Mercurial > repos > nml > spades
changeset 4:35cb17bd8bf9 draft
planemo upload commit ba4e93c036a072d6aac883bc1aba55e26256498c
| author | nml |
|---|---|
| date | Mon, 08 Aug 2016 15:56:56 -0400 |
| parents | 6dff6ed33cd7 |
| children | 909c315b656d |
| files | CHANGE output_dir/input_dataset.yaml spades.xml tool_dependencies.xml |
| diffstat | 4 files changed, 11 insertions(+), 11 deletions(-) [+] |
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--- a/CHANGE Wed Jul 06 16:01:02 2016 -0400 +++ b/CHANGE Mon Aug 08 15:56:56 2016 -0400 @@ -1,6 +1,10 @@ +1.4 +=== + - Supports SPAdes 3.9 + - CHANGE : Several minor bugs. 1.3 === - - Supports SPades 3.8 + - Supports SPAdes 3.8 - CHANGE: Improved running time and RAM consumption. 1.2
--- a/output_dir/input_dataset.yaml Wed Jul 06 16:01:02 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -- left reads: [/tmp/tmpwz6C_M/files/000/dataset_15.dat] - orientation: fr - right reads: [/tmp/tmpwz6C_M/files/000/dataset_16.dat] - type: paired-end
--- a/spades.xml Wed Jul 06 16:01:02 2016 -0400 +++ b/spades.xml Mon Aug 08 15:56:56 2016 -0400 @@ -1,7 +1,7 @@ -<tool id="spades" name="spades" version="1.3.2"> +<tool id="spades" name="spades" version="1.4"> <description>SPAdes genome assembler for regular and single-cell projects</description> <requirements> - <requirement type="package" version="3.8.0">spades</requirement> + <requirement type="package" version="3.9.0">spades</requirement> </requirements> <command interpreter="perl">spades.pl $out_contigs @@ -25,7 +25,7 @@ $careful -t \${GALAXY_SLOTS:-16} - #if str($kmer_choice.auto_kmer_choice) == 'False': + #if not $kmer_choice.auto_kmer_choice: -k "$kmer_choice.kmers" #else @@ -249,7 +249,7 @@ SPAdes – St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. See http://bioinf.spbau.ru/en/spades for more details on SPAdes. -This wrapper runs SPAdes 3.8, collects the output, and throws away all the temporary files. It also produces a tab file with contig names, length and coverage. +This wrapper runs SPAdes 3.9, collects the output, and throws away all the temporary files. It also produces a tab file with contig names, length and coverage. **License**
--- a/tool_dependencies.xml Wed Jul 06 16:01:02 2016 -0400 +++ b/tool_dependencies.xml Mon Aug 08 15:56:56 2016 -0400 @@ -1,6 +1,6 @@ <?xml version="1.0"?> <tool_dependency> - <package name="spades" version="3.8.0"> - <repository changeset_revision="c9eab59c0bc2" name="package_spades_3_8_0" owner="nml" toolshed="https://toolshed.g2.bx.psu.edu" /> + <package name="spades" version="3.9.0"> + <repository changeset_revision="d8c8c3dc8f9a" name="package_spades_3_9_0" owner="nml" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> </tool_dependency>