Mercurial > repos > mvdbeek > fermi2
diff fermi2.xml @ 4:a206c60df528 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 47795b03c956d0f239aede8e27d2aa4e3c4c1d27
| author | mvdbeek |
|---|---|
| date | Fri, 30 Dec 2016 12:10:15 -0500 |
| parents | 3ffa0a5cbd8c |
| children | b7f0625940a4 |
line wrap: on
line diff
--- a/fermi2.xml Fri Dec 30 11:56:08 2016 -0500 +++ b/fermi2.xml Fri Dec 30 12:10:15 2016 -0500 @@ -9,13 +9,13 @@ -s$genome_size -t\${GALAXY_SLOTS:-4} -l$readlength - -p prefix <(cat + -p prefix " #for fastq in $input1: '$fastq' #end for - ) - $T - $2 + " + -T $T + $two_pass_error $E > prefix.mak && make -f prefix.mak @@ -25,7 +25,7 @@ <param argument="-l" name="readlength" type="integer" label="primary read length" value="101" min="70"/> <param argument="-s" name="genome_size" type="integer" value="180000" min="1" label="approximate genome size in kilobases" help="Enter approximate genome size in kilobases. For a human genome of 3.2 gigabases enter 3200000"/> <param argument="-T" type="integer" value="61" label="use INT-mer for post-trimming/filtering" min="10"/> - <param argument="-2" type="boolean" checked="false" truevalue="-2" falsevalue="" label="Use 2-pass error correction"/> + <param argument="-2" name="two_pass_error" type="boolean" checked="false" truevalue="-2" falsevalue="" label="Use 2-pass error correction"/> <param argument="-E" type="boolean" checked="false" truevalue="-E" falsevalue="" label="Do not apply error correction"/> </inputs> <outputs> @@ -33,7 +33,7 @@ </outputs> <tests> <test> - <param name="input1" value="test.fastq.gz"/> + <param name="input1" value="test.fastq.gz,test.fastq.gz"/> <param name="readlength" value="150"/> <param name="genome_size" value="1"/> <output name="unitigs" file="unitigs.gz" compare="sim_size"/>