diff macros.xml @ 9:ef3ebaa70032 draft

planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit a54770771e567c7ad8a9dd75cc4689c3935ef11c

--- a/macros.xml	Mon May 27 13:21:48 2019 -0400
+++ b/macros.xml	Tue May 28 12:13:45 2019 -0400
@@ -26,7 +26,7 @@
     <token name="@DADA_UNIQUES@">dada2_derep,dada2_dada,dada2_mergepairs</token>
 
     <!-- function to read dada2 data types
-         - derep, dada, and mergepairs are simply read as RDS 
+         - derep, dada, and mergepairs are simply read as RDS
          - sequence_table is a named integer matrix (rows=samples, columns=ASVs)
          - uniques is a named integer vector (columns=ASVs, only one rows)-->
     <token name="@READ_FOO@"><![CDATA[
@@ -48,7 +48,7 @@
     #end def
     ]]></token>
     <!-- function to write dada2 data types (the content or the R variable 'out' is written)
-         - derep, dada, and mergepairs are written as RDS 
+         - derep, dada, and mergepairs are written as RDS
          - sequence_table is a named integer matrix (rows=samples, columns=ASVs)
          - uniques is a named integer vector (columns=ASVs, only one rows)-->
     <token name="@WRITE_FOO@"><![CDATA[
@@ -61,7 +61,27 @@
         saveRDS(data, file=fname)
     }
 }
-    ]]></token> 
+    ]]></token>
+
+    <xml name="fastq_input" token_multiple="" token_collection_type="" token_argument_fwd="" token_argument_rev="">
+        <conditional name="paired_cond">
+            <param name="paired_select" type="select" label="Paired reads">
+                <option value="paired">paired - in a data set pair</option>
+                <option value="separate">paired - in two separate data sets</option>
+                <option value="single">single</option>
+            </param>
+            <when value="paired">
+                <param name="reads" argument="@ARGUMENT_FWD@/@ARGUMENT_REV@" type="data_collection" collection_type="@COLLECTION_TYPE@" format="fastq,fastq.gz" label="Paired short read data"/>
+            </when>
+            <when value="separate">
+                <param name="reads" argument="@ARGUMENT_FWD@" type="data" format="fastq,fastq.gz" multiple="@MULTIPLE@" label="Forward read data"/>
+                <param name="sdaer" argument="@ARGUMENT_REV@" type="data" format="fastq,fastq.gz" multiple="@MULTIPLE@" label="Reverse read data"/>
+            </when>
+            <when value="single">
+                <param name="reads" argument="@ARGUMENT_FWD@" type="data" format="fastq,fastq.gz" multiple="@MULTIPLE@" label="Short read data"/>
+            </when>
+        </conditional>
+    </xml>
 
     <!-- for filterAndTrim -->
     <xml name="trimmers">
@@ -69,7 +89,7 @@
             <param argument="truncQ" type="integer" value="2" min="0" label="Truncate reads at quality threshold" help="Truncate reads at the first instance of a quality score less than or equal to this threshold"/>
             <param argument="trimLeft" type="integer" value="0" min="0" label="Trim start of each read" help="The number of nucleotides to remove from the start of each read."/>
             <param argument="trimRight" type="integer" value="0" min="0" label="Trim end of each read" help="The number of nucleotides to remove from the end of each read"/>
-			<param argument="truncLen" type="integer" value="0" min="0" label="Truncate read length" help="Truncate reads after this amount of bases. Reads shorter than this are discarded. (default 0: no truncation)"/>
+            <param argument="truncLen" type="integer" value="0" min="0" label="Truncate read length" help="Truncate reads after this amount of bases. Reads shorter than this are discarded. (default 0: no truncation)"/>
         </section>
     </xml>
     <xml name="filters">