# HG changeset patch
# User bebatut
# Date 1446035025 14400
# Node ID 9c19086ae6264a74d6cd691270cf8ce71060ee5a
# Parent  48ab7cdab700c4c0aa813490343884e041cbc5aa
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 4d9df680f128bc18183ebba6f85fc24f11207571-dirty

diff -r 48ab7cdab700 -r 9c19086ae626 sortmerna.xml
--- a/sortmerna.xml	Wed Oct 28 06:56:21 2015 -0400
+++ b/sortmerna.xml	Wed Oct 28 08:23:45 2015 -0400
@@ -41,12 +41,12 @@
     sortmerna
         --ref $ref
         --reads $input_sequence_file
+        --aligned aligned
 
         #if $fastx.test:
-            --aligned $aligned_sequence_file
             --fastx
             #if $fastx.rejected:
-                --other $rejected_sequence_file
+                --other other_file
             #end if
         #end if
 
@@ -58,9 +58,11 @@
 
         #if $blast.test:
             --aligned $blast_output_file
-            --blast '$blast.format'
+            --blast "$blast.format"
         #end if
 
+        $log.test
+
         #if $report.type == 'best':
             #if $report.best.type == '0':
                 --best 0
@@ -144,6 +146,10 @@
             </when>
         </conditional>
 
+        <conditional name="log">
+            <param name='test' type='boolean' checked="true" truevalue='--log' falsevalue='' label="Conserve overall statistic output into a log file?" help=""/>
+        </conditional>
+
         <conditional name="report">
             <param name="type" type="select" display="radio" label="Parameters for filtering and read mapping" help="">
                 <option value="best" selected="true">Report best alignments per read reaching E-value</option>
@@ -197,20 +203,27 @@
     </inputs>
     
     <outputs>
-        <data format="fastq,fasta" name="aligned_sequence_file" metadata="input_sequence_file">
+        <data format_source="input_sequence_file" name="aligned_sequence_file" metadata="input_sequence_file" from_work_dir="aligned.dat">
             <filter>((fastx['test']))</filter>
         </data>
 
-        <data format="fastq,fasta" name="rejected_sequence_file" metadata="input_sequence_file">
+        <data format_source="input_sequence_file" name="rejected_sequence_file" metadata="input_sequence_file" from_work_dir="other_file.dat">
             <filter>((fastx['test'] and fastx['rejected']))</filter>
         </data>
 
-        <data format="sam" name="sam_alignment_file" metadata="input_sequence_file">
+        <data format="sam" name="sam_alignment_file" metadata="input_sequence_file" from_work_dir="aligned.sam">
             <filter>((sam['test']]))</filter>
         </data>
 
-        <data format="text" name="blast_output_file" metadata="input_sequence_file">
+        <data format="tabular" name="blast_output_file" metadata="input_sequence_file" from_work_dir="aligned.blast">
             <filter>((blast['test']))</filter>
+            <change_format>
+                <when input="blast.format" value="0" format="txt" />
+            </change_format>
+        </data>
+
+        <data format="txt" name="output_log" metadata="input_sequence_file" from_work_dir="aligned.log">
+            <filter>log.test</filter>
         </data>
     </outputs>