Mercurial > repos > mvdbeek > wtdbg2
diff wtdbg2.xml @ 1:fe60b4299555 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/wtdbg2 commit e2f82dabda7848017302214b99404c8466351b08
| author | mvdbeek |
|---|---|
| date | Mon, 26 Nov 2018 09:10:05 -0500 |
| parents | 7bb3cf8b9a5d |
| children | 79430547460a |
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--- a/wtdbg2.xml Mon Nov 26 07:51:32 2018 -0500 +++ b/wtdbg2.xml Mon Nov 26 09:10:05 2018 -0500 @@ -12,7 +12,7 @@ wtdbg2 -t \${GALAXY_SLOTS:-1} -i '$inputs' -fo prefix -#if $preset +#if $preset.select_preset != 'manual' -x '$preset.select_preset' #else -k $preset.kmer_length @@ -40,19 +40,19 @@ <param name="inputs" type="data" format="fasta,fastq,fasta.gz,fastq.gz" help="Select input reads"/> <conditional name="preset"> <param name="select_preset" type="select"> - <option value="rsII/rs">PacBio RSII (-p 21 -S 4 -s 0.05 -L 5000)</option> - <option value="sequel/sq">Pacbio Sequel (-p 0 -k 15 -AS 2 -s 0.05 -L 5000)</option> - <option value="nanopore/ont">Nanopore (-p 19 -AS 2 -s 0.05 -L 5000)</option> - <option value="corrected/ccs">Corrected Reads (-p 0 -k 19 -AS 4 -s 0.5 -L 5000)</option> + <option value="rsII">PacBio RSII (-p 21 -S 4 -s 0.05 -L 5000)</option> + <option value="sequel">Pacbio Sequel (-p 0 -k 15 -AS 2 -s 0.05 -L 5000)</option> + <option value="nanopore">Nanopore (-p 19 -AS 2 -s 0.05 -L 5000)</option> + <option value="corrected">Corrected Reads (-p 0 -k 19 -AS 4 -s 0.5 -L 5000)</option> <option value="manual">Specify Options</option> </param> - <when value="rsII/rs"> + <when value="rsII"> </when> - <when value="sequel/sq"> + <when value="sequel"> </when> - <when value="nanopore/ont"> + <when value="nanopore"> </when> - <when value="corrected/ccs"> + <when value="corrected"> </when> <when value="manual"> <param name="kmer_length" argument="-k" type="integer" value="0" min="0" max="25" label="kmer fsize"/> @@ -80,7 +80,7 @@ <tests> <test> <param name="inputs" value="ecoli-reads.fasta" ftype="fasta"/> - <param name="preset|select_preset" value="rsII/rs"/> + <param name="preset|select_preset" value="rsII"/> <output name="contigs" value="contigs.txt"/> <output name="consensus" value="consensus.fa"/> <output name="polished_consensus" value="polished_consensus.fa"/>