# HG changeset patch
# User iuc
# Date 1444508672 14400
# Node ID 95b0695038c7aa765fc86d8f2fe8f7261571431a
# Parent  b01b13024dd12041d83e0c493afc2e39739e279a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 4a5952b2404c0821cf9895cb2a5036da62b14d6e-dirty

diff -r b01b13024dd1 -r 95b0695038c7 hisat2.xml
--- a/hisat2.xml	Sat Oct 10 14:51:00 2015 -0400
+++ b/hisat2.xml	Sat Oct 10 16:24:32 2015 -0400
@@ -113,7 +113,7 @@
                 <param format="fasta" label="Select the reference genome" metadata_name="dbkey" name="history_item" type="data" />
             </when>
         </conditional>
-        <param argument="-k" default="5" 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." label="Primary alignments" name="max_primary" optional="True" type="integer" value="5" />
+        <param argument="-k" name="max_primary" optional="True" type="integer" value="5" 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." label="Primary alignments" />
         <conditional name="alignment_options">
             <param label="Alignment options" name="alignment_options_selector" type="select">
                 <option value="defaults">Use default values</option>
@@ -134,10 +134,10 @@
             </param>
             <when value="defaults" />
             <when value="advanced">
-                <param argument="-s" default="0" min="0" label="Skip the first N reads or pairs in the input" name="skip" type="integer" value="0" />
-                <param argument="-u" default="0" min="0" help="Align the first N reads or read pairs from the input (after the first N reads or pairs have been skipped), then stop." label="Stop after aligning N reads" name="stop_after" type="integer" value="0" />
-                <param argument="-5" default="0" min="0" help="Trim N bases from 5' (left) end of each read before alignment" label="Trim 5' end" name="trim_five" type="integer" value="0" />
-                <param argument="-3" default="0" min="0" help="Trim N bases from 3' (right) end of each read before alignment" label="Trim 3' end" name="trim_three" type="integer" value="0" />
+                <param argument="-s" min="0" label="Skip the first N reads or pairs in the input" name="skip" type="integer" value="0" />
+                <param argument="-u" min="0" help="Align the first N reads or read pairs from the input (after the first N reads or pairs have been skipped), then stop." label="Stop after aligning N reads" name="stop_after" type="integer" value="0" />
+                <param argument="-5" min="0" help="Trim N bases from 5' (left) end of each read before alignment" label="Trim 5' end" name="trim_five" type="integer" value="0" />
+                <param argument="-3" min="0" help="Trim N bases from 3' (right) end of each read before alignment" label="Trim 3' end" name="trim_three" type="integer" value="0" />
             </when>
         </conditional>
         <conditional name="scoring_options">
@@ -148,16 +148,16 @@
             <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 argument="--ma" default="2" 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" label="Set match bonus" name="match_bonus" type="integer" value="2" />
-                <param argument="--mp" default="6" 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." label="Maximum mismatch penalty" name="max_mismatch" type="integer" value="6" />
-                <param argument="--mp" default="2" 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." label="Minimum mismatch penalty" name="min_mismatch" type="integer" value="2" />
-                <param argument="--np" default="1" help="Sets penalty for positions where the read, reference, or both, contain an ambiguous character such as N" label="Ambiguous read penalty" name="ambiguous_penalty" type="integer" value="1" />
-                <param argument="--sp" default="2" help="Sets the maximum (MX) penalty for soft-clipping per base. A number less than or equal to MX and greater than or equal to MN is subtracted from the alignment score for each position. The number subtracted is MN + floor( (MX-MN)(MIN(Q, 40.0)/40.0) ) where Q is the Phred quality value." label="Maximum soft-clipping penalty" name="soft_clip_penalty_max" type="integer" value="2" />
-                <param argument="--sp" default="1" help="Sets the minimum (MN) penalty for soft-clipping per base. A number less than or equal to MX and greater than or equal to MN is subtracted from the alignment score for each position. The number subtracted is MN + floor( (MX-MN)(MIN(Q, 40.0)/40.0) ) where Q is the Phred quality value." label="Minimum soft-clipping penalty" name="soft_clip_penalty_min" type="integer" value="1" />
-                <param argument="--rdg" default="5" help="A read gap of length N gets a penalty of [open_penalty] + N * [extend_penalty]" label="Read gap open penalty." name="read_open_penalty" type="integer" value="5" />
-                <param argument="--rdg" default="3" help="A read gap of length N gets a penalty of [open_penalty] + N * [extend_penalty]" label="Read gap extend penalty." name="read_extend_penalty" type="integer" value="3" />
-                <param argument="--rfg" default="5" help="A reference gap of length N gets a penalty of [open_penalty] + N * [extend_penalty]" label="Reference gap open penalty." name="ref_open_penalty" type="integer" value="5" />
-                <param argument="--rfg" default="3" help="A reference gap of length N gets a penalty of [open_penalty] + N * [extend_penalty]" label="Reference gap extend penalty." name="ref_extend_penalty" type="integer" value="3" />
+                <param argument="--ma" 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" label="Set match bonus" name="match_bonus" type="integer" value="2" />
+                <param argument="--mp" 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." label="Maximum mismatch penalty" name="max_mismatch" type="integer" value="6" />
+                <param argument="--mp" 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." label="Minimum mismatch penalty" name="min_mismatch" type="integer" value="2" />
+                <param argument="--np" help="Sets penalty for positions where the read, reference, or both, contain an ambiguous character such as N" label="Ambiguous read penalty" name="ambiguous_penalty" type="integer" value="1" />
+                <param argument="--sp" help="Sets the maximum (MX) penalty for soft-clipping per base. A number less than or equal to MX and greater than or equal to MN is subtracted from the alignment score for each position. The number subtracted is MN + floor( (MX-MN)(MIN(Q, 40.0)/40.0) ) where Q is the Phred quality value." label="Maximum soft-clipping penalty" name="soft_clip_penalty_max" type="integer" value="2" />
+                <param argument="--sp" help="Sets the minimum (MN) penalty for soft-clipping per base. A number less than or equal to MX and greater than or equal to MN is subtracted from the alignment score for each position. The number subtracted is MN + floor( (MX-MN)(MIN(Q, 40.0)/40.0) ) where Q is the Phred quality value." label="Minimum soft-clipping penalty" name="soft_clip_penalty_min" type="integer" value="1" />
+                <param argument="--rdg" help="A read gap of length N gets a penalty of [open_penalty] + N * [extend_penalty]" label="Read gap open penalty." name="read_open_penalty" type="integer" value="5" />
+                <param argument="--rdg" help="A read gap of length N gets a penalty of [open_penalty] + N * [extend_penalty]" label="Read gap extend penalty." name="read_extend_penalty" type="integer" value="3" />
+                <param argument="--rfg" help="A reference gap of length N gets a penalty of [open_penalty] + N * [extend_penalty]" label="Reference gap open penalty." name="ref_open_penalty" type="integer" value="5" />
+                <param argument="--rfg" help="A reference gap of length N gets a penalty of [open_penalty] + N * [extend_penalty]" label="Reference gap extend penalty." name="ref_extend_penalty" type="integer" value="3" />
             </when>
         </conditional>
         <conditional name="spliced_options">