# HG changeset patch
# User dfornika
# Date 1560888523 14400
# Node ID ae9dffe91f2094ade5e3c90613ec285b24c21859
# Parent  542d3c3d5a6e705669b677640af3fa4724a69a87
planemo upload commit 976a7fd83686e1fe0e4ca2ee9b7c98fff7241d6d-dirty

diff -r 542d3c3d5a6e -r ae9dffe91f20 snippy-core.xml
--- a/snippy-core.xml	Mon Jun 17 16:50:34 2019 -0400
+++ b/snippy-core.xml	Tue Jun 18 16:08:43 2019 -0400
@@ -45,7 +45,7 @@
 
     <tests>
         <test><!-- Test #1 - test with 3 zipped directories -->
-            <param name="indirs" value="a.dat,b.dat,c.dat" />
+            <param name="indirs" value="a.tgz,b.tgz,c.tgz" />
             <param name="ref" value="reference.fasta" />
             <param name="outputs" value="outtxt" />
             <output name="alignment_summary" ftype="txt" file="a_b_c.core.txt" />
diff -r 542d3c3d5a6e -r ae9dffe91f20 snippy.xml
--- a/snippy.xml	Mon Jun 17 16:50:34 2019 -0400
+++ b/snippy.xml	Tue Jun 18 16:08:43 2019 -0400
@@ -10,6 +10,17 @@
 
     <command detect_errors="exit_code"><![CDATA[
 
+        #import re
+        #if str( $fastq_input.fastq_input_selector ) == "paired"
+            #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input1.element_identifier)
+        #elif str( $fastq_input.fastq_input_selector ) == "paired_collection"
+            #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input.name)
+        #elif str( $fastq_input.fastq_input_selector ) == "single"
+            #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input_single.element_identifier)
+        #elif str( $fastq_input.fastq_input_selector ) == "paired_iv"
+            #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input_interleaved.element_identifier)
+        #end if
+
         #if $ref.is_of_type("fasta")
             cp '$ref' 'ref.fna' &&
         #end if
@@ -17,7 +28,7 @@
             cp '$ref' 'ref.gbk' &&
         #end if
         snippy
-            --outdir 'out'
+            --outdir '$dir_name'
             --cpus \${GALAXY_SLOTS:-1}
             --ram \$((\${GALAXY_MEMORY_MB:-4096}/1024))
             #if $ref.is_of_type("fasta")
@@ -51,18 +62,6 @@
 
         &&
 
-        #import re
-        #if str( $fastq_input.fastq_input_selector ) == "paired"
-            #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input1.element_identifier)
-        #elif str( $fastq_input.fastq_input_selector ) == "paired_collection"
-            #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input.name)
-        #elif str( $fastq_input.fastq_input_selector ) == "single"
-            #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input_single.element_identifier)
-        #elif str( $fastq_input.fastq_input_selector ) == "paired_iv"
-            #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input_interleaved.element_identifier)
-        #end if
-
-        mkdir -p ${dir_name} && cp -r out/reference out/snps.tab out/snps.aligned.fa out/snps.vcf ${dir_name}/ &&
         tar -czf out.tgz ${dir_name}
         #if "outcon" in str($outputs) and $adv.rename_cons
           && sed -i 's/>.*/>${dir_name}/' out/snps.consensus.fa
@@ -124,31 +123,31 @@
 
     <outputs>
 
-        <data format="vcf" name="snpvcf" label="${tool.name} on ${on_string} snps vcf file" from_work_dir="out/snps.vcf">
+        <data format="vcf" name="snpvcf" label="${tool.name} on ${on_string} snps vcf file" from_work_dir="${dir_name}/snps.vcf">
             <filter>outputs and 'outvcf' in outputs</filter>
         </data>
-        <data format="gff3" name="snpgff" label="${tool.name} on ${on_string} snps gff file" from_work_dir="out/snps.gff">
+        <data format="gff3" name="snpgff" label="${tool.name} on ${on_string} snps gff file" from_work_dir="${dir_name}/snps.gff">
             <filter>outputs and 'outgff' in outputs</filter>
         </data>
-        <data format="tabular" name="snptab" label="${tool.name} on ${on_string} snps table" from_work_dir="out/snps.tab">
+        <data format="tabular" name="snptab" label="${tool.name} on ${on_string} snps table" from_work_dir="${dir_name}/snps.tab">
             <filter>outputs and 'outtab' in outputs</filter>
         </data>
-        <data format="tabular" name="snpsum" label="${tool.name} on ${on_string} snps summary" from_work_dir="out/snps.txt">
+        <data format="tabular" name="snpsum" label="${tool.name} on ${on_string} snps summary" from_work_dir="${dir_name}/snps.txt">
             <filter>outputs and 'outsum' in outputs</filter>
         </data>
-        <data format="txt" name="snplog" label="${tool.name} on ${on_string} log file" from_work_dir="out/snps.log">
+        <data format="txt" name="snplog" label="${tool.name} on ${on_string} log file" from_work_dir="${dir_name}/snps.log">
             <filter>outputs and 'outlog' in outputs</filter>
         </data>
-        <data format="fasta" name="snpalign" label="${tool.name} on ${on_string} aligned fasta" from_work_dir="out/snps.aligned.fa">
+        <data format="fasta" name="snpalign" label="${tool.name} on ${on_string} aligned fasta" from_work_dir="${dir_name}/snps.aligned.fa">
             <filter>outputs and 'outaln' in outputs</filter>
         </data>
-        <data format="fasta" name="snpconsensus" label="${tool.name} on ${on_string} consensus fasta" from_work_dir="out/snps.consensus.fa">
+        <data format="fasta" name="snpconsensus" label="${tool.name} on ${on_string} consensus fasta" from_work_dir="${dir_name}/snps.consensus.fa">
             <filter>outputs and 'outcon' in outputs</filter>
         </data>
-        <data format="tabular" name="snpsdepth" label="${tool.name} on ${on_string} mapping depth" from_work_dir="out/snps.depth">
+        <data format="tabular" name="snpsdepth" label="${tool.name} on ${on_string} mapping depth" from_work_dir="${dir_name}/snps.depth">
             <filter>outputs and 'outdep' in outputs</filter>
         </data>
-        <data format="bam" name="snpsbam" label="${tool.name} on ${on_string} mapped reads (bam)" from_work_dir="out/snps.bam">
+        <data format="bam" name="snpsbam" label="${tool.name} on ${on_string} mapped reads (bam)" from_work_dir="${dir_name}/snps.bam">
             <filter>outputs and 'outbam' in outputs</filter>
         </data>
         <data format="tar" name="outdir" label="${tool.name} on ${on_string} dir for snippy core" from_work_dir="out.tgz">
diff -r 542d3c3d5a6e -r ae9dffe91f20 test-data/a.dat
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diff -r 542d3c3d5a6e -r ae9dffe91f20 test-data/a.tgz
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diff -r 542d3c3d5a6e -r ae9dffe91f20 test-data/b.dat
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diff -r 542d3c3d5a6e -r ae9dffe91f20 test-data/b.tgz
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diff -r 542d3c3d5a6e -r ae9dffe91f20 test-data/c.dat
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diff -r 542d3c3d5a6e -r ae9dffe91f20 test-data/c.tgz
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