diff macros.xml @ 8:65c38d020fea draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 1739cab238d13107d96acd9f87700869fa9d3193-dirty

--- a/macros.xml	Tue Jun 13 10:41:34 2017 -0400
+++ b/macros.xml	Sun Sep 24 14:28:47 2017 -0400
@@ -1,4 +1,35 @@
 <?xml version="1.0" ?>
 <macros>
     <token name="@VERSION@">2.1b</token>
+    <xml name="db_prep">
+        <param name="seed_length" type="integer" min="0" max="100" value="18" label="Seed length for database indexing" help="(-L)"/>
+        <param name="max_pos" type="integer" min="0" max="100000" value="10000" label="Maximum number of positions to store for each k-mer for database indexing" help="With 0, all positions are stored (--max_pos)"/>
+    </xml>
+    <xml name="output_alignments">
+        <param name="print_all_reads" type="boolean" checked="false" truevalue="--print_all_reads" falsevalue="" label="Output null alignment strings for non-aligned reads"/>
+        <conditional name="blast">
+            <param name="blast_output" type="select" label="Output BLAST report?">
+                <option value="True">Yes</option>
+                <option value="False" selected="True">No</option>
+            </param>
+            <when value="True">
+                <param name="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="False"/>
+        </conditional>
+    </xml>
+    <token name="@ALIGNMENTS@">
+        $report.print_all_reads
+        --sam
+        --SQ
+        #if $report.blast.blast_output == 'True'
+            --blast '$report.blast.blast_format'
+        #end if
+    </token>
 </macros>
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