diff nanostat.xml @ 1:845458a694e0 draft default tip

planemo upload

--- a/nanostat.xml	Tue May 14 05:36:34 2019 -0400
+++ b/nanostat.xml	Fri May 17 09:23:59 2019 -0400
@@ -10,9 +10,21 @@
     ## Galaxy creates xyz.dat but nanostat relies on suffix to detect compressed fasta/fastq; otoh Galaxy provides 'element_identifier'
     #if str($input_type.type) == "fastq" or str($input_type.type) == "fasta"
       #set $named_input_files = ''
-      #for $i_file in $input_type.file
-        ## Add single quotes around each input file identifier
-        #set $_input_file = "'{}'".format($i_file.element_identifier)
+      #for $counter, $i_file in enumerate($input_type.file):
+        #if $i_file.is_of_type('fastqsanger', 'fastq'):
+            #set $ext = 'fastq'
+        #elif $i_file.is_of_type('fastqsanger.gz', 'fastq.gz'):
+            #set $ext = 'fastq.gz'
+        #elif $i_file.is_of_type('fastqsanger.bz2', 'fastq.bz2'):
+            #set $ext = 'fastq.bz2'
+        #elif $i_file.is_of_type('fasta'):
+            #set $ext = 'fasta'
+        #elif $i_file.is_of_type('fasta.gz'):
+            #set $ext = 'fasta.gz'
+        #elif $i_file.is_of_type('fasta.bz2'):
+            #set $ext = 'fasta.bz2'
+        #end if
+        #set $_input_file = "./input_" + str($counter) + "." + $ext
         #set $named_input_files = $named_input_files + ' ' + $_input_file
         ln -s '${i_file}' ${_input_file} &&
       #end for
@@ -45,16 +57,16 @@
         <option value="summary">Use albacore or guppy summary file for quality scores</option>
       </param>
       <when value="fastq">
-        <param type="data" name="file" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2, fastqsanger.bgz" multiple="true" label="One or more (compressed) fastq file(s)." optional="true"/>
+        <param type="data" multiple="true" name="file" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2, fastqsanger.bgz" label="One or more (compressed) fastq file(s)." optional="true"/>
       </when>
       <when value="fasta">
-        <param type="data" name="file" format="fasta, fasta.gz, fasta.bz2, fasta.bgz" multiple="true" label="One or more (compressed) fasta file(s)." optional="true"/>
+        <param type="data" multiple="true" name="file" format="fasta, fasta.gz, fasta.bz2, fasta.bgz" label="One or more (compressed) fasta file(s)." optional="true"/>
       </when>
       <when value="bam">
-        <param type="data" name="file" format="bam" label="One or more sorted bam file(s)." multiple="true" optional="true"/>
+        <param type="data" multiple="true" name="file" format="bam" label="One or more sorted bam file(s)." optional="true"/>
       </when>
       <when value="summary">
-        <param type="data" name="file" format="tabular" label="Summary file generated by albacore or guppy." multiple="true" optional="true"/>
+        <param type="data" multiple="true" name="file" format="tabular" label="Summary file generated by albacore or guppy." optional="true"/>
         <param name="barcoded" argument="--barcoded" type="boolean" truevalue="--barcode" falsevalue="" checked="false" label="Do you want to split the summary file by barcode?" help="Default:No"/>
         <param name="readtype" argument="--readtype" type="select" label="Which read type to extract information about from summary?">
           <option value="1D" selected="true">1D</option>