# HG changeset patch
# User rnateam
# Date 1465983070 14400
# Node ID bf2866308fbd25cc76b73b05355ff9573d3b8fb0
# Parent  97f73e0566c9de242d5407cc485b3943180d377e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 5a8ffc52b7076d8d4fbc9649703bb4c0155b726c

diff -r 97f73e0566c9 -r bf2866308fbd sortmerna.xml
--- a/sortmerna.xml	Tue Mar 29 06:53:28 2016 -0400
+++ b/sortmerna.xml	Wed Jun 15 05:31:10 2016 -0400
@@ -1,4 +1,4 @@
-<tool id="bg_sortmerna" name="Filter with SortMeRNA" version="2.1b.0">
+<tool id="bg_sortmerna" name="Filter with SortMeRNA" version="2.1b.1">
     <description>Fast and accurate filtering of ribosomal RNAs in metatranscriptomic data</description>
     <requirements>
         <requirement type="package" version="2.1b">sortmerna</requirement>
@@ -75,7 +75,9 @@
     	#if $aligned_sam.aligned_sam_selector == '--sam'
         	$aligned_sam.sq
     	#end if
-    	$aligned_blast
+    	#if $aligned_blast.aligned_blast_selector == '--blast'
+        	--blast "$aligned_blast.aligned_blast_format"
+    	#end if
 
     	$log
 
@@ -179,14 +181,23 @@
             </when>
             <when value="" />
         </conditional>
-        <param name="aligned_blast" type="select" label="Include alignments in BLAST-like format">
-            <option value="--blast 0">pairwise (--blast 0)</option>
-            <option value="--blast 1">tabular BLAST -m 8 format (--blast 1)</option>
-            <option value="--blast 2">tabular + column for CIGAR (--blast 2)</option>
-            <option value="--blast 3">tabular + columns for CIGAR and query coverage (--blast 3)</option>
-            <option value="" selected="true">No</option>
-        </param>
-        <param name="log" type="boolean" checked="False" truevalue="--log" falsevalue="" label="Generate statistics file"
+        <conditional name="aligned_blast">
+            <param name="aligned_blast_selector" type="select" label="Include alignments in BLAST-like format?">
+                <option value="--blast">Yes</option>
+                <option value="" selected="true">No</option>
+            </param>
+            <when value="--blast">
+                <param name="aligned_blast_format" type="select" label="BLAST-like format?">
+                    <option value="0">pairwise (--blast '0')</option>
+                    <option value="1">tabular BLAST -m 8 format (--blast '1')</option>
+                    <option value="1 cigar">tabular + column for CIGAR (--blast '1 cigar')</option>
+                    <option value="1 cigar qcov">tabular + columns for CIGAR and query coverage (--blast '1 cigar qcov')</option>
+                    <option value="1 cigar qcov qstrand">tabular + columns for CIGAR, query coverage and strand (--blast '1 cigar qcov qstrand')</option>
+                </param>
+            </when>
+            <when value="" />
+        </conditional>
+        <param name="log" type="boolean" checked="false" truevalue="--log" falsevalue="" label="Generate statistics file"
                help="Generates statistics for the rRNA content of reads, as well as rRNA subunit distribution. (--log)">
         </param>
 	<conditional name="report">
@@ -247,9 +258,9 @@
         </data>
         <data format="tabular" name="output_blast" from_work_dir="aligned.blast"
             label="Alignments on ${on_string} (BLAST)">
-            <filter>aligned_blast</filter>
+            <filter>aligned_blast['aligned_blast_selector']</filter>
             <change_format>
-                <when input="aligned_blast" value="--blast 0" format="txt" />
+                <when input="aligned_blast.aligned_blast_format" value="0" format="txt" />
             </change_format>
         </data>
         <data format="txt" name="output_log" label="${tool.name} statistics (txt)" from_work_dir="aligned.log">
@@ -263,8 +274,20 @@
             <param name="strand_search" value="" />
             <param name="databases_selector" value="history" />
             <param name="database_name" value="ref_small.fasta" />
+            <param name="aligned_fastx_selector" value="--fastx" />
             <param name="other" value="True" />
+            <param name="aligned_sam_selector" value="--sam" />
+            <param name="aligned_blast_selector" value="--blast"/>
+            <param name="aligned_blast_format" value="1 cigar qcov" />
             <param name="log" value="" />
+            <param name="report_type" value="best" />
+            <param name="report_best_type" value="1" />
+            <param name="e_value" value="1"/>
+            <param name="match" value="2"/>
+            <param name="mismatch" value="-3" />
+            <param name="gap_open" value="5"/>
+            <param name="gap_ext" value="2"/>
+            <param name="ambiguous_letter" value="-3"/>
             <output name="output_fastx" file="sortmerna_wrapper_accept1.fastq" />
             <output name="output_other" file="sortmerna_wrapper_other1.fastq" />
             <output name="output_sam" file="sortmerna_wrapper_sam1.sam" lines_diff="2" />
@@ -275,8 +298,21 @@
             <param name="strand_search" value="" />
             <param name="databases_selector" value="history" />
             <param name="database_name" value="ref_small.fasta" />
+            <param name="aligned_fastx_selector" value="--fastx" />
             <param name="other" value="True" />
+            <param name="aligned_sam_selector" value="--sam" />
+            <param name="aligned_blast" value="" />
             <param name="log" value="" />
+            <param name="report_type" value="best" />
+            <param name="report_best_type" value="1" />
+            <param name="report_type" value="best" />
+            <param name="report_best_type" value="1" />
+            <param name="e_value" value="1"/>
+            <param name="match" value="2"/>
+            <param name="mismatch" value="-3" />
+            <param name="gap_open" value="5"/>
+            <param name="gap_ext" value="2"/>
+            <param name="ambiguous_letter" value="-3"/>
             <output name="output_fastx" file="sortmerna_wrapper_accept2.fasta" />
             <output name="output_other" file="sortmerna_wrapper_other2.fasta" />
             <output name="output_sam" file="sortmerna_wrapper_sam2.sam" lines_diff="2" />