diff velveth.xml @ 3:920677cd220f draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvet commit ccce07eb8b612cbe09702214d3184b0085c055a8"

--- a/velveth.xml	Tue Jun 16 12:58:20 2020 -0400
+++ b/velveth.xml	Sun Jan 24 15:40:17 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="velveth" name="velveth" version="@WRAPPER_VERSION@.2">
+<tool id="velveth" name="velveth" version="@WRAPPER_VERSION@.3">
   <description>Prepare a dataset for the Velvet velvetg Assembler</description>
   <macros>
     <import>macros.xml</import>
@@ -15,20 +15,20 @@
       '$outfile.extra_files_path'
       $hash_length
       #for $i in $inputs
-          -${i.input_type.input.ext}
-          ${i.input_type.read_type}
-          #if str( $i.input_type.input_type_selector ) == "paireds":
-              -separate '${i.input_type.input}' '${i.input_type.input2}'
-          #else if str( $i.input_type.input_type_selector ) == "pairedi":
-              -interleaved '${i.input_type.input}'
-          #else:
-              '${i.input_type.input}'
-          #end if
+        -fmtAuto 
+        ${i.input_type.read_type}
+        #if str( $i.input_type.input_type_selector ) == "paireds":
+          -separate '${i.input_type.input}' '${i.input_type.input2}'
+        #else if str( $i.input_type.input_type_selector ) == "pairedi":
+          -interleaved '${i.input_type.input}'
+        #else:
+          '${i.input_type.input}'
+        #end if
       #end for
       $strand_specific
   ]]></command>
   <inputs>
-      <param label="Hash Length" name="hash_length" type="integer" value="21" min="11" max="191" help="k-mer length in base pairs of the words being hashed."/>
+    <param label="Hash Length" name="hash_length" type="integer" value="21" min="11" max="191" help="k-mer length in base pairs of the words being hashed."/>
     <param name="strand_specific" type="boolean" checked="false" truevalue="-strand_specific" falsevalue="" label="Use strand specific transcriptome sequencing" help="If you are using a strand specific transcriptome sequencing protocol, you may wish to use this option for better results."/>
     <repeat name="inputs" title="Input Files">
       <conditional name="input_type">
@@ -81,8 +81,8 @@
         <conditional name="input_type">
           <param name="input_type_selector" value="paireds" />
           <param name="read_type" value="-shortPaired" />
-          <param name="input1" value="R1.fastq" ftype="fastq" />
-          <param name="input2" value="R2.fastq" ftype="fastq" />
+          <param name="input1" value="R1.fastq" ftype="fastqsanger" />
+          <param name="input2" value="R2.fastq" ftype="fastqsanger" />
         </conditional>
       </repeat>
       <param name="strand_specific" value="" />
@@ -97,7 +97,7 @@
         <conditional name="input_type">
           <param name="input_type_selector" value="single" />
           <param name="read_type" value="-short" />
-          <param name="input" value="R1.fastq" ftype="fastq" />
+          <param name="input" value="R1.fastq" ftype="fastqillumina" />
         </conditional>
       </repeat>
       <param name="strand_specific" value="" />