diff nanopolish_variants.xml @ 3:bc79b5b0fe04 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 89078a214cefd31d28da75ddebb21f546fba79df-dirty

--- a/nanopolish_variants.xml	Tue Jun 05 18:28:16 2018 -0400
+++ b/nanopolish_variants.xml	Wed Jun 19 03:46:05 2019 -0400
@@ -9,12 +9,28 @@
         
         #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':
@@ -29,7 +45,7 @@
         -g genome.fa
         -o variants.vcf
         #if $consensus:
-            --consensus polished.fa
+            --consensus 
         #end if
 
         $snps
@@ -73,11 +89,16 @@
           --models-fofn '$input_models_fofn'
         #end if
 
+        && 
+
+        nanopolish vcf2fasta --skip-checks -g genome.fa variants.vcf > polished.fa
+
+
     ]]></command>
     <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" />
@@ -143,37 +164,47 @@
             <param name="input_reads_raw" ftype="fast5.tar.gz" value="fast5_files.tar.gz" />
             <param name="b" value="reads.sorted.bam" />
             <param name="reference_source_selector" value="history" />
-            <param name="ref_file" value="draft.fa" />
+            <param name="ref_file" value="draft_single_seq.fa" />
             <param name="w" value="tig00000001:200000-202000" />
             <output name="output_polished" file="polished.fa" />
             <output name="output_variants" file="variants.vcf"/>
         </test>
         <test>
             <param name="input_merged" ftype="fasta" value="reads.fasta" />
+            <param name="input_reads_raw" ftype="fast5.tar.bz2" value="fast5_files.tar.bz2" />
+            <param name="b" value="reads.sorted.bam" />
+            <param name="reference_source_selector" value="history" />
+            <param name="ref_file" value="draft_single_seq.fa" />
+            <param name="w" value="tig00000001:200000-202000" />
+            <output name="output_polished" file="t3_polished.fa" />
+            <output name="output_variants" file="t3_variants.vcf"/>
+        </test>
+        <test>
+            <param name="input_merged" ftype="fasta" value="reads.fasta" />
+            <param name="input_reads_raw" ftype="fast5.tar" value="fast5_files.tar" />
+            <param name="b" value="reads.sorted.bam" />
+            <param name="reference_source_selector" value="history" />
+            <param name="ref_file" value="draft_single_seq.fa" />
+            <param name="w" value="tig00000001:200000-202000" />
+            <output name="output_polished" file="t4_polished.fa" />
+            <output name="output_variants" file="t4_variants.vcf"/>
+        </test>
+        <test>
+            <param name="input_merged" ftype="fasta" value="reads.fasta" />
             <param name="input_reads_raw" ftype="fast5.tar.gz" value="fast5_files.tar.gz" />
             <param name="b" value="reads.sorted.bam" />
             <param name="reference_source_selector" value="history" />
-            <param name="ref_file" value="draft.fa" />
-            <param name="w" value="tig00000001:200000-202000" />
+            <param name="ref_file" value="draft_single_seq.fa" />
+            <param name="w" value="tig00000001:198000-202000" />
             <param name="ploidy" value="2" />
             <param name="snps" value="true" />            
             <param name="faster" value="true" />            
             <param name="all_bases" value="true" /> 
             <param name="consensus" value="false" /> 
-            <param name="min_flanking_sequence" value="30" />
+            <param name="min_flanking_sequence" value="10" />
             <output name="output_polished" file="t2-polished.fa" />
             <output name="output_variants" file="t2-variants.vcf"/>
         </test>
-        <test>
-            <param name="input_merged" ftype="fasta" value="reads.fasta" />
-            <param name="input_reads_raw" ftype="fast5.tar.gz" value="fast5_files.tar.gz" />
-            <param name="b" value="reads.sorted.bam" />
-            <param name="reference_source_selector" value="cached" />
-            <param name="ref_file" value="draft"/>
-            <param name="w" value="tig00000001:200000-202000" />
-            <output name="output_polished" file="polished.fa" />
-            <output name="output_variants" file="variants.vcf"/>
-        </test>
     </tests>
     <help><![CDATA[