Mercurial > repos > iuc > abyss
diff abyss-pe.xml @ 2:2b89471cca20 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
| author | iuc |
|---|---|
| date | Sun, 01 Sep 2019 11:57:51 -0400 |
| parents | 0a5c7992b1ac |
| children | f4fb67b97a63 |
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--- 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) > 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) > 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>