| Previous changeset 2:d71e007323d4 (2015-08-04) Next changeset 4:f0606dfd5195 (2016-02-23) |
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Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit 3dadc4bd6bf2f20b34794c767dfc6d541031914c-dirty |
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modified:
mafft.xml |
| b |
| diff -r d71e007323d4 -r a681631ccee6 mafft.xml --- a/mafft.xml Tue Aug 04 04:01:23 2015 -0400 +++ b/mafft.xml Thu Feb 18 12:05:37 2016 -0500 |
| [ |
| b'@@ -1,4 +1,4 @@\n-<tool id="rbc_mafft" name="MAFFT" version="7.221.1">\n+<tool id="rbc_mafft" name="MAFFT" version="7.221.3">\n <description>Multiple alignment program for amino acid or nucleotide sequences</description>\n <requirements>\n <requirement type="package" version="7.221">mafft</requirement>\n@@ -16,35 +16,50 @@\n <![CDATA[\n #if $cond_flavour.flavourType != \'custom\'\n $cond_flavour.flavourType\n+ \n #elif $cond_flavour.flavourType == \'custom\'\n ### full parameter options\n mafft\n+ $cond_flavour.distance_method\n+ --ep $cond_flavour.ep\n+ --retree $cond_flavour.retree\n+ --maxiterate $cond_flavour.iterations\n #end if\n \n ## specify threads to use\n --thread \\${GALAXY_SLOTS:-1}\n \n+ $datatype\n+ --op $op\n $adjustdirection\n \n- #if $outputFormat.value == \'clustalw\'\n- --clustalout\n+ #if $matrix_condition.matrix == "BLOSUM"\n+ --bl ${matrix_condition.BLOSUM}\n+ #elif $matrix_condition.matrix == "PAM"\n+ --jtt ${matrix_condition.PAM}\n #end if\n \n- $inputSequences > \n+ $reorder\n+ $getTree \n+ $outputFormat\n+ $inputSequences > $outputAlignment;\n \n- #if $outputFormat.value == \'fasta\'\n- $outputFasta\n- #elif $outputFormat.value == \'clustalw\'\n- $outputClustalW\n+ #if $getTree == "--treeout"\n+ mv ${inputSequences}.tree $outputTree;\n #end if\n ]]>\n </command>\n <inputs>\n <param name="inputSequences" type="data" format="fasta" label="Sequences to align" help="Amino acid or nucleotide sequences in FASTA format."/>\n+ <param name="datatype" type="select" label="Data type">\n+ <option value="">Auto detection</option>\n+ <option value="--nuc">Nucleic acids</option>\n+ <option value="--amino">Amino acids</option>\n+ </param>\n <conditional name="cond_flavour">\n <param name="flavourType" type="select" label="MAFFT flavour" help="Run mafft with pre-defined input parameters. Specification of these parameters can be found in the help section.">\n+ <option value="mafft --auto">auto</option>\n <option value="mafft-fftns" selected="true">fftns</option>\n- <option value="mafft --auto">auto</option>\n <option value="mafft-fftnsi">fftnsi</option>\n <option value="mafft-nwns">nwns</option>\n <option value="mafft-nwnsi">nwnsi</option>\n@@ -53,7 +68,7 @@\n <option value="mafft-linsi">linsi</option>\n <option value="mafft-qinsi">qinsi</option>\n <option value="mafft-xinsi">xinsi</option>\n- <!-- <option value="custom">Custom Parameters</option> this should trigger tweaking of all parameters -->\n+ <option value="custom">Custom Parameters</option>\n </param>\n <when value="mafft-fftns"/>\n <when value="mafft --auto"/>\n@@ -65,36 +80,73 @@\n <when value="mafft-linsi"/>\n <when value="mafft-qinsi"/>\n <when value="mafft-xinsi"/>\n+ <when value="custom">\n+ <param name="distance_method" type="select" display="radio" label="Distance method" help="Distance method must be chosen regarding your data">\n+ <option value="--6merpair" selected="true">Shared 6mers distance (fastest)</option>\n+ <option value="--globalpair">Global alignment (Needleman-Wunsch)</option>\n+ <option value="--localpair">Local alignment (Smith-Waterman)</option>\n+ <option value="--genafpair">Local, affine gap cost</option>\n+ </param>\n+ <param name="retree" type="integer" value="2" min="1" max="100" label="Guide tree is built'..b'tion value="BLOSUM">BLOSUM</option>\n+ <option value="PAM">PAM</option>\n </param>\n+ <when value=""/>\n+ <when value="BLOSUM">\n+ <param name="BLOSUM" type="select" display="radio" label="Coefficient of the BLOSUM matrix">\n+ <option value="30">30</option>\n+ <option value="45">45</option>\n+ <option value="62" selected="true">62</option>\n+ <option value="80">80</option>\n+ </param>\n+ </when>\n+ <when value="PAM">\n+ <param name="PAM" type="integer" value="80" min="1" max="350" label="Coefficient of the PAM matrix" />\n+ </when>\n+ </conditional>\n+ <param name="reorder" type="boolean" truevalue="--reorder" falsevalue="" checked="False" label="Reorder output?" />\n+ <param name="getTree" type="boolean" truevalue="--treeout" falsevalue="" checked="False" label="Display alignment tree ?" />\n <param name="outputFormat" type="select" label="Output format" help="Either FASTA or ClustalW">\n- <option value="fasta" selected="true">FASTA</option>\n- <option value="clustalw">ClustalW</option>\n+ <option value="" selected="true">FASTA</option>\n+ <option value="--clustalout">ClustalW</option>\n+ <option value="--phylipout">Phylip</option>\n </param>\n </inputs>\n <outputs>\n- <data format="fasta" name="outputFasta" label="${tool.name} on ${on_string}">\n- <filter>outputFormat == \'fasta\'</filter>\n+ <data format="fasta" name="outputAlignment" label="${tool.name} on ${on_string}">\n+ <change_format>\n+ <when input="outputFormat" value="--clustalout" format="clustal"/>\n+ <when input="outputFormat" value="--phylipout" format="phylip"/>\n+ </change_format>\n </data>\n- <data format="clustal" name="outputClustalW" label="${tool.name} on ${on_string}">\n- <filter>outputFormat == \'clustalw\'</filter>\n+ <data name="outputTree" format="txt" label="${tool.name} Guide Tree">\n+ <filter>getTree == True</filter>\n </data>\n </outputs>\n <tests>\n <test>\n <param name="inputSequences" value="sample.fa"/>\n <param name="flavourType" value="mafft-fftns"/>\n- <param name="outputFormat" value="fasta"/>\n- <output name="outputFasta" ftype="fasta" file="mafft_fftns_result.aln"/>\n+ <param name="outputFormat" value=""/>\n+ <output name="outputAlignment" ftype="fasta" file="mafft_fftns_result.aln"/>\n </test>\n <test>\n <param name="inputSequences" value="sample.fa"/>\n <param name="flavourType" value="mafft-nwns"/>\n- <param name="outputFormat" value="clustalw"/>\n- <output name="outputClustalW" ftype="clustal" file="mafft_nwns_result.aln"/>\n+ <param name="outputFormat" value="--clustalout"/>\n+ <output name="outputAlignment" ftype="clustal" file="mafft_nwns_result.aln"/>\n </test>\n </tests>\n <help>\n@@ -158,6 +210,18 @@\n Automatically selects an appropriate strategy from L-INS-i, FFT-NS-i and FFT-NS-2, according to data size. Default: off (always FFT-NS-2)\n --adjustdirection\n Generate reverse complement sequences, as necessary, and align them together with the remaining sequences. In the case of protein alignment, these options are just ignored.\n+--op\n+ Gap opening penalty, default: 1.53\n+--ep\n+ Offset (works like gap extension penalty), default: 0.0\n+--maxiterate\n+ Maximum number of iterative refinement, default: 0\n+--clustalout\n+ Output: clustal format, default: fasta\n+--thread\n+ Number of threads (if unsure, --thread -1)\n+--retree number\n+ Guide tree is built number times in the progressive stage. Valid with 6mer distance. Default: 2\n ]]>\n </help>\n <citations>\n' |