# HG changeset patch
# User iuc
# Date 1606385372 0
# Node ID dba4db64c3acecf58b2a8d38a1ceca4af1b41f89
# Parent  5df3ed4a855993d83aadc08df3219a83db66d754
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 0c0447365a23d4382b04745f22290608b47e5ff5"

diff -r 5df3ed4a8559 -r dba4db64c3ac hisat2.xml
--- a/hisat2.xml	Wed Nov 04 20:02:12 2020 +0000
+++ b/hisat2.xml	Thu Nov 26 10:09:32 2020 +0000
@@ -1,4 +1,4 @@
-<tool id="hisat2" name="HISAT2" version="2.1.0+galaxy5" profile="17.01">
+<tool id="hisat2" name="HISAT2" version="2.1.0+galaxy6" profile="17.01">
     <description>A fast and sensitive alignment program</description>
     <macros>
         <import>hisat2_macros.xml</import>
@@ -280,11 +280,11 @@
     --min-intronlen ${adv.spliced_options.min_intron}
     --max-intronlen ${adv.spliced_options.max_intron}
     ${adv.spliced_options.tma}
-	
+
     #if str($adv.spliced_options.novel_splicesite_outfile) == "true":
        --novel-splicesite-outfile '$novel_splicesite_output'
     #end if
-	
+
     #if str($adv.spliced_options.notmplen):
         ${adv.spliced_options.notmplen}
     #end if
@@ -439,12 +439,7 @@
                 </param>
                 <when value="defaults" />
                 <when value="advanced">
-                    <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>
+                    <expand macro="nc_function" name="function_type" argument="--n-ceil" 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" lselected="true"/>
                     <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" />
@@ -472,12 +467,7 @@
                     <param argument="--rdg" name="read_extend_penalty" type="integer" value="3" min="0" label="Read gap extend penalty" help="A read gap of length N gets a penalty of [open_penalty] + N * [extend_penalty]" />
                     <param argument="--rfg" name="ref_open_penalty" type="integer" value="5" min="0" label="Reference gap open penalty" help="A reference gap of length N gets a penalty of [open_penalty] + N * [extend_penalty]" />
                     <param argument="--rfg" name="ref_extend_penalty" type="integer" value="3" min="0" label="Reference gap extend penalty" help="A reference gap of length N gets a penalty of [open_penalty] + N * [extend_penalty]" />
-                    <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>
+                    <expand macro="nc_function" name="function_type" argument="--score-min" 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" lselected="true"/>
                 </when>
             </conditional>
 
@@ -490,20 +480,10 @@
                 <when value="advanced">
                     <param name="canonical_penalty" argument="--pen-cansplice" type="integer" value="0" min="0" label="Penalty for canonical splice sites" />
                     <param name="noncanonical_penalty" argument="--pen-noncansplice" type="integer" value="12" min="0" 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>
+                    <expand macro="nc_function" name="function_type" argument="--pen-canintronlen" label="Penalty function for long introns with canonical splice sites" help="Alignments with shorter introns are preferred to those with longer ones" gselected="true"/>
                     <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>
+                    <expand macro="nc_function" name="nc_function_type" argument="--pen-noncanintronlen" label="Penalty function for long introns with non-canonical splice sites" help="Alignments with shorter introns are preferred to those with longer ones" gselected="true"/>
                     <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" min="0" label="Minimum intron length" />
@@ -1197,7 +1177,7 @@
 
     --no-templatelen-adjustment
             Disables template length adjustment for RNA-seq reads.
-    
+
     --novel-splicesite-outfile
 			In this mode, HISAT2 reports a list of splice sites in the file :
 				chromosome name <tab> genomic position of the flanking base on the left side of an intron <tab> genomic position of the flanking base on the right <tab> strand (+, -, and .) '.' indicates an unknown strand for non-canonical splice sites.
diff -r 5df3ed4a8559 -r dba4db64c3ac hisat2_macros.xml
--- a/hisat2_macros.xml	Wed Nov 04 20:02:12 2020 +0000
+++ b/hisat2_macros.xml	Thu Nov 26 10:09:32 2020 +0000
@@ -44,5 +44,14 @@
               </when>
         </conditional>
     </xml>
+    
+    <xml name= "nc_function" token_name="NO NAME GIVEN" token_argument="NO ARGUMENT GIVEN" token_label="NO LABEL GIVEN" token_help="" token_cselected="false" token_lselected="false" token_sselected="false" token_gselected="false">
+        <param name="@NAME@" argument="@ARGUMENT@" type="select" display="radio" label="@LABEL@" help="@HELP@">
+            <option value="C" selected="@CSELECTED@">Constant [f(x) = B]</option>
+            <option value="L" selected="@LSELECTED@">Linear [f(x) = B + A * x]</option>
+            <option value="S" selected="@SSELECTED@">Square root [f(x) = B + A * &#8730;x]</option>
+            <option value="G" selected="@GSELECTED@">Natural logarithm [f(x) = B + A * log(x)]</option>
+        </param>
+   </xml>
 
 </macros>