# HG changeset patch
# User iuc
# Date 1536152642 14400
# Node ID 6daca6da305925af452b65bdc73f86f0c0f57b6a
# Parent  a26ed87f444c429ecc412f3f714ca1bc134799bc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 048a871cbca11489fb27478f233555106cfb5f22

diff -r a26ed87f444c -r 6daca6da3059 hisat2.xml
--- a/hisat2.xml	Tue Jul 24 09:29:27 2018 -0400
+++ b/hisat2.xml	Wed Sep 05 09:04:02 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="hisat2" name="HISAT2" version="2.1.0+galaxy2" profile="17.01">
+<tool id="hisat2" name="HISAT2" version="2.1.0+galaxy3" profile="17.01">
     <description>A fast and sensitive alignment program</description>
     <macros>
         <import>hisat2_macros.xml</import>
@@ -291,8 +291,6 @@
 
 #if str($adv.reporting_options.reporting_options_selector) == "advanced":
     -k ${adv.reporting_options.max_primary}
-    --max-seeds ${adv.reporting_options.max_seeds}
-    $adv.reporting_options.secondary
 #end if
 
 
@@ -534,8 +532,6 @@
                 <when value="defaults" />
                 <when value="advanced">
                     <param name="max_primary" argument="-k" type="integer" min="0" optional="true" label="Primary alignments" help="Search for at most K distinct, primary alignments for each read. Primary alignments mean alignments whose alignment score is equal or higher than any other alignments. The search terminates when it can't find more distinct valid alignments, or when it finds K, whichever happens first. The alignment score for a paired-end alignment equals the sum of the alignment scores of the individual mates. Each reported read or pair alignment beyond the first has the SAM 'secondary' bit (which equals 256) set in its FLAGS field. For reads that have more than K distinct, valid alignments, HISAT2 does not guarantee that the K alignments reported are the best possible in terms of alignment score. HISAT2 is not designed with large values for -k in mind, so when aligning reads to long repetitive genomes, a large K can be very, very slow. Default: 5 (HFM) or 10 (HGFM)" />
-                    <param name="max_seeds" argument="--max-seeds" type="integer" min="0" optional="true" label="Maximum number of seeds that will be extended" help="HISAT2, like other aligners, uses seed-and-extend approaches. HISAT2 tries to extend seeds to full-length alignments. HISAT2 extends up to these many seeds and skips the rest of the seeds. Large values for --max-seeds may improve alignment sensitivity, but HISAT2 is not designed with large values for --max-seeds in mind, and when aligning reads to long repetitive genomes, a large --max-seeds can be very, very slow. Default: 5 (HFM) or 10 (HGFM)" />
-                    <param name="secondary" argument="--secondary" type="boolean" truevalue="--secondary" falsevalue="" label="Report secondary alignments" />
                 </when>
             </conditional>
 
@@ -1083,12 +1079,6 @@
 
             Note: HISAT2 is not designed with large values for `-k` in mind, and when aligning reads to long, repetitive genomes large `-k` can be very, very slow.
 
-    -max-seeds
-            HISAT2, like other aligners, uses seed-and-extend approaches. HISAT2 tries to extend seeds to full-length alignments. In HISAT2, `--max-seeds` is used to control the maximum number of seeds that will be extended. HISAT2 extends up to these many seeds and skips the rest of the seeds. Large values for `--max-seeds` may improve alignment sensitivity, but HISAT2 is not designed with large values for `--max-seeds` in mind, and when aligning reads to long, repetitive genomes large `--max-seeds` can be very, very slow. The default value is the maximum of 5 and the value that comes with `-k`.
-
-    --secondary
-            Report secondary alignments.
-
 -----
 
 **Paired-end options**::