diff ectyper.xml @ 18:b4fe4085b240 draft

Uploaded

--- a/ectyper.xml	Wed Jan 10 13:22:00 2018 -0500
+++ b/ectyper.xml	Wed Jan 10 13:33:23 2018 -0500
@@ -3,14 +3,22 @@
       <requirement type="package" version="0.1">ectyper</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
+      #if $jobtype.select == "asm"
+        ln -s $jobtype.draft sample.fasta;  
+      #else if $jobtype.select == "se"
+        ln -s $jobtype.fastq1 sample_1.fastq;  
+      #else if $jobtype.select == "pe"
+        ln -s $jobtype.fastq1 sample_1.fastq;  
+        ln -s $jobtype.fastq2 sample_2.fastq;  
+      #end if
 
 	  $__tool_directory__/ectyper 
       #if $jobtype.select == "asm"
-        -i $draft
+        -i sample.fasta
       #else if $jobtype.select == "se"
-        -i $fastq1
+        -i sample_1.fastq
       #else if $jobtype.select == "pe"
-        -i $fastq1 $fastq2
+        -i sample_1.fastq sample_2.fastq
       #end if
       -d $percent_identity
 	  -l $percent_length
@@ -41,7 +49,7 @@
     
     </inputs>
     <outputs>
-            <data format="csv" label="ectyper Results" name="#{tool_input_name}.ectperResults" from_work_dir="*.csv"/>
+            <data format="csv" label="${input1.name}" name="${input1.name}.ectperResults" from_work_dir="*.csv"/>
     </outputs>
 
     <help><![CDATA[