| Previous changeset 1:0a5c7992b1ac (2017-03-01) Next changeset 3:f4fb67b97a63 (2019-11-28) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852" |
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modified:
abyss-pe.xml test-data/abyss-stats1.tab test-data/abyss-stats2.tab test-data/abyss-stats3.tab |
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| 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 |
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| b'@@ -1,6 +1,7 @@\n-<tool id="abyss-pe" name="ABySS" version="2.0.1.0">\n+<tool id="abyss-pe" name="ABySS" version="@TOOL_VERSION@">\n <description>de novo sequence assembler</description>\n <macros>\n+ <token name="@TOOL_VERSION@">2.2.1</token>\n <xml name="reads_conditional">\n <conditional name="reads">\n <param name="reads_selector" type="select" label="Type of paired-end datasets">\n@@ -22,7 +23,8 @@\n </xml>\n </macros>\n <requirements>\n- <requirement type="package" version="2.0.1">abyss</requirement>\n+ <requirement type="package" version="@TOOL_VERSION@">abyss</requirement>\n+ <requirement type="package" version="0.7.17">bwa</requirement>\n </requirements>\n <stdio>\n <!-- Anything other than zero is an error -->\n@@ -33,144 +35,144 @@\n </stdio>\n <version_command>ABYSS --version | head -n 1</version_command>\n <command>\n- abyss-pe\n- name=abyss\n- j=\\${GALAXY_SLOTS:-1}\n- k=$k\n+abyss-pe\n+name=abyss\n+j=\\${GALAXY_SLOTS:-1}\n+k=$k\n \n- #if str($K)\n- K=$K\n- #end if\n- #if str($q)\n- q=$q\n- #end if\n- #if str($Q)\n- Q=$Q\n- #end if\n- #if str($e)\n- e=$e\n- #end if\n- #if str($E)\n- E=$E\n- #end if\n- #if str($t)\n- t=$t\n- #end if\n- #if str($c)\n- c=$c\n- #end if\n- #if str($b)\n- b=$b\n- #end if\n- #if $SS\n- SS=--SS\n- #end if\n- #if str($m)\n- m=$m\n- #end if\n- #if str($p)\n- p=$p\n- #end if\n- #if str($a)\n- a=$a\n- #end if\n- #if str($l)\n- l=$l\n- #end if\n- #if str($s)\n- s=$s\n- #end if\n- #if str($n)\n- n=$n\n- #end if\n- #if str($d)\n- d=$d\n- #end if\n- #if str($S)\n- S=$S\n- #end if\n- #if str($N)\n- N=$N\n- #end if\n- #if $lib_repeat\n- lib=\'\n- #for $i in range(len($lib_repeat))\n- lib$i\n- #end for\n- \'\n- #for $i, $v in enumerate($lib_repeat)\n- #if $v.reads.reads_selector == \'paired\'\n- lib${i}=\'${v.reads.reads1} ${v.reads.reads2}\'\n- #elif $v.reads.reads_selector == \'paired_collection\'\n- lib${i}=\'${v.reads.reads_coll.forward} ${v.reads.reads_coll.reverse}\'\n- #else\n- lib${i}=\'${v.reads.reads_il}\'\n- #end if\n- #end for\n- #end if\n- #if str($se_reads) != \'None\'\n- se=\'\n- #for $v in $se_reads\n- $v\n- #end for\n- \'\n- #end if\n- #if $mp_repeat\n- mp=\'\n- #for $i in range(len($mp_repeat))\n- mp$i\n- #end for\n- \'\n- #for $i, $v in enumerate($mp_repeat)\n- #if $v.reads.reads_selector == \'paired\'\n- mp${i}=\'${v.reads.reads1} ${v.reads.reads2}\'\n- #elif $v.reads.reads_selector == \'paired_collection\'\n- mp${i}=\'${v.reads.reads_coll.forward} ${v.reads.reads_coll.reverse}\'\n- #else\n- mp${i}=\'${v.reads.reads_il}\'\n- #end if\n- #end for\n- #end if\n- #if str($long_seqs) != \'None\'\n- long=\'\n- #for $i in range(len($long_seqs))\n- long$i\n- #end for\n- \'\n- #for $i, $v in enumerate($long_seqs)\n- long${i}=\'$v\'\n- '..b' <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)" />\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" />\n+ <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)" />\n+ <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" />\n+ <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" />\n+ <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\'" />\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))" />\n+ <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) > 2 else 0" />\n+ <param argument="t" type="integer" value="" optional="true" label="Maximum length of blunt contigs to trim" help="Defaults to the value of k" />\n+ <param argument="c" type="float" value="" optional="true" label="Minimum mean k-mer coverage of a unitig" help="Defaults to sqrt(median)" />\n+ <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" />\n+ <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" />\n+ <param argument="m" type="integer" value="50" min="0" optional="true" label="Minimum overlap of two unitigs (in bp)" />\n+ <param argument="p" type="float" value="0.9" optional="true" label="Minimum sequence identity of a bubble" />\n+ <param argument="a" type="integer" value="2" min="0" optional="true" label="Maximum number of branches of a bubble" />\n+ <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" />\n+ <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" />\n+ <param argument="n" type="integer" value="10" min="0" optional="true" label="Minimum number of pairs required for building contigs" />\n+ <param argument="d" type="integer" value="6" min="0" optional="true" label="Allowable error of a distance estimate (in bp)" />\n+ <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" />\n+ <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" />\n </inputs>\n \n <outputs>\n' |
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| 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 |
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| @@ -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 |
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| 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 |
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| @@ -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 |
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| 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 |
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| @@ -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 |