# HG changeset patch
# User iuc
# Date 1500402313 14400
# Node ID f4fa77189eb0a1a7a2bb4a4129d21ec5bff35c0a
# Parent  2ec097c8e843265ef60e38de5b062c08e214e232
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 24fd129248023df91579027d9061468d01fc2350

diff -r 2ec097c8e843 -r f4fa77189eb0 hisat2.xml
--- a/hisat2.xml	Mon Apr 10 23:28:31 2017 -0400
+++ b/hisat2.xml	Tue Jul 18 14:25:13 2017 -0400
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="hisat2" name="HISAT2" version="2.0.5.1" profile="17.01">
+<tool id="hisat2" name="HISAT2" version="2.0.5.2" profile="17.01">
     <description>A fast and sensitive alignment program</description>
     <macros>
         <import>hisat2_macros.xml</import>
@@ -86,10 +86,13 @@
         #end if
         #if str($alignment_options.alignment_options_selector) == "advanced":
             --n-ceil ${alignment_options.function_type},${alignment_options.constant_term},${alignment_options.coefficient}
-            ${alignment_options.skip_forward} ${alignment_options.skip_reverse} ${alignment_options.ignore_quals}
+            ${alignment_options.ignore_quals}
+            ${alignment_options.skip_forward}
+            ${alignment_options.skip_reverse}
         #end if
         #if str($spliced_options.spliced_options_selector) == "advanced":
-            --pen-cansplice ${spliced_options.canonical_penalty} --pen-noncansplice ${spliced_options.noncanonical_penalty}
+            --pen-cansplice ${spliced_options.canonical_penalty}
+            --pen-noncansplice ${spliced_options.noncanonical_penalty}
             --pen-canintronlen ${spliced_options.function_type},${spliced_options.constant_term},${spliced_options.coefficient}
             --pen-noncanintronlen ${spliced_options.nc_function_type},${spliced_options.nc_constant_term},${spliced_options.nc_coefficient}
             #if str($spliced_options.known_splice_gtf) != 'None':
@@ -167,7 +170,14 @@
             </param>
             <when value="defaults" />
             <when value="advanced">
-                <expand macro="function" helptext="Sets a function governing the maximum number of ambiguous characters" />
+                <param name="function_type" argument="--n-ceil" type="select" display="radio" label="Function governing the maximum number of ambiguous characters (usually Ns and/or .s) allowed in a read as a function of read length" help="Reads exceeding this ceiling are filtered out">
+                    <option value="C">Constant [f(x) = B]</option>
+                    <option value="L" selected="true">Linear [f(x) = B + A * x]</option>
+                    <option value="S">Square root [f(x) = B + A * x&#178;]</option>
+                    <option value="G">Natural logarithm [f(x) = B + A * log(x)]</option>
+                </param>
+                <param name="constant_term" type="float" value="0" label="Constant term (B)" help="Constant term for the above function" />
+                <param name="coefficient" type="float" value="0.15" label="Coefficient (A)" help="Coefficient for the above function" />
                 <param argument="--ignore-quals" name="ignore_quals" type="boolean" truevalue="--ignore-quals" falsevalue="" label="Ignore quality values" help="When calculating a mismatch penalty, always consider the quality value at the mismatched position to be the highest possible, regardless of the actual value. I.e. input is treated as though all quality values are high. This is also the default behavior when the input doesn't specify quality values" />
                 <param argument="--nofw" name="skip_forward" type="boolean" truevalue="--nofw" falsevalue="" label="Skip forward strand of reference" help="If --nofw is specified, hisat2 will not attempt to align unpaired reads to the forward (Watson) reference strand. In paired-end mode, --nofw and --norc pertain to the fragments; i.e. specifying --nofw causes hisat2 to explore only those paired-end configurations corresponding to fragments from the reverse-complement (Crick) strand" />
                 <param argument="--norc" name="skip_reverse" type="boolean" truevalue="--norc" falsevalue="" label="Skip reverse strand of reference" help="If --norc is specified, hisat2 will not attempt to align unpaired reads against the reverse-complement (Crick) reference strand. In paired-end mode, --nofw and --norc pertain to the fragments; i.e. specifying --norc causes hisat2 to explore only those paired-end configurations corresponding to fragments from the forward-complement (Watson) strand" />
@@ -193,7 +203,14 @@
             </param>
             <when value="defaults" />
             <when value="advanced">
-                <expand macro="function" helptext="Sets a function governing the minimum alignment score needed for an alignment to be considered &quot;valid&quot; (i.e. good enough to report)" />
+                <param name="function_type" argument="--score-min" type="select" display="radio" label="Function governing the minimum alignment score needed for an alignment to be considered &quot;valid&quot; (i.e. good enough to report)" help="This is a function of read length">
+                    <option value="C">Constant [f(x) = B]</option>
+                    <option value="L" selected="true">Linear [f(x) = B + A * x]</option>
+                    <option value="S">Square root [f(x) = B + A * x&#178;]</option>
+                    <option value="G">Natural logarithm [f(x) = B + A * log(x)]</option>
+                </param>
+                <param name="constant_term" type="float" value="0" label="Constant term (B)" help="Constant term for the above function" />
+                <param name="coefficient" type="float" value="-0.2" label="Coefficient (A)" help="Coefficient for the above function" />
                 <param argument="--ma" name="match_bonus" type="integer" value="2" label="Set match bonus" help="In local mode N is added to the alignment score for each position where a read character aligns to a reference character and the characters match. Not used in end-to-end mode" />
                 <param argument="--mp" name="max_mismatch" type="integer" value="6" label="Maximum mismatch penalty" help="Sets the maximum mismatch penalty. A number less than or equal to MX and greater than or equal to MN is subtracted from the alignment score for each position where a read character aligns to a reference character, the characters do not match, and neither is an N. If --ignore-quals is specified, the number subtracted quals MX. Otherwise, the number subtracted is MN + floor( (MX-MN)(MIN(Q, 40.0)/40.0) ) where Q is the Phred quality value" />
                 <param argument="--mp" name="min_mismatch" type="integer" value="2" label="Minimum mismatch penalty" help="Sets the minimum mismatch penalty. A number less than or equal to MX and greater than or equal to MN is subtracted from the alignment score for each position where a read character aligns to a reference character, the characters do not match, and neither is an N. If --ignore-quals is specified, the number subtracted quals MX. Otherwise, the number subtracted is MN + floor( (MX-MN)(MIN(Q, 40.0)/40.0) ) where Q is the Phred quality value" />
@@ -214,24 +231,24 @@
             </param>
             <when value="defaults" />
             <when value="advanced">
-                <param name="canonical_penalty" type="integer" value="0" label="Penalty for canonical splice sites" />
-                <param name="noncanonical_penalty" type="integer" value="3" label="Penalty for non-canonical splice sites" />
-                <param name="function_type" type="select" display="radio" label="Penalty for long introns with canonical splice sites">
-                    <option value="C">Constant</option>
-                    <option value="L">Linear [f(x) = y + z * x]</option>
-                    <option value="S">Square root [f(x) = y + z * x&#178;]</option>
-                    <option value="G">Natural logarithm [f(x) = y + z * log(x)]</option>
+                <param name="canonical_penalty" argument="--pen-cansplice" type="integer" value="0" label="Penalty for canonical splice sites" />
+                <param name="noncanonical_penalty" argument="--pen-noncansplice" type="integer" value="12" label="Penalty for non-canonical splice sites" />
+                <param name="function_type" argument="--pen-canintronlen" type="select" display="radio" label="Penalty function for long introns with canonical splice sites" help="Alignments with shorter introns are preferred to those with longer ones">
+                    <option value="C">Constant [f(x) = B]</option>
+                    <option value="L">Linear [f(x) = B + A * x]</option>
+                    <option value="S">Square root [f(x) = B + A * x&#178;]</option>
+                    <option value="G" selected="true">Natural logarithm [f(x) = B + A * log(x)]</option>
                 </param>
-                <param name="constant_term" type="integer" value="0" label="Constant term (y)" help="Constant term for long canonical introns" />
-                <param name="coefficient" type="integer" value="0" label="Coefficient (z)" help="Coefficient for long canonical introns" />
-                <param name="nc_function_type" type="select" display="radio" label="Penalty for long introns with noncanonical splice sites">
-                    <option value="C">Constant</option>
-                    <option value="L">Linear [f(x) = y + z * x]</option>
-                    <option value="S">Square root [f(x) = y + z * x&#178;]</option>
-                    <option value="G" selected="True">Natural logarithm [f(x) = y + z * log(x)]</option>
+                <param name="constant_term" type="float" value="-8" label="Constant term (B)" help="Constant term for the above function" />
+                <param name="coefficient" type="float" value="1" label="Coefficient (A)" help="Coefficient for the above function" />
+                <param name="nc_function_type" argument="--pen-noncanintronlen" type="select" display="radio" label="Penalty function for long introns with non-canonical splice sites" help="Alignments with shorter introns are preferred to those with longer ones">
+                    <option value="C">Constant [f(x) = B]</option>
+                    <option value="L">Linear [f(x) = B + A * x]</option>
+                    <option value="S">Square root [f(x) = B + A * x&#178;]</option>
+                    <option value="G" selected="true">Natural logarithm [f(x) = B + A * log(x)]</option>
                 </param>
-                <param name="nc_constant_term" type="integer" value="-8" label="Constant term (y)" help="Constant term for long non-canonical introns" />
-                <param name="nc_coefficient" type="integer" value="1" label="Coefficient (z)" help="Coefficient for long non-canonical introns" />
+                <param name="nc_constant_term" type="float" value="-8" label="Constant term (B)" help="Constant term for the above function" />
+                <param name="nc_coefficient" type="float" value="1" label="Coefficient (A)" help="Coefficient for the above function" />
                 <param name="min_intron" type="integer" value="20" label="Minimum intron length" />
                 <param name="max_intron" type="integer" value="500000" label="Maximum intron length" />
                 <param argument="--rna-strandness" name="rna_strandness" type="select" label="Specify strand-specific information"
diff -r 2ec097c8e843 -r f4fa77189eb0 hisat2_macros.xml
--- a/hisat2_macros.xml	Mon Apr 10 23:28:31 2017 -0400
+++ b/hisat2_macros.xml	Tue Jul 18 14:25:13 2017 -0400
@@ -1,15 +1,5 @@
 <?xml version="1.0"?>
 <macros>
-    <xml name="function" tokens="helptext">
-        <param display="radio" help="@HELPTEXT@" label="Function type" name="function_type" type="select">
-            <option value="C">Constant</option>
-            <option value="L">Linear [f(x) = y + z * x]</option>
-            <option value="S">Square root [f(x) = y + z * x&#178;]</option>
-            <option value="G">Natural logarithm [f(x) = y + z * log(x)]</option>
-        </param>
-        <param help="@HELPTEXT@" label="Constant term (y)" name="constant_term" type="integer" value="0" />
-        <param help="@HELPTEXT@" label="Coefficient (z)" name="coefficient" type="integer" value="0" />
-    </xml>
     <xml name="single_paired_selector">
         <param label="Single end or paired reads?" name="paired_selector" type="select">
             <option value="paired_collection">Collection of paired reads</option>