# HG changeset patch
# User iuc
# Date 1567353471 14400
# Node ID 2b89471cca20c7b90f02179cda8a5e1d78010c44
# Parent  0a5c7992b1ac5c0d2ed36e49f0d3daffa1f9ecf5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"

diff -r 0a5c7992b1ac -r 2b89471cca20 abyss-pe.xml
--- a/abyss-pe.xml	Wed Mar 01 15:17:12 2017 -0500
+++ b/abyss-pe.xml	Sun Sep 01 11:57:51 2019 -0400
@@ -1,6 +1,7 @@
-<tool id="abyss-pe" name="ABySS" version="2.0.1.0">
+<tool id="abyss-pe" name="ABySS" version="@TOOL_VERSION@">
     <description>de novo sequence assembler</description>
     <macros>
+        <token name="@TOOL_VERSION@">2.2.1</token>
         <xml name="reads_conditional">
             <conditional name="reads">
                 <param name="reads_selector" type="select" label="Type of paired-end datasets">
@@ -22,7 +23,8 @@
         </xml>
     </macros>
     <requirements>
-        <requirement type="package" version="2.0.1">abyss</requirement>
+        <requirement type="package" version="@TOOL_VERSION@">abyss</requirement>
+        <requirement type="package" version="0.7.17">bwa</requirement>
     </requirements>
     <stdio>
         <!-- Anything other than zero is an error -->
@@ -33,144 +35,144 @@
     </stdio>
     <version_command>ABYSS --version | head -n 1</version_command>
     <command>
-        abyss-pe
-            name=abyss
-            j=\${GALAXY_SLOTS:-1}
-            k=$k
+abyss-pe
+name=abyss
+j=\${GALAXY_SLOTS:-1}
+k=$k
 
-            #if str($K)
-              K=$K
-            #end if
-            #if str($q)
-              q=$q
-            #end if
-            #if str($Q)
-              Q=$Q
-            #end if
-            #if str($e)
-              e=$e
-            #end if
-            #if str($E)
-              E=$E
-            #end if
-            #if str($t)
-              t=$t
-            #end if
-            #if str($c)
-              c=$c
-            #end if
-            #if str($b)
-              b=$b
-            #end if
-            #if $SS
-              SS=--SS
-            #end if
-            #if str($m)
-              m=$m
-            #end if
-            #if str($p)
-              p=$p
-            #end if
-            #if str($a)
-              a=$a
-            #end if
-            #if str($l)
-              l=$l
-            #end if
-            #if str($s)
-              s=$s
-            #end if
-            #if str($n)
-              n=$n
-            #end if
-            #if str($d)
-              d=$d
-            #end if
-            #if str($S)
-              S=$S
-            #end if
-            #if str($N)
-              N=$N
-            #end if
-            #if $lib_repeat
-              lib='
-              #for $i in range(len($lib_repeat))
-                lib$i
-              #end for
-              '
-              #for $i, $v in enumerate($lib_repeat)
-                #if $v.reads.reads_selector == 'paired'
-                  lib${i}='${v.reads.reads1} ${v.reads.reads2}'
-                #elif $v.reads.reads_selector == 'paired_collection'
-                  lib${i}='${v.reads.reads_coll.forward} ${v.reads.reads_coll.reverse}'
-                #else
-                  lib${i}='${v.reads.reads_il}'
-                #end if
-              #end for
-            #end if
-            #if str($se_reads) != 'None'
-              se='
-              #for $v in $se_reads
-                $v
-              #end for
-              '
-            #end if
-            #if $mp_repeat
-              mp='
-              #for $i in range(len($mp_repeat))
-                mp$i
-              #end for
-              '
-              #for $i, $v in enumerate($mp_repeat)
-                #if $v.reads.reads_selector == 'paired'
-                  mp${i}='${v.reads.reads1} ${v.reads.reads2}'
-                #elif $v.reads.reads_selector == 'paired_collection'
-                  mp${i}='${v.reads.reads_coll.forward} ${v.reads.reads_coll.reverse}'
-                #else
-                  mp${i}='${v.reads.reads_il}'
-                #end if
-              #end for
-            #end if
-            #if str($long_seqs) != 'None'
-              long='
-              #for $i in range(len($long_seqs))
-                long$i
-              #end for
-              '
-              #for $i, $v in enumerate($long_seqs)
-                long${i}='$v'
-              #end for
-            #end if
+#if str($K)
+    K=$K
+#end if
+#if str($q)
+    q=$q
+#end if
+#if str($Q)
+    Q=$Q
+#end if
+#if str($e)
+    e=$e
+#end if
+#if str($E)
+    E=$E
+#end if
+#if str($t)
+    t=$t
+#end if
+#if str($c)
+    c=$c
+#end if
+#if str($b)
+    b=$b
+#end if
+#if $SS
+    SS=--SS
+#end if
+#if str($m)
+    m=$m
+#end if
+#if str($p)
+    p=$p
+#end if
+#if str($a)
+    a=$a
+#end if
+#if str($l)
+    l=$l
+#end if
+#if str($s)
+    s=$s
+#end if
+#if str($n)
+    n=$n
+#end if
+#if str($d)
+    d=$d
+#end if
+#if str($S)
+    S=$S
+#end if
+#if str($N)
+    N=$N
+#end if
+#if $lib_repeat
+    lib='
+    #for $i in range(len($lib_repeat))
+        lib$i
+    #end for
+    '
+    #for $i, $v in enumerate($lib_repeat)
+        #if $v.reads.reads_selector == 'paired'
+            lib${i}='${v.reads.reads1} ${v.reads.reads2}'
+        #elif $v.reads.reads_selector == 'paired_collection'
+            lib${i}='${v.reads.reads_coll.forward} ${v.reads.reads_coll.reverse}'
+        #else
+            lib${i}='${v.reads.reads_il}'
+        #end if
+    #end for
+#end if
+#if str($se_reads) != 'None'
+    se='
+    #for $v in $se_reads
+        $v
+    #end for
+    '
+#end if
+#if $mp_repeat
+    mp='
+    #for $i in range(len($mp_repeat))
+        mp$i
+    #end for
+    '
+    #for $i, $v in enumerate($mp_repeat)
+        #if $v.reads.reads_selector == 'paired'
+            mp${i}='${v.reads.reads1} ${v.reads.reads2}'
+        #elif $v.reads.reads_selector == 'paired_collection'
+            mp${i}='${v.reads.reads_coll.forward} ${v.reads.reads_coll.reverse}'
+        #else
+            mp${i}='${v.reads.reads_il}'
+        #end if
+    #end for
+#end if
+#if str($long_seqs) != 'None'
+    long='
+    #for $i in range(len($long_seqs))
+        long$i
+    #end for
+    '
+    #for $i, $v in enumerate($long_seqs)
+        long${i}='$v'
+    #end for
+#end if
     </command>
 
     <inputs>
         <repeat name="lib_repeat" title="Paired-end library" help="(lib)">
             <expand macro="reads_conditional" />
         </repeat>
-        <param name="se_reads" type="data" multiple="true" optional="true" format="fasta,fastq,fastqsanger,fastqillumina" label="Single-end reads" help="(se)" />
+        <param name="se_reads" argument="se" type="data" multiple="true" optional="true" format="fasta,fastq,fastqsanger,fastqillumina" label="Single-end reads" />
         <repeat name="mp_repeat" title="Mate-pair library" help="The mate-pair libraries are used only for scaffolding and do not contribute towards the consensus sequence (mp)">
             <expand macro="reads_conditional" />
         </repeat>
-        <param name="long_seqs" type="data" multiple="true" optional="true" format="fasta,fastq,fastqsanger,fastqillumina" label="Long sequences" help="Long sequence libraries are used only for rescaffolding and do not contribute towards the consensus sequence (long)" />
-        <param name="k" type="integer" value="41" label="K-mer length (in bp)" help="The length of a k-mer (when -K is not set) or the span of a k-mer pair (when K is set) (k)" />
-        <param name="K" type="integer" value="" optional="true" label="The length (in bp) of a single k-mer in a k-mer pair" help="Optional (K)" />
-        <param name="q" type="integer" value="3" max="40" optional="true" label="Minimum base quality when trimming" help="Trim bases from the ends of reads whose quality is less than this value (q)" />
-        <param name="Q" type="integer" value="0" max="40" optional="true" label="Minimum base quality" help="Mask all bases of reads whose quality is less than this value as 'N' (Q)" />
-        <param name="e" type="integer" value="" min="0" optional="true" label="Minimum erosion k-mer coverage" help="Erode bases at the ends of blunt contigs with coverage less than this value. Defaults to round(sqrt(median)) (e)" />
-        <param name="E" type="integer" value="" min="0" optional="true" label="Minimum erosion k-mer coverage per strand" help="Erode bases at the ends of blunt contigs with coverage less than this value on either strand. Defaults to 1 if sqrt(median) &gt; 2 else 0 (E)" />
-        <param name="t" type="integer" value="" optional="true" label="Maximum length of blunt contigs to trim" help="Defaults to the value of k (t)" />
-        <param name="c" type="float" value="" optional="true" label="Minimum mean k-mer coverage of a unitig" help="Defaults to sqrt(median) (c)" />
-        <param name="b" type="integer" value="" optional="true" label="Maximum length of a bubble (in bp)" help="abyss-pe has two bubble popping stages. The default limits are 3*k bp for ABYSS and 10000 bp for PopBubbles (b)" />
-        <param name="SS" type="boolean" label="Assemble in strand-specific mode" help="Requires that all libraries are strand-specific RNA-Seq libraries. Assumes that the first read in a read pair is reveresed with respect to the transcripts sequenced (SS)" />
-        <param name="m" type="integer" value="50" min="0" optional="true" label="Minimum overlap of two unitigs (in bp)" help="(m)" />
-        <param name="p" type="float" value="0.9" optional="true" label="Minimum sequence identity of a bubble" help="(p)" />
-        <param name="a" type="integer" value="2" min="0" optional="true" label="Maximum number of branches of a bubble" help="(a)" />
-        <param name="l" type="integer" value="" min="1"  optional="true" label="Minimum alignment length of a read (in bp)" help="Defaults to the value of k (l)" />
-        <param name="s" type="integer" value="200" min="0" optional="true" label="Minimum unitig length required for building contigs (in bp)" help="The seed length should be at least twice the value of k. If more sequence is assembled than the expected genome size, try increasing this value (s)" />
-        <param name="n" type="integer" value="10" min="0" optional="true" label="Minimum number of pairs required for building contigs" help="(n)" />
-        <param name="d" type="integer" value="6" min="0" optional="true" label="Allowable error of a distance estimate (in bp)" help="(d)" />
-        <param name="S" type="integer" value="" min="0" optional="true" label="Minimum contig length required for building scaffolds (in bp)" help="Defaults to the value of s (S)" />
-        <param name="N" type="integer" value="" min="0" optional="true" label="Minimum number of pairs required for building scaffolds" help="Defaults to the value of n (N)" />
+        <param name="long_seqs" argument="long" type="data" multiple="true" optional="true" format="fasta,fastq,fastqsanger,fastqillumina" label="Long sequences" help="Long sequence libraries are used only for rescaffolding and do not contribute towards the consensus sequence" />
+        <param argument="k" type="integer" value="41" label="K-mer length (in bp)" help="The length of a k-mer (when -K is not set) or the span of a k-mer pair (when K is set)" />
+        <param argument="K" type="integer" value="" optional="true" label="The length (in bp) of a single k-mer in a k-mer pair" help="Optional" />
+        <param argument="q" type="integer" value="3" max="40" optional="true" label="Minimum base quality when trimming" help="Trim bases from the ends of reads whose quality is less than this value" />
+        <param argument="Q" type="integer" value="0" max="40" optional="true" label="Minimum base quality" help="Mask all bases of reads whose quality is less than this value as 'N'" />
+        <param argument="e" type="integer" value="" min="0" optional="true" label="Minimum erosion k-mer coverage" help="Erode bases at the ends of blunt contigs with coverage less than this value. Defaults to round(sqrt(median))" />
+        <param argument="E" type="integer" value="" min="0" optional="true" label="Minimum erosion k-mer coverage per strand" help="Erode bases at the ends of blunt contigs with coverage less than this value on either strand. Defaults to 1 if sqrt(median) &gt; 2 else 0" />
+        <param argument="t" type="integer" value="" optional="true" label="Maximum length of blunt contigs to trim" help="Defaults to the value of k" />
+        <param argument="c" type="float" value="" optional="true" label="Minimum mean k-mer coverage of a unitig" help="Defaults to sqrt(median)" />
+        <param argument="b" type="integer" value="" optional="true" label="Maximum length of a bubble (in bp)" help="abyss-pe has two bubble popping stages. The default limits are 3*k bp for ABYSS and 10000 bp for PopBubbles" />
+        <param argument="SS" type="boolean" label="Assemble in strand-specific mode" help="Requires that all libraries are strand-specific RNA-Seq libraries. Assumes that the first read in a read pair is reveresed with respect to the transcripts sequenced" />
+        <param argument="m" type="integer" value="50" min="0" optional="true" label="Minimum overlap of two unitigs (in bp)" />
+        <param argument="p" type="float" value="0.9" optional="true" label="Minimum sequence identity of a bubble" />
+        <param argument="a" type="integer" value="2" min="0" optional="true" label="Maximum number of branches of a bubble" />
+        <param argument="l" type="integer" value="" min="1"  optional="true" label="Minimum alignment length of a read (in bp)" help="Defaults to the value of k" />
+        <param argument="s" type="integer" value="200" min="0" optional="true" label="Minimum unitig length required for building contigs (in bp)" help="The seed length should be at least twice the value of k. If more sequence is assembled than the expected genome size, try increasing this value" />
+        <param argument="n" type="integer" value="10" min="0" optional="true" label="Minimum number of pairs required for building contigs" />
+        <param argument="d" type="integer" value="6" min="0" optional="true" label="Allowable error of a distance estimate (in bp)" />
+        <param argument="S" type="integer" value="" min="0" optional="true" label="Minimum contig length required for building scaffolds (in bp)" help="Defaults to the value of s" />
+        <param argument="N" type="integer" value="" min="0" optional="true" label="Minimum number of pairs required for building scaffolds" help="Defaults to the value of n" />
     </inputs>
 
     <outputs>
diff -r 0a5c7992b1ac -r 2b89471cca20 test-data/abyss-stats1.tab
--- a/test-data/abyss-stats1.tab	Wed Mar 01 15:17:12 2017 -0500
+++ b/test-data/abyss-stats1.tab	Sun Sep 01 11:57:51 2019 -0400
@@ -1,4 +1,4 @@
-n	n:500	L50	min	N80	N50	N20	E-size	max	sum	name
+n	n:500	L50	min	N75	N50	N25	E-size	max	sum	name
 1	1	1	556	556	556	556	556	556	556	abyss-unitigs.fa
 1	1	1	556	556	556	556	556	556	556	abyss-contigs.fa
 1	1	1	556	556	556	556	556	556	556	abyss-scaffolds.fa
diff -r 0a5c7992b1ac -r 2b89471cca20 test-data/abyss-stats2.tab
--- a/test-data/abyss-stats2.tab	Wed Mar 01 15:17:12 2017 -0500
+++ b/test-data/abyss-stats2.tab	Sun Sep 01 11:57:51 2019 -0400
@@ -1,2 +1,2 @@
-n	n:500	L50	min	N80	N50	N20	E-size	max	sum	name
+n	n:500	L50	min	N75	N50	N25	E-size	max	sum	name
 1	1	1	556	556	556	556	556	556	556	abyss-unitigs.fa
diff -r 0a5c7992b1ac -r 2b89471cca20 test-data/abyss-stats3.tab
--- a/test-data/abyss-stats3.tab	Wed Mar 01 15:17:12 2017 -0500
+++ b/test-data/abyss-stats3.tab	Sun Sep 01 11:57:51 2019 -0400
@@ -1,3 +1,3 @@
-n	n:500	L50	min	N80	N50	N20	E-size	max	sum	name
+n	n:500	L50	min	N75	N50	N25	E-size	max	sum	name
 1	1	1	556	556	556	556	556	556	556	abyss-unitigs.fa
 1	1	1	556	556	556	556	556	556	556	abyss-long-scaffs.fa