diff nanopolish_eventalign.xml @ 3:ec4ac1a63682 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 4478b7f7e16d56ff6c1ffa24ded1fc106f2379c6

--- a/nanopolish_eventalign.xml	Tue Jun 05 18:06:17 2018 -0400
+++ b/nanopolish_eventalign.xml	Fri Jun 14 08:36:58 2019 -0400
@@ -6,15 +6,31 @@
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
         ln -s '$input_merged' reads.fasta && 
-        
+ 
         #if $input_reads_raw.extension == 'fast5':
             mkdir fast5_files && ln -s '$input_reads_raw' fast5_files/read1.fast5 &&
-        #else
+
+        #else if $input_reads_raw.extension == 'fast5.tar':
+            ln -s '$input_reads_raw' fast5_files.tar &&
+            mkdir fast5_files && tar -xf fast5_files.tar -C fast5_files &&
+
+        #else if $input_reads_raw.extension == 'fast5.tar.bz2':
+            ln -s '$input_reads_raw' fast5_files.tar.bz2 &&
+            mkdir fast5_files && tar -xjf fast5_files.tar.bz2 -C fast5_files &&
+
+        #else:
             ln -s '$input_reads_raw' fast5_files.tar.gz &&
             mkdir fast5_files && tar -xzf fast5_files.tar.gz -C fast5_files &&
+
         #end if
 
-        nanopolish index -d fast5_files/ reads.fasta &&
+        nanopolish index 
+        -d fast5_files/
+        #if $adv.input_seq_summary:
+          -s '$adv.input_seq_summary'
+        #end if 
+        reads.fasta &&
+
         ln -s '$b' reads.bam &&
         ln -s '${b.metadata.bam_index}' reads.bam.bai &&
         #if $reference_source.reference_source_selector == 'history':
@@ -51,7 +67,7 @@
     <inputs>
       <!-- index inputs -->
         <param type="data" name="input_merged" format="fasta,fastq" label="Basecalled merged reads.fa"/>
-        <param type="data" name="input_reads_raw" format="h5,fast5.tar.gz" label="Flat archive file of raw fast5 files"/>
+        <param type="data" name="input_reads_raw" format="h5,fast5.tar.gz,fast5.tar.bz2,fast5.tar" label="Flat archive file of raw fast5 files"/>
 
         <!-- variants consensus inputs -->
         <param type="data" argument="-b" format="bam" label="Reads aligned to the reference genome" />
@@ -72,6 +88,11 @@
           </when>
         </conditional>
 
+        <section name="adv" title="Optional data inputs">
+            <!-- optional inputs -->
+            <param type="data" name="input_seq_summary" format="txt" optional="true" label="Sequencing summary file from albacore" help="(-s)"/>       
+        </section>
+
         <!-- optional inputs -->
         <param type="data" name="input_models_fofn" argument="--models-fofn" format="txt" optional="true"
             label="Read alternative k-mer models (optional)" />