Update cutadapt v.3.4

tools/cutadapt/macros.xml

@@ -1,18 +1,42 @@
 <macros>
-
+    <token name="@TOOL_VERSION@">3.4</token>
+    <token name="@GALAXY_TOOL_VERSION@">galaxy0</token>
+    <xml name="edam_ontology">
+        <edam_topics>                                                                                  
+            <edam_topic>topic_0632</edam_topic>
+        </edam_topics>
+        <edam_operations>
+            <edam_operation>operation_0231</edam_operation>
+        </edam_operations>
+    </xml>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@TOOL_VERSION@">cutadapt</requirement>
+        </requirements>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.14806/ej.17.1.200</citation>
+        </citations>
+    </xml>
+    <xml name="xrefs">
+        <xrefs>
+            <xref type='bio.tools'>cutadapt</xref>
+        </xrefs>
+    </xml>
      <token name="@read1_options@"><![CDATA[
 
         ## Read1 trimming
 
         #for $a in $library.r1.adapters
             #if $a.adapter_source.adapter_source_list == 'builtin':
-                -a '${a.adapter_source.adapter.fields.name}'='${a.adapter_source.adapter}'
+                -a '${a.adapter_source.adapter.fields.name}'='${a.adapter_source.adapter}${adapter_options.internal}'
             #else if $a.adapter_source.adapter_source_list == 'file':
-                -a file:'${a.adapter_source.adapter_file}'
+                -a file:'${a.adapter_source.adapter_file}${adapter_options.internal}'
             #else if str($a.adapter_source.adapter_name) != "":
-                -a '${a.adapter_source.adapter_name}'='${a.adapter_source.adapter}'
+                -a '${a.adapter_source.adapter_name}'='${a.adapter_source.adapter}${adapter_options.internal}'
             #else
-                -a '${a.adapter_source.adapter}'
+                -a '${a.adapter_source.adapter}${adapter_options.internal}'
             #end if
         #end for
         #for $aa in $library.r1.anywhere_adapters
@@ -28,13 +52,13 @@
         #end for
         #for $fa in $library.r1.front_adapters
             #if $fa.front_adapter_source.front_adapter_source_list == 'builtin':
-                -g '${fa.front_adapter_source.front_adapter.fields.name}'='${fa.front_adapter_source.front_adapter}'
+                -g '${fa.front_adapter_source.front_adapter.fields.name}'='${adapter_options.internal}${fa.front_adapter_source.front_adapter}'
             #else if $fa.front_adapter_source.front_adapter_source_list == 'file':
-                -g file:'${fa.front_adapter_source.front_adapter_file}'
+                -g file:'${adapter_options.internal}${fa.front_adapter_source.front_adapter_file}'
             #else if str($fa.front_adapter_source.front_adapter_name) != "":
-                -g '${fa.front_adapter_source.front_adapter_name}'='${fa.front_adapter_source.front_adapter}'
+                -g '${adapter_options.internal}${fa.front_adapter_source.front_adapter_name}'='${fa.front_adapter_source.front_adapter}'
             #else
-                -g '${fa.front_adapter_source.front_adapter}'
+                -g '${adapter_options.internal}${fa.front_adapter_source.front_adapter}'
             #end if
         #end for
 
@@ -44,22 +68,22 @@
 
         ## Additional Outputs
 
-        #if $output_options.info_file:
+        #if 'info_file' in $output_selector:
             --info-file=$info_file
         #end if
-        #if $output_options.rest_file:
+        #if 'rest_file' in $output_selector:
             --rest-file='${rest_output}'
         #end if
-        #if $output_options.wildcard_file:
+        #if 'wildcard_file' in $output_selector:
             --wildcard-file='${wild_output}'
         #end if
-        #if $output_options.too_short_file:
+        #if 'too_short_file' in $output_selector:
             --too-short-output='${too_short_output}'
         #end if
-        #if $output_options.too_long_file:
+        #if 'too_long_file' in $output_selector:
             --too-long-output='${too_long_output}'
         #end if
-        #if $output_options.untrimmed_file:
+        #if 'untrimmed_file' in $output_selector:
             --untrimmed-output='${untrimmed_output}'
         #end if
 
@@ -71,13 +95,13 @@
 
         #for $a in $library.r2.adapters2
             #if $a.adapter_source2.adapter_source_list2 == 'builtin':
-                -A '${a.adapter_source2.adapter2.fields.name}'='${a.adapter_source2.adapter2}'
+                -A '${a.adapter_source2.adapter2.fields.name}'='${a.adapter_source2.adapter2}${adapter_options.internal}'
             #else if $a.adapter_source2.adapter_source_list2 == 'file':
-                -A file:'${a.adapter_source2.adapter_file2}'
+                -A file:'${a.adapter_source2.adapter_file2}${adapter_options.internal}'
             #else if str($a.adapter_source2.adapter_name2) != "":
-                -A '${a.adapter_source2.adapter_name2}'='${a.adapter_source2.adapter2}'
+                -A '${a.adapter_source2.adapter_name2}'='${a.adapter_source2.adapter2}${adapter_options.internal}'
             #else
-                -A '${a.adapter_source2.adapter2}'
+                -A '${a.adapter_source2.adapter2}${adapter_options.internal}'
             #end if
         #end for
         #for $aa in $library.r2.anywhere_adapters2
@@ -93,13 +117,13 @@
         #end for
         #for $fa in $library.r2.front_adapters2
             #if $fa.front_adapter_source2.front_adapter_source_list2 == 'builtin':
-                -G '${fa.front_adapter_source2.front_adapter2.fields.name}'='${fa.front_adapter_source2.front_adapter2}'
+                -G '${adapter_options.internal}${fa.front_adapter_source2.front_adapter2.fields.name}'='${fa.front_adapter_source2.front_adapter2}'
             #else if $fa.front_adapter_source2.front_adapter_source_list2  == 'file':
-                -G file:'${fa.front_adapter_source2.front_adapter_file2}'
+                -G file:'${adapter_options.internal}${fa.front_adapter_source2.front_adapter_file2}'
             #else if str($fa.front_adapter_source2.front_adapter_name2) != "":
-                -G '${fa.front_adapter_source2.front_adapter_name2}'='${fa.front_adapter_source2.front_adapter2}'
+                -G '${fa.front_adapter_source2.front_adapter_name2}'='${adapter_options.internal}${fa.front_adapter_source2.front_adapter2}'
             #else
-                -G '${fa.front_adapter_source2.front_adapter2}'
+                -G '${adapter_options.internal}${fa.front_adapter_source2.front_adapter2}'
             #end if
         #end for
 
@@ -109,13 +133,13 @@
 
         ## Additional Outputs - Read 2
 
-        #if $output_options.too_short_file:
+        #if 'too_short_file' in $output_selector:
             --too-short-paired-output='${too_short_paired_output}'
         #end if
-        #if $output_options.too_long_file:
+        #if 'too_long_file' in $output_selector:
             --too-long-paired-output='${too_long_paired_output}'
         #end if
-        #if $output_options.untrimmed_file:
+        #if 'untrimmed_file' in $output_selector:
             --untrimmed-paired-output='${untrimmed_paired_output}'
         #end if
 
@@ -181,7 +205,7 @@
                         <param name="adapter_source_list" type="select" label="Source" >
                             <option value="builtin" selected="True">Standard (select from the list below)</option>
                             <option value="user">Enter custom sequence</option>
-                            <option value="file">File From History</option>
+                            <option value="file">File from history</option>
                         </param>
 
                         <when value="user">
@@ -204,7 +228,7 @@
                         <param name="front_adapter_source_list" type="select" label="Source">
                             <option value="builtin" selected="True">Standard (select from the list below)</option>
                             <option value="user">Enter custom sequence</option>
-                            <option value="file">File From History</option>
+                            <option value="file">File from history</option>
                         </param>
 
                         <when value="user">
@@ -225,7 +249,7 @@
                         <param name="anywhere_adapter_source_list" type="select" label="Source">
                             <option value="builtin" selected="True">Standard (select from the list below)</option>
                             <option value="user">Enter custom sequence</option>
-                            <option value="file">File From History</option>
+                            <option value="file">File from history</option>
                         </param>
 
                         <when value="user">
@@ -260,7 +284,7 @@
                         <param name="adapter_source_list2" type="select" label="Source" >
                             <option value="builtin" selected="True">Standard (select from the list below)</option>
                             <option value="user">Enter custom sequence</option>
-                            <option value="file">File From History</option>
+                            <option value="file">File from history</option>
                         </param>
 
                         <when value="user">
@@ -282,7 +306,7 @@
                         <param name="front_adapter_source_list2" type="select" label="Source">
                             <option value="builtin" selected="True">Standard (select from the list below)</option>
                             <option value="user">Enter custom sequence</option>
-                            <option value="file">File From History</option>
+                            <option value="file">File from history</option>
                         </param>
 
                         <when value="user">
@@ -303,7 +327,7 @@
                         <param name="anywhere_adapter_source_list2" type="select" label="Source">
                             <option value="builtin" selected="True">Standard (select from the list below)</option>
                             <option value="user">Enter custom sequence</option>
-                            <option value="file">File From History</option>
+                            <option value="file">File from history</option>
                         </param>
 
                         <when value="user">

tools/cutadapt/test-data/cutadapt_action_lowercase.out

@@ -0,0 +1,12 @@
+@prefix:1_13_573/1
+cgtccgaantagctaccaccctgattagacaaat
++
+)3%)&&&&!.1&(6:<'67..*,:75)'77&&&5
+@prefix:1_13_1259/1
+AGCCGCTANGACGGGTTGGCCCTTAGACGTATCT
++
+;<:&:A;A!9<<<,7:<=3=;:<&<?<?8<;=<&
+@prefix:1_13_1440/1
+CAAGATCTNCCCTGCCACATTGCCCTAGTTAAAC
++
+<=A:A=57!7<';<6?5;;6:+:=)71>70<,=:

tools/cutadapt/test-data/cutadapt_action_mask.out

@@ -0,0 +1,12 @@
+@prefix:1_13_573/1
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
++
+)3%)&&&&!.1&(6:<'67..*,:75)'77&&&5
+@prefix:1_13_1259/1
+AGCCGCTANGACGGGTTGGCCCTTAGACGTATCT
++
+;<:&:A;A!9<<<,7:<=3=;:<&<?<?8<;=<&
+@prefix:1_13_1440/1
+CAAGATCTNCCCTGCCACATTGCCCTAGTTAAAC
++
+<=A:A=57!7<';<6?5;;6:+:=)71>70<,=:

tools/cutadapt/test-data/cutadapt_action_none.out

@@ -0,0 +1,12 @@
+@prefix:1_13_573/1
+CGTCCGAANTAGCTACCACCCTGATTAGACAAAT
++
+)3%)&&&&!.1&(6:<'67..*,:75)'77&&&5
+@prefix:1_13_1259/1
+AGCCGCTANGACGGGTTGGCCCTTAGACGTATCT
++
+;<:&:A;A!9<<<,7:<=3=;:<&<?<?8<;=<&
+@prefix:1_13_1440/1
+CAAGATCTNCCCTGCCACATTGCCCTAGTTAAAC
++
+<=A:A=57!7<';<6?5;;6:+:=)71>70<,=:

tools/cutadapt/test-data/cutadapt_action_retain.out

@@ -0,0 +1,12 @@
+@prefix:1_13_573/1
+CGTCCGAANTAG
++
+)3%)&&&&!.1&
+@prefix:1_13_1259/1
+AGCCGCTANGACGGGTTGGCCCTTAGACGTATCT
++
+;<:&:A;A!9<<<,7:<=3=;:<&<?<?8<;=<&
+@prefix:1_13_1440/1
+CAAGATCTNCCCTGCCACATTGCCCTAGTTAAAC
++
+<=A:A=57!7<';<6?5;;6:+:=)71>70<,=:

tools/cutadapt/test-data/cutadapt_builtin_internal_adapter.out

@@ -0,0 +1,12 @@
+@prefix:1_13_573/1
+CGTCCGAANTAGCTACCACCCTGATTAGACAAAT
++
+)3%)&&&&!.1&(6:<'67..*,:75)'77&&&5
+@prefix:1_13_1259/1
+AGCCGCTANGACGGGTTGGCCCTTAGACGTATCT
++
+;<:&:A;A!9<<<,7:<=3=;:<&<?<?8<;=<&
+@prefix:1_13_1440/1
+CAAGATCTNCCCTGCCACATTGCCCTAGTTAAAC
++
+<=A:A=57!7<';<6?5;;6:+:=)71>70<,=:

tools/cutadapt/test-data/cutadapt_revcomp.out

@@ -0,0 +1,12 @@
+@prefix:1_13_573/1
+CGTCCGAANTAGCTACCACCCTGATTAGACAAAT
++
+)3%)&&&&!.1&(6:<'67..*,:75)'77&&&5
+@prefix:1_13_1259/1
+AGCCGCTANGACGGGTTGGCCCTTAGACGTATCT
++
+;<:&:A;A!9<<<,7:<=3=;:<&<?<?8<;=<&
+@prefix:1_13_1440/1
+CAAGATCTNCCCTGCCACATTGCCCTAGT
++
+<=A:A=57!7<';<6?5;;6:+:=)71>7

tools/cutadapt/test-data/cutadapt_shorten_3prime.out

@@ -0,0 +1,12 @@
+@prefix:1_13_573/1
+CGTCCGAANT
++
+)3%)&&&&!.
+@prefix:1_13_1259/1
+
++
+
+@prefix:1_13_1440/1
+CAAGATCTNC
++
+<=A:A=57!7

tools/cutadapt/test-data/cutadapt_shorten_5prime.out

@@ -0,0 +1,12 @@
+@prefix:1_13_573/1
+TTAGACAAAT
++
+75)'77&&&5
+@prefix:1_13_1259/1
+
++
+
+@prefix:1_13_1440/1
+CTAGTTAAAC
++
+)71>70<,=:

tools/cutadapt/test-data/cutadapt_shorten_expected_errors.out

@@ -0,0 +1,12 @@
+@prefix:1_13_573/1
+CGTCCGAANTAGCTACCACCCTGATTAGACAAAT
++
+)3%)&&&&!.1&(6:<'67..*,:75)'77&&&5
+@prefix:1_13_1259/1
+AGCCGCTANGACGGGTTGGCCCTTAGACGTATCT
++
+;<:&:A;A!9<<<,7:<=3=;:<&<?<?8<;=<&
+@prefix:1_13_1440/1
+CAAGATCTNCCCTGCCACATTGCCCTAGTTAAAC
++
+<=A:A=57!7<';<6?5;;6:+:=)71>70<,=:

tools/cutadapt/test-data/cutadapt_shorten_internal_adapters.out

@@ -0,0 +1,12 @@
+@prefix:1_13_573/1
+CGTCCGAANTAGCTACCACCCTGATTAGACAAAT
++
+)3%)&&&&!.1&(6:<'67..*,:75)'77&&&5
+@prefix:1_13_1259/1
+AGCCGCTANGACGGGTTGGCCCTTAGACGTATCT
++
+;<:&:A;A!9<<<,7:<=3=;:<&<?<?8<;=<&
+@prefix:1_13_1440/1
+CAAGATCTNCCCTGCCACATTGCCCTAGTTAAAC
++
+<=A:A=57!7<';<6?5;;6:+:=)71>70<,=:

tools/cutadapt/test-data/cutadapt_small_cut.out

@@ -0,0 +1,12 @@
+@prefix:1_13_573/1
+GAANTAGCTACCACCCTGATTAGACAAAT
++
+&&&!.1&(6:<'67..*,:75)'77&&&5
+@prefix:1_13_1259/1
+CTANGACGGGTTGGCCCTTAGACGTATCT
++
+A;A!9<<<,7:<=3=;:<&<?<?8<;=<&
+@prefix:1_13_1440/1
+TCTNCCCTGCCACATTGCCCTAGTTAAAC
++
+=57!7<';<6?5;;6:+:=)71>70<,=:

tools/cutadapt/test-data/cutadapt_small_rename.out

@@ -0,0 +1,12 @@
+@__oc__prefix:1_13_1259/1__cc__ barcode=__oc__AGATC__cc__ adapter=__oc__illumina_adapter__cc__
+GAANTAGCTACCACCCTGATTAGACAAAT
++
+&&&!.1&(6:<'67..*,:75)'77&&&5
+@__oc__prefix:1_13_1259/1__cc__ barcode=__oc__AGATC__cc__ adapter=__oc__illumina_adapter__cc__
+CTANGACGGGTTGGCCCTTAGACGTATCT
++
+A;A!9<<<,7:<=3=;:<&<?<?8<;=<&
+@__oc__prefix:1_13_1259/1__cc__ barcode=__oc__AGATC__cc__ adapter=__oc__illumina_adapter__cc__
+TCTNCCCTGCCACATTGCCCTAGTTAAAC
++
+=57!7<';<6?5;;6:+:=)71>70<,=: