diff snippy.xml @ 1:82f2b6f20fa2 draft

planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61

--- a/snippy.xml	Fri Feb 16 13:40:16 2018 -0500
+++ b/snippy.xml	Sat Jan 26 14:36:48 2019 -0500
@@ -1,4 +1,4 @@
-<tool id="snippy" name="snippy" version="@VERSION@">
+<tool id="snippy" name="snippy" version="@VERSION@+galaxy1">
   <description>
       Snippy finds SNPs between a haploid reference genome and your NGS sequence reads.
   </description>
@@ -40,14 +40,14 @@
                 --pe2 '$fastq_input.fastq_input2'
             #end if
             #if str( $fastq_input.fastq_input_selector ) == "paired_collection"
-                --pe1 '$fastq_input.fastq_input1.forward'
-                --pe2 '$fastq_input.fastq_input1.reverse'
+                --pe1 '$fastq_input.fastq_input.forward'
+                --pe2 '$fastq_input.fastq_input.reverse'
             #end if
             #if str( $fastq_input.fastq_input_selector ) == "single"
-                --se '$fastq_input.fastq_input1'
+                --se '$fastq_input.fastq_input'
             #end if
             #if str( $fastq_input.fastq_input_selector ) == "paired_iv"
-                --peil '$fastq_input.fastq_input1'
+                --peil '$fastq_input.fastq_input'
             #end if
 
         &&
@@ -57,9 +57,13 @@
         &&
 
         #import re
-        #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input1.element_identifier)
-        mkdir -p ${dir_name}/reference && cp out/snps.tab out/snps.aligned.fa ${dir_name}/ && cp out/reference/ref.fa ${dir_name}/reference/ &&
+        #if str( $fastq_input.fastq_input_selector ) == "paired"
+            #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input1.element_identifier)
+        #else
+            #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input.element_identifier)
+        #end if
 
+        mkdir -p ${dir_name} && cp -r out/reference out/snps.tab out/snps.aligned.fa ${dir_name}/ &&
         tar -czf out.tgz ${dir_name}
 
 
@@ -81,13 +85,13 @@
                 <param name="fastq_input2" type="data" format="fastqsanger,fasta" label="Select second set of reads" help="Specify dataset with reverse reads"/>
             </when>
             <when value="single">
-                <param name="fastq_input1" type="data" format="fastqsanger,fasta" label="Select fastq dataset" help="Specify dataset with single reads"/>
+                <param name="fastq_input" type="data" format="fastqsanger,fasta" label="Select fastq dataset" help="Specify dataset with single reads"/>
             </when>
             <when value="paired_collection">
-                <param name="fastq_input1" format="fastqsanger,fasta" type="data_collection" collection_type="paired" label="Select a paired collection" help="See help section for an explanation of dataset collections"/>
+                <param name="fastq_input" format="fastqsanger,fasta" type="data_collection" collection_type="paired" label="Select a paired collection" help="See help section for an explanation of dataset collections"/>
             </when>
             <when value="paired_iv">
-                <param name="fastq_input1" type="data" format="fastqsanger" label="Select fastq dataset" help="Specify dataset with interleaved reads"/>
+                <param name="fastq_input" type="data" format="fastqsanger" label="Select fastq dataset" help="Specify dataset with interleaved reads"/>
             </when>
         </conditional>
 
@@ -204,6 +208,20 @@
             <output name="snpgff" ftype="gff3" file="min_frac/snps.gff" />
         </test>
 
+        <test> <!-- test 6 - fasta ref default paired_collection -->
+	    <param name="ref" value="wildtype.fna" ftype="fasta" />
+            <param name="fastq_input_selector" value="paired_collection" />
+            <param name="fastq_input">
+                <collection type="paired">
+                    <element name="forward" ftype="fastqsanger" value="mutant_R1.fastq" />
+                    <element name="reverse" ftype="fastqsanger" value="mutant_R2.fastq" />
+                </collection>
+            </param>
+            <param name="outputs" value="outgff,outsum" />
+            <output name="snpsum" ftype="tabular" file="fna_ref/snps.txt" lines_diff="6" />
+            <output name="snpgff" ftype="gff3" file="fna_ref/snps.gff" />
+        </test>
+
     </tests>