| Previous changeset 0:f048033da666 (2015-06-19) Next changeset 2:2b89471cca20 (2019-09-01) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty |
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modified:
abyss-pe.xml |
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added:
test-data/abyss-long-scaffolds3.fa test-data/abyss-stats3.tab test-data/abyss-unitigs3.fa test-data/coverage3.hist |
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removed:
tool_dependencies.xml |
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| diff -r f048033da666 -r 0a5c7992b1ac abyss-pe.xml --- a/abyss-pe.xml Fri Jun 19 09:26:16 2015 -0400 +++ b/abyss-pe.xml Wed Mar 01 15:17:12 2017 -0500 |
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| @@ -1,4 +1,4 @@ -<tool id="abyss-pe" name="ABySS" version="1.9.0.0"> +<tool id="abyss-pe" name="ABySS" version="2.0.1.0"> <description>de novo sequence assembler</description> <macros> <xml name="reads_conditional"> @@ -22,7 +22,7 @@ </xml> </macros> <requirements> - <requirement type="package" version="1.9.0">abyss</requirement> + <requirement type="package" version="2.0.1">abyss</requirement> </requirements> <stdio> <!-- Anything other than zero is an error --> @@ -33,107 +33,114 @@ </stdio> <version_command>ABYSS --version | head -n 1</version_command> <command> -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 $v in $long_seqs - $v - #end for - ' -#end if + abyss-pe + name=abyss + j=\${GALAXY_SLOTS:-1} + k=$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 </command> <inputs> @@ -174,6 +181,9 @@ <data name="scaffolds" format="fasta" label="${tool.name} on ${on_string}: scaffolds" from_work_dir="abyss-scaffolds.fa"> <filter>lib_repeat or mp_repeat</filter> </data> + <data name="long_scaffolds" format="fasta" label="${tool.name} on ${on_string}: scaffolds" from_work_dir="abyss-long-scaffs.fa"> + <filter>long_seqs</filter> + </data> <data name="bubbles" format="fasta" label="${tool.name} on ${on_string}: bubbles" from_work_dir="abyss-bubbles.fa" /> <data name="indels" format="fasta" label="${tool.name} on ${on_string}: indels" from_work_dir="abyss-indel.fa" /> <data name="coverage_histogram_outfile" format="tabular" label="${tool.name} on ${on_string}: coverage histogram" from_work_dir="coverage.hist" /> @@ -207,6 +217,17 @@ <output name="coverage_histogram_outfile" file="coverage2.hist" /> <output name="stats" file="abyss-stats2.tab" /> </test> + <test> + <param name="se_reads" ftype="fastqsanger" value="assembly_sample-R1.fastq,assembly_sample-R2.fastq" /> + <param name="long_seqs" ftype="fastqsanger" value="assembly_sample-R2.fastq" /> + <param name="k" value="50" /> + <output name="unitigs" file="abyss-unitigs3.fa" /> + <output name="long_scaffolds" file="abyss-long-scaffolds3.fa" /> + <output name="bubbles" file="empty_file.fasta" /> + <output name="indels" file="empty_file.fasta" /> + <output name="coverage_histogram_outfile" file="coverage3.hist" /> + <output name="stats" file="abyss-stats3.tab" /> + </test> </tests> <help> **What it does** @@ -229,10 +250,10 @@ **License and citation** -This Galaxy tool is Copyright © 2015 `The Genome Analysis Centre (TGAC)`_ and is released under the `MIT license`_. +This Galaxy tool is Copyright © 2015-2016 `Earlham Institute`_ and is released under the `MIT license`_. -.. _The Genome Analysis Centre (TGAC): http://www.tgac.ac.uk/ -.. _MIT license: http://opensource.org/licenses/MIT +.. _Earlham Institute: http://www.earlham.ac.uk/ +.. _MIT license: https://opensource.org/licenses/MIT You can use this tool only if you agree to the license terms of: `ABySS`_. |
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| diff -r f048033da666 -r 0a5c7992b1ac test-data/abyss-long-scaffolds3.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/abyss-long-scaffolds3.fa Wed Mar 01 15:17:12 2017 -0500 |
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| @@ -0,0 +1,2 @@ +>0 556 6128 +GAGTCGTCGGTATATCTGAATGGAGATACGACAATCAGCGGAGAATTCCCTCTGGGGTTTGCCGGGGTTATTCGGGTACAGGATAAAGCTTTGCTGGAAATTGGCAGTGGCGCTACGCTAACAATGCAGGATATTGACAGTTTTGAACATCATGGGACAAGAACCCTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCCTCTGCAAGGTTCTTTGCTGCCGTTAACCCGTCTGGTTTGGGCATGATACTGATGTAGTCACGCTTTATCGTTTTCACGAAGCTCTCTGCTATTCCGTTACTCTCCGGACTCCGCACCGCCGTGTTCTTCGGTTCAAGTCCCAACATCCGGGCGAACTGGCGTGTTTCATTAGCCCGGTAGCATGAACCATTATCCGTCAGCCACTCCACTGGAGACGACGGAAGATCGTTGCCGAAGCGGCGTTCCACCGCTCCCAGC |
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| diff -r f048033da666 -r 0a5c7992b1ac test-data/abyss-stats3.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/abyss-stats3.tab Wed Mar 01 15:17:12 2017 -0500 |
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| @@ -0,0 +1,3 @@ +n n:500 L50 min N80 N50 N20 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 |
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| diff -r f048033da666 -r 0a5c7992b1ac test-data/abyss-unitigs3.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/abyss-unitigs3.fa Wed Mar 01 15:17:12 2017 -0500 |
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| @@ -0,0 +1,2 @@ +>0 556 6128 +GAGTCGTCGGTATATCTGAATGGAGATACGACAATCAGCGGAGAATTCCCTCTGGGGTTTGCCGGGGTTATTCGGGTACAGGATAAAGCTTTGCTGGAAATTGGCAGTGGCGCTACGCTAACAATGCAGGATATTGACAGTTTTGAACATCATGGGACAAGAACCCTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCCTCTGCAAGGTTCTTTGCTGCCGTTAACCCGTCTGGTTTGGGCATGATACTGATGTAGTCACGCTTTATCGTTTTCACGAAGCTCTCTGCTATTCCGTTACTCTCCGGACTCCGCACCGCCGTGTTCTTCGGTTCAAGTCCCAACATCCGGGCGAACTGGCGTGTTTCATTAGCCCGGTAGCATGAACCATTATCCGTCAGCCACTCCACTGGAGACGACGGAAGATCGTTGCCGAAGCGGCGTTCCACCGCTCCCAGC |
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| diff -r f048033da666 -r 0a5c7992b1ac test-data/coverage3.hist --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/coverage3.hist Wed Mar 01 15:17:12 2017 -0500 |
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| @@ -0,0 +1,27 @@ +1 4 +2 8 +3 6 +4 13 +5 20 +6 36 +7 70 +8 56 +9 60 +10 66 +11 56 +12 32 +13 27 +14 44 +15 24 +16 25 +17 39 +18 28 +19 23 +20 11 +21 12 +22 5 +23 5 +24 2 +25 2 +26 2 +27 16 |
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| diff -r f048033da666 -r 0a5c7992b1ac tool_dependencies.xml --- a/tool_dependencies.xml Fri Jun 19 09:26:16 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,6 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="abyss" version="1.9.0"> - <repository changeset_revision="ded58f1da91c" name="package_abyss_1_9_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency> |