# HG changeset patch
# User bgruening
# Date 1447204763 18000
# Node ID 06646e81c543eb2a61f2a2a44fcdd404d901cdda
# Parent  3b4ed0e473dcefd1f8d0cf4ca5692b15b5d38854
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sailfish commit 326fbf6e8070a792e3bda3256e5465c2d5b1eb71

diff -r 3b4ed0e473dc -r 06646e81c543 sailfish.xml
--- a/sailfish.xml	Fri Oct 16 15:09:03 2015 -0400
+++ b/sailfish.xml	Tue Nov 10 20:19:23 2015 -0500
@@ -6,9 +6,9 @@
     <macros>
         <xml name="strandedness">
             <param name="strandedness" type="select" label="Specify the strandedness of the reads">
-                <option value="U" selected="True">Not stranded</option>
-                <option value="SF">read 1 (or single-end read) comes from the forward strand</option>
-                <option value="SR">read 1 (or single-end read) comes from the reverse strand</option>
+                <option value="U" selected="True">Not stranded (U)</option>
+                <option value="SF">read 1 (or single-end read) comes from the forward strand (SF)</option>
+                <option value="SR">read 1 (or single-end read) comes from the reverse strand (SR)</option>
             </param>
         </xml>
     </macros>
@@ -17,6 +17,7 @@
         <exit_code range=":-1" />
         <regex match="Error:" />
         <regex match="Exception:" />
+        <regex match="Exception :" />
     </stdio>
     <version_command>sailfish -version</version_command>
     <command>
@@ -36,10 +37,24 @@
         &&
 
         #if $single_or_paired.single_or_paired_opts == 'single':
-            ln -s $single_or_paired.input_singles ./single.$single_or_paired.input_singles.ext &&
+
+            #if $single_or_paired.input_singles.ext == 'fasta':
+                #set $ext = 'fasta'
+            #else:
+                #set $ext = 'fastq'
+            #end if
+
+            ln -s $single_or_paired.input_singles ./single.$ext &&
         #else:
-            ln -s $single_or_paired.input_mate1 ./mate1.$single_or_paired.input_mate1.ext &&
-            ln -s $single_or_paired.input_mate2 ./mate2.$single_or_paired.input_mate2.ext &&
+
+            #if $single_or_paired.input_mate1.ext == 'fasta':
+                #set $ext = 'fasta'
+            #else:
+                #set $ext = 'fastq'
+            #end if
+
+            ln -s $single_or_paired.input_mate1 ./mate1.$ext &&
+            ln -s $single_or_paired.input_mate2 ./mate2.$ext &&
         #end if
 
 
@@ -50,11 +65,11 @@
         sailfish quant
             --index $index_path
             #if $single_or_paired.single_or_paired_opts == 'single':
-                --libType "${single_or_paired.orientation}${single_or_paired.strandedness}"
-                --unmated_reads ./single.$single_or_paired.input_singles.ext
+                --libType ${single_or_paired.strandedness}
+                --unmatedReads ./single.$ext
             #else:
-                --mates1 ./mate1.$single_or_paired.input_mate1.ext
-                --mates2 ./mate2.$single_or_paired.input_mate2.ext
+                --mates1 ./mate1.$ext
+                --mates2 ./mate2.$ext
                 --libType "${single_or_paired.orientation}${single_or_paired.strandedness}"
             #end if
             --output ./ 
@@ -173,7 +188,7 @@
     <outputs>
         <data name="output_quant" format="tabular" from_work_dir="quant.sf" label="${tool.name} on ${on_string} (Quantification)" />
         <data name="output_bias_corrected_quant" format="tabular" from_work_dir="quant_bias_corrected.sf" label="${tool.name} on ${on_string} (Bias corrected Quantification)">
-            <filter>bias_correct == '--biasCorrect'</filter>
+            <filter>biasCorrect is True</filter>
         </data>
         <data name="output_gene_quant" format="tabular" from_work_dir="quant.genes.sf" label="${tool.name} on ${on_string} (Gene Quantification)">
             <filter>geneMap is True</filter>