="${tool.name} on ${on_string}: Read 1 Output">
             <filter>library['type'] != 'paired_collection' and 'multiple_output' not in output_selector</filter>
             <expand macro="inherit_format_1" />
         </data>
 
-        <data name="out2" format="fastqsanger" metadata_source="input_2" from_work_dir="out2.*" label="${tool.name} on ${on_string}: Read 2 Output" >
+        <data name="out2" format="fastqsanger" metadata_source="library|input_2" default_identifier_source="library|input_2" from_work_dir="out2.*" label="${tool.name} on ${on_string}: Read 2 Output" >
             <filter>library['type'] == 'paired' and 'multiple_output' not in output_selector</filter>
             <expand macro="inherit_format_2" />
         </data>
 
-        <collection name="out_pairs" type="paired" format_source="input_1" label="${tool.name} on ${on_string}: Reads">
+        <collection name="out_pairs" type="paired" format_source="library|input_1" label="${tool.name} on ${on_string}: Reads">
             <filter>library['type'] == 'paired_collection' and 'multiple_output' not in output_selector</filter>
             <data name="forward" from_work_dir="out1.*" />
             <data name="reverse" from_work_dir="out2.*" />
@@ -338,43 +339,43 @@
         <data name="report" format="txt" from_work_dir="report.txt" label="${tool.name} on ${on_string}: Report">
             <filter>output_selector and 'report' in output_selector</filter>
         </data>
-        <data  name="info_file" format="txt" metadata_source="input_1" label="${tool.name} on ${on_string}: Info File" >
+        <data  name="info_file" format="txt" metadata_source="library|input_1" label="${tool.name} on ${on_string}: Info File" >
             <filter>output_selector and 'info_file' in output_selector</filter>
         </data>
 
-        <data name="rest_output" format="fastqsanger" metadata_source="input_1" from_work_dir="rest_output*" label="${tool.name} on ${on_string}: Rest of Reads (R1 only)" >
+        <data name="rest_output" format="fastqsanger" metadata_source="library|input_1" from_work_dir="rest_output*" label="${tool.name} on ${on_string}: Rest of Reads (R1 only)" >
             <filter>output_selector and 'rest_file' in output_selector</filter>
             <expand macro="inherit_format_1" />
         </data>
 
-        <data name="wild_output" format="txt" metadata_source="input_1" from_work_dir="wild_output*" label="${tool.name} on ${on_string}: Wildcard File" >
+        <data name="wild_output" format="txt" metadata_source="library|input_1" from_work_dir="wild_output*" label="${tool.name} on ${on_string}: Wildcard File" >
             <filter>output_selector and 'wildcard_file' in output_selector</filter>
         </data>
 
-        <data name="untrimmed_output" format="fastqsanger" metadata_source="input_1" from_work_dir="untrimmed_output*" label="${tool.name} on ${on_string}: Untrimmed Read 1" >
+        <data name="untrimmed_output" format="fastqsanger" metadata_source="library|input_1" default_identifier_source="library|input_1" from_work_dir="untrimmed_output*" label="${tool.name} on ${on_string}: Untrimmed Read 1" >
             <filter>output_selector and 'untrimmed_file' in output_selector</filter>
             <expand macro="inherit_format_1" />
         </data>
-        <data name="untrimmed_paired_output" format="fastqsanger" metadata_source="input_2" from_work_dir="untrimmed_paired_output*" label="${tool.name} on ${on_string}: Untrimmed Read 2" >
+        <data name="untrimmed_paired_output" format="fastqsanger" metadata_source="library|input_2" default_identifier_source="library|input_2" from_work_dir="untrimmed_paired_output*" label="${tool.name} on ${on_string}: Untrimmed Read 2" >
             <filter>library['type'] == 'paired' or library['type'] == 'paired_collection'</filter>
             <filter>output_selector and 'untrimmed_file' in output_selector </filter>
             <expand macro="inherit_format_2" />
         </data>
 
-        <data name="too_short_output" format="fastqsanger" metadata_source="input_1" from_work_dir="too_short_output*" label="${tool.name} on ${on_string}: Too Short Read 1" >
+        <data name="too_short_output" format="fastqsanger" metadata_source="library|input_1" default_identifier_source="library|input_1" from_work_dir="too_short_output*" label="${tool.name} on ${on_string}: Too Short Read 1" >
             <filter>output_selector and 'too_short_file' in output_selector</filter>
             <expand macro="inherit_format_1" />
         </data>
-        <data name="too_short_paired_output" format="fastqsanger" metadata_source="input_2" from_work_dir="too_short_paired_output*" label="${tool.name} on ${on_string}: Too Short Read 2" >
+        <data name="too_short_paired_output" format="fastqsanger" metadata_source="library|input_2" default_identifier_source="library|input_2" from_work_dir="too_short_paired_output*" label="${tool.name} on ${on_string}: Too Short Read 2" >
             <filter>library['type'] == 'paired' or library['type'] == 'paired_collection'</filter>
             <filter>output_selector and 'too_short_file' in output_selector</filter>
             <expand macro="inherit_format_2" />
         </data>
-        <data name="too_long_output" format="fastqsanger" metadata_source="input_1" from_work_dir="too_long_output*" label="${tool.name} on ${on_string}: Too Long Read 1" >
+        <data name="too_long_output" format="fastqsanger" metadata_source="library|input_1" default_identifier_source="library|input_1" from_work_dir="too_long_output*" label="${tool.name} on ${on_string}: Too Long Read 1" >
             <filter>output_selector and 'too_long_file' in output_selector</filter>
             <expand macro="inherit_format_1" />
         </data>
-        <data name="too_long_paired_output" format="fastqsanger" metadata_source="input_2" from_work_dir="too_long_paired_output*" label="${tool.name} on ${on_string}: Too Long Read 2" >
+        <data name="too_long_paired_output" format="fastqsanger" metadata_source="library|input_2" default_identifier_source="library|input_2" from_work_dir="too_long_paired_output*" label="${tool.name} on ${on_string}: Too Long Read 2" >
             <filter>library['type'] == 'paired' or library['type'] == 'paired_collection'</filter>
             <filter>output_selector and 'too_long_file' in output_selector</filter>
             <expand macro="inherit_format_2" />
@@ -1333,9 +1334,9 @@
                     </conditional>
                 </repeat>
             </section>
-            <assert_stdout>
+            <assert_stderr>
                 <has_text text="Reads are improperly paired"/>
-            </assert_stdout>
+            </assert_stderr>
         </test>
     </tests>
 
diff -r 64172f1c1202 -r 944ae523bacb macros.xml
--- a/macros.xml	Thu Jan 04 18:44:12 2024 +0000
+++ b/macros.xml	Thu Mar 21 10:46:29 2024 +0000
@@ -1,6 +1,6 @@
 <macros>
-    <token name="@TOOL_VERSION@">4.6</token>
-    <token name="@VERSION_SUFFIX@">1</token>
+    <token name="@TOOL_VERSION@">4.7</token>
+    <token name="@VERSION_SUFFIX@">0</token>
     <token name="@FASTQ_TYPES@">fastq.bz2,fastq.gz,fastq,fasta.bz2,fasta.gz,fasta</token>
     <xml name="edam_ontology">
         <edam_topics>