diff cutadapt.xml @ 18:5c7e7d905b33 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b58d6ff959a1d920fd0d9b02e43d2482667d61e8

--- a/cutadapt.xml	Fri Nov 09 11:33:40 2018 -0500
+++ b/cutadapt.xml	Thu Dec 13 20:54:04 2018 -0500
@@ -82,7 +82,7 @@
 #if str( $library.type ) == "single":
     @read1_options@
     #if $output_options.multiple_output:
-        --output='split/{name}.fastq'
+        --output='split/{name}.${input_1.ext}'
     #else:
         --output='$out1'
     #end if
@@ -236,6 +236,7 @@
 
     <outputs>
         <data name="out1" format="fastqsanger" metadata_source="input_1" from_work_dir="out1*" label="${tool.name} on ${on_string}: Read 1 Output">
+            <filter>(output_options['multiple_output'] is False)</filter>
             <expand macro="inherit_format_1" />
         </data>
         <data name="out2" format="fastqsanger" metadata_source="input_2" from_work_dir="out2*" label="${tool.name} on ${on_string}: Read 2 Output" >
@@ -290,8 +291,8 @@
             <expand macro="inherit_format_2" />
         </data>
 
-        <collection name="split_output" type="list" format_source="input" label="${tool.name} on ${on_string}: Split outputs">
-            <discover_datasets pattern="__designation_and_ext__" directory="split" visible="false"   />
+        <collection name="split_output" type="list" label="${tool.name} on ${on_string}: Split outputs"  >
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.(?P&lt;ext&gt;fastq.*)" directory="split" />
             <filter>(output_options['multiple_output'] is True)</filter>
         </collection>
 
@@ -422,7 +423,7 @@
                     </repeat>
                 </section>
             </conditional>
-            <param name="report" value="True" />
+            <param name="report" value="False" />
             <param name="info_file" value="False" />
             <param name="multiple_output" value="True" />
             <output_collection name="split_output" type="list" count="3">
@@ -433,14 +434,43 @@
                    <element name="unknown" value="unknown.fastq" ftype="fastq">
                    </element>
              </output_collection>
-            <output name="report">
-                <assert_contents>
-                    <has_text text="Summary"/>
-                </assert_contents>
-            </output>
         </test>
 
 
+            <test>
+                <conditional name="library">
+                    <param name="type" value="single" />
+                    <param name="input_1" ftype="fastq.gz" value="cutadapt_in_split.fastq.gz" />
+                    <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" />
+                            </conditional>
+                        </repeat>
+                    </section>
+                </conditional>
+                <param name="report" value="False" />
+                <param name="info_file" value="False" />
+                <param name="multiple_output" value="True" />
+                <output_collection name="split_output" type="list" count="3">
+                       <element name="A1"  decompress="True" file="A1.fastq.gz" ftype="fastq.gz">
+                       </element>
+                       <element name="A2" decompress="True" file="A2.fastq.gz" ftype="fastq.gz">
+                       </element>
+                       <element name="unknown" decompress="True" file="unknown.fastq.gz" ftype="fastq.gz">
+                       </element>
+                 </output_collection>
+            </test>
+
     </tests>
 
     <help><![CDATA[