# HG changeset patch
# User iuc
# Date 1545160193 18000
# Node ID 49370cb85f0ff8a78499dbffdad32451292e7263
# Parent  5c7e7d905b331ae44c7e9500d8a5e5965cc3982b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 6318c53e772ed592862729f3048ed9bd3a711969

diff -r 5c7e7d905b33 -r 49370cb85f0f cutadapt.xml
--- a/cutadapt.xml	Thu Dec 13 20:54:04 2018 -0500
+++ b/cutadapt.xml	Tue Dec 18 14:09:53 2018 -0500
@@ -1,4 +1,4 @@
-<tool id="cutadapt" name="Cutadapt" version="1.16.4" profile="17.09">
+<tool id="cutadapt" name="Cutadapt" version="1.16.5" profile="17.09">
     <description>Remove adapter sequences from Fastq/Fasta</description>
     <macros>
         <import>macros.xml</import>
@@ -444,16 +444,8 @@
                     <section name="r1" >
                         <repeat name="front_adapters">
                             <conditional name="front_adapter_source">
-                                <param name="front_adapter_source_list" value="user"/>
-                                <param name="front_adapter_name" value="A1" />
-                                <param name="front_adapter" value="^GTCGGTAA" />
-                            </conditional>
-                        </repeat>
-                        <repeat name="front_adapters">
-                            <conditional name="front_adapter_source">
-                                <param name="front_adapter_source_list" value="user"/>
-                                <param name="front_adapter_name" value="A2" />
-                                <param name="front_adapter" value="^AGGTCACT" />
+                                <param name="front_adapter_source_list" value="file"/>
+                                <param name="front_adapter_file" ftype="fasta"  value="barcodes.fasta" />
                             </conditional>
                         </repeat>
                     </section>
@@ -499,7 +491,7 @@
 
 - FASTQ.GZ, FASTQ.BZ2, FASTQ or FASTA
 
-To trim an adapter, input the ADAPTER sequence e.g. AACCGGTT (with the characters: **$**, **^**, **...**, if anchored or linked).
+To trim an adapter, input the ADAPTER sequence in plain text or in a FASTA file e.g. AACCGGTT (with the characters: **$**, **^**, **...**, if anchored or linked).
 
     =============================================   ===================
     **Option**                                      **Sequence**
diff -r 5c7e7d905b33 -r 49370cb85f0f macros.xml
--- a/macros.xml	Thu Dec 13 20:54:04 2018 -0500
+++ b/macros.xml	Tue Dec 18 14:09:53 2018 -0500
@@ -7,6 +7,8 @@
         #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}'
+            #else if $a.adapter_source.adapter_source_list == 'file':
+                -a file:'${a.adapter_source.adapter_file}'
             #else if str($a.adapter_source.adapter_name) != "":
                 -a '${a.adapter_source.adapter_name}'='${a.adapter_source.adapter}'
             #else
@@ -16,6 +18,8 @@
         #for $aa in $library.r1.anywhere_adapters
             #if $aa.anywhere_adapter_source.anywhere_adapter_source_list == 'builtin':
                 -b ${aa.anywhere_adapter_source.anywhere_adapter.fields.name}"='${aa.anywhere_adapter_source.anywhere_adapter}'
+            #else if $aa.anywhere_adapter_source.anywhere_adapter_source_list == 'file':
+                -b file:'${aa.anywhere_adapter_source.anywhere_adapter_file}'
             #else if str($aa.anywhere_adapter_source.anywhere_adapter_name) != "":
                 -b '${aa.anywhere_adapter_source.anywhere_adapter_name}'='${aa.anywhere_adapter_source.anywhere_adapter}'
             #else
@@ -25,6 +29,8 @@
         #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}'
+            #else if $fa.front_adapter_source.front_adapter_source_list == 'file':
+                -g file:'${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}'
             #else
@@ -66,6 +72,8 @@
         #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}'
+            #else if $a.adapter_source2.adapter_source_list2 == 'file':
+                -A file:'${a.adapter_source2.adapter_file2}'
             #else if str($a.adapter_source2.adapter_name2) != "":
                 -A '${a.adapter_source2.adapter_name2}'='${a.adapter_source2.adapter2}'
             #else
@@ -75,6 +83,8 @@
         #for $aa in $library.r2.anywhere_adapters2
             #if $aa.anywhere_adapter_source2.anywhere_adapter_source_list2 == 'builtin':
                 -B "${aa.anywhere_adapter_source2.anywhere_adapter2.fields.name}"='${aa.anywhere_adapter_source2.anywhere_adapter2}'
+            #else if $aa.anywhere_adapter_source2.anywhere_adapter_source_list2 == 'file':
+                -B file:'${aa.anywhere_adapter_source2.anywhere_adapter_file2}'
             #else if str($aa.anywhere_adapter_source2.anywhere_adapter_name2) != "":
                 -B '${aa.anywhere_adapter_source2.anywhere_adapter_name2}'='${aa.anywhere_adapter_source2.anywhere_adapter2}'
             #else
@@ -84,6 +94,8 @@
         #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}'
+            #else if $fa.front_adapter_source2.front_adapter_source_list2  == 'file':
+                -G file:'${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}'
             #else
@@ -118,6 +130,7 @@
                         <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>
                         </param>
 
                         <when value="user">
@@ -132,6 +145,10 @@
                                 </options>
                             </param>
                         </when>
+
+                        <when value="file">
+                            <param name="adapter_file" argument="-a" format="fasta" type="data" help="Should be of datatype FASTA" label="Choose file containing 3' adapters" />
+                        </when>
                     </conditional>
                 </repeat>
 
@@ -140,6 +157,7 @@
                         <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>
                         </param>
 
                         <when value="user">
@@ -153,6 +171,9 @@
                                 </options>
                             </param>
                         </when>
+                        <when value="file">
+                            <param name="front_adapter_file" argument="-g" format="fasta" type="data" help="Should be of datatype &quot;FASTA&quot;" label="Choose file containing 5' adapters" />
+                        </when>
                     </conditional>
                 </repeat>
 
@@ -161,6 +182,7 @@
                         <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>
                         </param>
 
                         <when value="user">
@@ -174,6 +196,9 @@
                                 </options>
                             </param>
                         </when>
+                        <when value="file">
+                            <param name="anywhere_adapter_file" argument="-b" format="fasta" type="data" help="Should be of datatype &quot;FASTA&quot;" label="Choose file containing 3' or 5' adapters" />
+                        </when>
                     </conditional>
                 </repeat>
 
@@ -196,6 +221,7 @@
                         <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>
                         </param>
 
                         <when value="user">
@@ -210,6 +236,9 @@
                                 </options>
                             </param>
                         </when>
+                        <when value="file">
+                            <param name="adapter_file2" argument="-a" format="fasta" type="data" help="Should be of datatype &quot;FASTA&quot;" label="Choose file containing 3' adapters" />
+                        </when>
                     </conditional>
                 </repeat>
 
@@ -218,6 +247,7 @@
                         <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>
                         </param>
 
                         <when value="user">
@@ -231,6 +261,9 @@
                                 </options>
                             </param>
                         </when>
+                        <when value="file">
+                            <param name="front_adapter_file2" argument="-g" format="fasta" type="data" help="Should be of datatype &quot;FASTA&quot;" label="Choose file containing 5' adapters" />
+                        </when>
                     </conditional>
                 </repeat>
 
@@ -239,6 +272,7 @@
                         <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>
                         </param>
 
                         <when value="user">
@@ -252,6 +286,9 @@
                                 </options>
                             </param>
                         </when>
+                        <when value="file">
+                            <param name="anywhere_adapter_file2" argument="-b" format="fasta" type="data" help="Should be of datatype &quot;FASTA&quot;" label="Choose file containing 3' or 5' adapters" />
+                        </when>
                     </conditional>
                 </repeat>
 
diff -r 5c7e7d905b33 -r 49370cb85f0f test-data/barcodes.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/barcodes.fasta	Tue Dec 18 14:09:53 2018 -0500
@@ -0,0 +1,4 @@
+>A2
+^AGGTCACT
+>A1
+^GTCGGTAA