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Committing EMBOSS v5 tools: epestfind, est2genome extractseq freak fuzzpro garnier geecee
This commit is contained in:
Chinmay Rao
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<tool id="EMBOSS_epestfind29" name="epestfind">
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<description>Finds PEST motifs as potential proteolytic cleavage sites</description>
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<command interpreter="perl">emboss_single_outputfile_wrapper.pl epestfind -sequence $input1 -goutfile $ofile2 -outfile $ofile1 -window $window -order $order -potential $potential -poor $poor
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-invalid $invalid -map $map -graph png -auto</command>
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<inputs>
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<param format="data" name="input1" type="data">
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<label>Sequence</label>
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</param>
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<param name="window" size="4" type="text" value="10">
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<label>Minimal distance between positively charged amino acids</label>
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</param>
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<param name="order" type="select">
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<label>Sort by</label>
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<option value="3">Score</option>
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<option value="1">Length</option>
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<option value="2">Position</option>
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</param>
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<param name="threshold" size="4" type="text" value="5.0">
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<label>Threshold value to discriminate weak from potential PEST motifs.</label>
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</param>
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<param name="potential" type="select">
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<label>Decide whether potential PEST motifs should be printed</label>
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<option value="yes">Yes</option>
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<option value="no">No</option>
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</param>
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<param name="poor" type="select">
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<label>Decide whether poor PEST motifs should be printed</label>
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<option value="yes">Yes</option>
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<option value="no">No</option>
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</param>
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<param name="invalid" type="select">
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<label>Decide whether invalid PEST motifs should be printed</label>
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<option value="no">No</option>
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<option value="yes">Yes</option>
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</param>
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<param name="map" type="select">
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<label>Decide whether PEST motifs should be mapped to sequence</label>
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<option value="yes">Yes</option>
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<option value="no">No</option>
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</param>
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</inputs>
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<outputs>
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<data format="png" name="ofile2" />
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<data format="epestfind" name="ofile1" />
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</outputs>
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<!-- <tests>
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<test>
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<param name="input1" value="2.fasta"/>
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<param name="window" value="10"/>
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<param name="order" value="3"/>
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<param name="threshold" value="5.0"/>
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<param name="potential" value="yes"/>
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<param name="poor" value="yes"/>
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<param name="invalid" value="no"/>
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<param name="map" value="yes"/>
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<output name="ofile1" file="emboss_epestfind_out.epestfind"/>
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</test>
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</tests> output file contains file location info -->
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<help>
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You can view the original documentation here_.
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.. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/epestfind.html
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</help>
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</tool>
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<tool id="EMBOSS_est2genome32" name="est2genome">
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<description>Align EST and genomic DNA sequences</description>
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<command>est2genome -estsequence $input1 -genomesequence $input2 -outfile $out_file1 -match $match -mismatch $mismatch -gappenalty $gappenalty -intronpenalty $intronpenalty -splicepenalty
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$splicepenalty -minscore $minscore -reverse $reverse -splice $splice -mode $mode -best $best -shuffle $shuffle -seed $seed -align $align -width $width -auto</command>
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<inputs>
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<param format="fasta" name="input1" type="data">
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<label>EST sequence(s)</label>
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</param>
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<param format="data" name="input2" type="data">
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<label>Genomic sequence</label>
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</param>
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<param name="match" size="4" type="text" value="1">
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<label>Score for matching two bases</label>
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</param>
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<param name="mismatch" size="4" type="text" value="1">
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<label>Cost for mismatching two bases</label>
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</param>
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<param name="gappenalty" size="4" type="text" value="2">
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<label>Cost for deleting a single base in either sequence, excluding introns</label>
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</param>
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<param name="intronpenalty" size="4" type="text" value="40">
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<label>Cost for an intron, independent of length</label>
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</param>
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<param name="splicepenalty" size="4" type="text" value="20">
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<label>Cost for an intron, independent of length and starting/ending on donor-acceptor sites</label>
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</param>
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<param name="minscore" size="4" type="text" value="30">
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<label>Exclude alignments with scores below this threshold score</label>
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</param>
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<param name="reverse" type="select">
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<label>Reverse the orientation of the EST sequence</label>
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<option value="no">No</option>
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<option value="yes">Yes</option>
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</param>
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<param name="splice" type="select">
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<label>Use donor and acceptor splice sites</label>
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<option value="yes">Yes</option>
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<option value="no">No</option>
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</param>
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<param name="mode" type="select">
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<label>Comparison mode</label>
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<option value="both">Both strands</option>
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<option value="forward">Forward strand only</option>
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<option value="reverse">Reverse strand only</option>
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</param>
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<param name="best" type="select">
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<label>Only best comparisons</label>
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<option value="yes">Yes</option>
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<option value="no">No</option>
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</param>
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<param name="shuffle" size="4" type="text" value="0">
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<label>Shuffle</label>
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</param>
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<param name="seed" size="4" type="text" value="20825">
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<label>Random number seed</label>
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</param>
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<param name="align" type="select">
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<label>Show the alignment</label>
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<option value="no">No</option>
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<option value="yes">Yes</option>
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</param>
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<param name="width" size="4" type="text" value="50">
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<label>Alignment width</label>
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</param>
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</inputs>
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<outputs>
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<data format="est2genome" name="out_file1" />
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</outputs>
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<tests>
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<test>
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<param name="input1" value="2.fasta"/>
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<param name="input2" value="1.fasta"/>
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<param name="match" value="1"/>
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<param name="mismatch" value="1"/>
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<param name="match" value="1"/>
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<param name="gappenalty" value="2"/>
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<param name="intronpenalty" value="40"/>
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<param name="splicepenalty" value="20"/>
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<param name="minscore" value="30"/>
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<param name="reverse" value="no"/>
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<param name="splice" value="yes"/>
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<param name="mode" value="both"/>
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<param name="best" value="yes"/>
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<param name="shuffle" value="0"/>
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<param name="seed" value="20825"/>
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<param name="align" value="no"/>
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<param name="width" value="50"/>
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<output name="out_file1" file="emboss_est2genome_out.est2genome"/>
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</test>
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</tests>
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<help>
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.. class:: warningmark
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The input dataset needs to be sequences.
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-----
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You can view the original documentation here_.
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.. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/est2genome.html
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</help>
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</tool>
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@@ -0,0 +1,95 @@
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<tool id="EMBOSS_extractfeat34" name="extractfeat">
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<!-- tool tested with documentation, functional test not designed due to empty files resulting from test input sequences -->
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<description>Extract features from a sequence</description>
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<command>extractfeat -sequence $input1 -outseq $out_file1 -before $before -after $after -source "$source" -type "$type" -sense $sense -minscore $minscore -maxscore $maxscore -tag "$tag" -value
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"$value" -join $join -featinname $featinname -describe "$describe" -osformat2 $out_format1 -auto</command>
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<inputs>
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<param format="data" name="input1" type="data">
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<label>Sequences</label>
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</param>
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<param name="before" size="4" type="text" value="0">
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<label>Number of bases or residues before the feature to include in the extracted sequence</label>
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</param>
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<param name="after" size="4" type="text" value="0">
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<label>Number of bases or residues after the feature to include in the extracted sequence</label>
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</param>
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<param name="source" size="4" type="text" value="*">
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<label>Feature source</label>
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</param>
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<param name="type" size="4" type="text" value="*">
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<label>Feature type</label>
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</param>
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<param name="sense" type="select">
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<label>Feature sense</label>
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<option value="0">Any sense</option>
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<option value="1">Forward sense</option>
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<option value="-1">Reverse sense</option>
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</param>
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<param name="minscore" size="4" type="text" value="0.0">
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<label>Minimum score</label>
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</param>
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<param name="maxscore" size="4" type="text" value="0.0">
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<label>Maximum score</label>
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</param>
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<param name="tag" size="4" type="text" value="*">
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<label>Feature tags</label>
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</param>
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<param name="value" size="4" type="text" value="*">
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<label>Tag values</label>
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</param>
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<param name="join" type="select">
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<label>Join features</label>
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<option value="no">No</option>
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<option value="yes">Yes</option>
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</param>
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<param name="featinname" type="select">
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<label>Put feature type in sequence name</label>
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<option value="no">No</option>
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<option value="yes">Yes</option>
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</param>
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<param name="describe" size="4" type="text" value="">
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<label>Specify one or more tag names that should be added to the output sequence Description text</label>
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</param>
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<param name="out_format1" type="select">
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<label>Output Sequence File Format</label>
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<option value="fasta">FASTA (m)</option>
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<option value="acedb">ACeDB (m)</option>
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<option value="asn1">ASN.1 (m)</option>
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<option value="clustal">Clustal (m)</option>
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<option value="codata">CODATA (m)</option>
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<option value="embl">EMBL (m)</option>
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<option value="fitch">Fitch (m)</option>
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<option value="gcg">Wisconsin Package GCG 9.x and 10.x (s)</option>
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<option value="genbank">GENBANK (m)</option>
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<option value="gff">GFF (m)</option>
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<option value="hennig86">Hennig86 (m)</option>
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<option value="ig">Intelligenetics (m)</option>
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<option value="jackknifer">Jackknifer (m)</option>
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<option value="jackknifernon">Jackknifernon (m)</option>
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<option value="mega">Mega (m)</option>
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<option value="meganon">Meganon (m)</option>
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<option value="msf">Wisconsin Package GCG's MSF (m)</option>
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<option value="pir">NBRF (PIR) (m)</option>
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<option value="ncbi">NCBI style FASTA (m)</option>
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<option value="nexus">Nexus/PAUP (m)</option>
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<option value="nexusnon">Nexusnon/PAUPnon (m)</option>
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<option value="phylip">PHYLIP interleaved (m)</option>
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<option value="phylipnon">PHYLIP non-interleaved (m)</option>
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<option value="selex">SELEX (m)</option>
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<option value="staden">Staden (s)</option>
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<option value="strider">DNA strider (m)</option>
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<option value="swiss">SwisProt entry (m)</option>
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<option value="text">Plain sequence (s)</option>
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<option value="treecon">Treecon (m)</option>
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</param>
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</inputs>
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<outputs>
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<data format="fasta" name="out_file1" />
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</outputs>
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<code file="emboss_format_corrector.py" />
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<help>
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You can view the original documentation here_.
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.. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/extractfeat.html
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</help>
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</tool>
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@@ -0,0 +1,67 @@
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<tool id="EMBOSS_extractseq35" name="extractseq">
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<description>Extract regions from a sequence</description>
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<command>extractseq -sequence $input1 -outseq $out_file1 -regions $regions -separate $separate -osformat2 $out_format1 -auto</command>
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<inputs>
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<param format="data" name="input1" type="data">
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<label>Sequences</label>
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</param>
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<param name="regions" size="20" type="text" value="1-9999999">
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<label>Regions to extract</label>
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</param>
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<param name="separate" type="select">
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<label>Write each specified region as a separate sequence</label>
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<option value="no">No</option>
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<option value="yes">Yes</option>
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</param>
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<param name="out_format1" type="select">
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<label>Output Sequence File Format</label>
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<option value="fasta">FASTA (m)</option>
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<option value="acedb">ACeDB (m)</option>
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<option value="asn1">ASN.1 (m)</option>
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<option value="clustal">Clustal (m)</option>
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<option value="codata">CODATA (m)</option>
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<option value="embl">EMBL (m)</option>
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<option value="fitch">Fitch (m)</option>
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<option value="gcg">Wisconsin Package GCG 9.x and 10.x (s)</option>
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<option value="genbank">GENBANK (m)</option>
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<option value="gff">GFF (m)</option>
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<option value="hennig86">Hennig86 (m)</option>
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<option value="ig">Intelligenetics (m)</option>
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<option value="jackknifer">Jackknifer (m)</option>
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<option value="jackknifernon">Jackknifernon (m)</option>
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<option value="mega">Mega (m)</option>
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<option value="meganon">Meganon (m)</option>
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<option value="msf">Wisconsin Package GCG's MSF (m)</option>
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<option value="pir">NBRF (PIR) (m)</option>
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<option value="ncbi">NCBI style FASTA (m)</option>
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<option value="nexus">Nexus/PAUP (m)</option>
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<option value="nexusnon">Nexusnon/PAUPnon (m)</option>
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<option value="phylip">PHYLIP interleaved (m)</option>
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<option value="phylipnon">PHYLIP non-interleaved (m)</option>
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<option value="selex">SELEX (m)</option>
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<option value="staden">Staden (s)</option>
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<option value="strider">DNA strider (m)</option>
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<option value="swiss">SwisProt entry (m)</option>
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<option value="text">Plain sequence (s)</option>
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<option value="treecon">Treecon (m)</option>
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</param>
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</inputs>
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<outputs>
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<data format="fasta" name="out_file1" />
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</outputs>
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<tests>
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<test>
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<param name="input1" value="2.fasta"/>
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<param name="regions" value="1-9999999"/>
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<param name="separate" value="no"/>
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<param name="out_format1" value="fasta"/>
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<output name="out_file1" file="emboss_extractseq_out.fasta"/>
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</test>
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</tests>
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<code file="emboss_format_corrector.py" />
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<help>
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You can view the original documentation here_.
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||||
.. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/extractseq.html
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</help>
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</tool>
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@@ -0,0 +1,50 @@
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#EMBOSS format corrector
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import operator
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#from galaxy import datatypes
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#Properly set file formats after job run
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def exec_after_process( app, inp_data, out_data, param_dict,tool, stdout, stderr):
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#Properly set file formats before job run
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#def exec_before_job(trans, inp_data, out_data, param_dict,tool):
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#why isn't items an ordered list?
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items = out_data.items()
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#lets sort it ourselves....
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items = sorted(items, key=operator.itemgetter(0))
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#items is now sorted...
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#normal filetype correction
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data_count=1
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for name, data in items:
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outputType = param_dict.get( 'out_format'+str(data_count), None )
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#print "data_count",data_count, "name", name, "outputType", outputType
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if outputType !=None:
|
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if outputType == 'ncbi':
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outputType = "fasta"
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elif outputType == 'excel':
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outputType = "tabular"
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elif outputType == 'text':
|
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outputType = "txt"
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data = app.datatypes_registry.change_datatype(data, outputType)
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data.flush()
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data_count+=1
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||||
|
||||
#html filetype correction
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||||
data_count=1
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for name, data in items:
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wants_plot = param_dict.get( 'html_out'+str(data_count), None )
|
||||
ext = "html"
|
||||
if wants_plot == "yes":
|
||||
data = app.datatypes_registry.change_datatype(data, ext)
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data.flush()
|
||||
data_count+=1
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||||
|
||||
#png file correction
|
||||
data_count=1
|
||||
for name, data in items:
|
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wants_plot = param_dict.get( 'plot'+str(data_count), None )
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||||
ext = "png"
|
||||
if wants_plot == "yes":
|
||||
data = app.datatypes_registry.change_datatype(data, ext)
|
||||
data.flush()
|
||||
data_count+=1
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@@ -0,0 +1,35 @@
|
||||
<tool id="EMBOSS_freak36" name="freak">
|
||||
<description>Residue/base frequency table or plot</description>
|
||||
<command>freak -seqall $input1 -outfile $out_file1 -window $window -letters $letters -graph png -step $step -auto</command>
|
||||
<inputs>
|
||||
<param format="data" name="input1" type="data">
|
||||
<label>Sequences</label>
|
||||
</param>
|
||||
<param name="letters" size="5" type="text" value="gc">
|
||||
<label>Residue letters</label>
|
||||
</param>
|
||||
<param name="step" size="5" type="text" value="1">
|
||||
<label>Stepping value</label>
|
||||
</param>
|
||||
<param name="window" size="5" type="text" value="30">
|
||||
<label>Averaging window</label>
|
||||
</param>
|
||||
</inputs>
|
||||
<outputs>
|
||||
<data format="freak" name="out_file1" />
|
||||
</outputs>
|
||||
<tests>
|
||||
<test>
|
||||
<param name="input1" value="2.fasta"/>
|
||||
<param name="letters" value="gc"/>
|
||||
<param name="step" value="1"/>
|
||||
<param name="window" value="30"/>
|
||||
<output name="out_file1" file="emboss_freak_out.freak"/>
|
||||
</test>
|
||||
</tests>
|
||||
<help>
|
||||
You can view the original documentation here_.
|
||||
|
||||
.. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/freak.html
|
||||
</help>
|
||||
</tool>
|
||||
@@ -0,0 +1,43 @@
|
||||
<tool id="EMBOSS: fuzzpro38" name="fuzzpro">
|
||||
<description>Protein pattern search</description>
|
||||
<command>fuzzpro -sequence $input1 -outfile $out_file1 -pattern "$pattern" -mismatch $mismatch -rformat2 $out_format1 -auto</command>
|
||||
<inputs>
|
||||
<param format="data" name="input1" type="data">
|
||||
<label>Sequences</label>
|
||||
</param>
|
||||
<param name="pattern" size="5" type="text" value="">
|
||||
<label>Search pattern</label>
|
||||
</param>
|
||||
<param name="mismatch" size="5" type="text" value="0">
|
||||
<label>Number of mismatches</label>
|
||||
</param>
|
||||
<param name="out_format1" type="select">
|
||||
<label>Output Report File Format</label>
|
||||
<option value="seqtable">SeqTable</option>
|
||||
<option value="embl">EMBL</option>
|
||||
<option value="genbank">GENBANK</option>
|
||||
<option value="gff">GFF</option>
|
||||
<option value="pir">PIR</option>
|
||||
<option value="swiss">SwissProt</option>
|
||||
<option value="dbmotif">DbMotif</option>
|
||||
<option value="diffseq">Diffseq</option>
|
||||
<option value="excel">Excel (tab delimited)</option>
|
||||
<option value="feattable">FeatTable</option>
|
||||
<option value="motif">Motif</option>
|
||||
<option value="regions">Regions</option>
|
||||
<option value="simple">SRS Simple</option>
|
||||
<option value="srs">SRS</option>
|
||||
<option value="table">Table</option>
|
||||
<option value="tagseq">TagSeq</option>
|
||||
</param>
|
||||
</inputs>
|
||||
<outputs>
|
||||
<data format="fuzzpro" name="out_file1" />
|
||||
</outputs>
|
||||
<code file="emboss_format_corrector.py" />
|
||||
<help>
|
||||
You can view the original documentation here_.
|
||||
|
||||
.. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/fuzzpro.html
|
||||
</help>
|
||||
</tool>
|
||||
@@ -0,0 +1,57 @@
|
||||
<tool id="EMBOSS_garnier40" name="garnier">
|
||||
<description>Predicts protein secondary structure</description>
|
||||
<command>garnier -sequence $input1 -outfile $out_file1 -idc $idc -rformat2 $out_format1 -auto</command>
|
||||
<inputs>
|
||||
<param format="data" name="input1" type="data">
|
||||
<label>Sequences</label>
|
||||
</param>
|
||||
<param name="idc" type="select">
|
||||
<label>In their paper, GOR mention that if you know something about the secondary structure content of the protein you are analyzing, you can do better in prediction. 'idc' is an index into a
|
||||
set of arrays, dharr[] and dsarr[], which provide 'decision constants' (dch, dcs), which are offsets that are applied to the weights for the helix and sheet (extend) terms. So, idc=0 says don't
|
||||
use the decision constant offsets, and idc=1 to 6 indicates that various combinations of dch,dcs offsets should be used</label>
|
||||
<option value="0">idc 0</option>
|
||||
<option value="1">idc 1</option>
|
||||
<option value="2">idc 2</option>
|
||||
<option value="3">idc 3</option>
|
||||
<option value="4">idc 4</option>
|
||||
<option value="5">idc 5</option>
|
||||
<option value="6">idc 6</option>
|
||||
</param>
|
||||
<param name="out_format1" type="select">
|
||||
<label>Output Report File Format</label>
|
||||
<option value="tagseq">TagSeq</option>
|
||||
<option value="embl">EMBL</option>
|
||||
<option value="genbank">GENBANK</option>
|
||||
<option value="gff">GFF</option>
|
||||
<option value="pir">PIR</option>
|
||||
<option value="swiss">SwissProt</option>
|
||||
<option value="dbmotif">DbMotif</option>
|
||||
<option value="diffseq">Diffseq</option>
|
||||
<option value="excel">Excel (tab delimited)</option>
|
||||
<option value="feattable">FeatTable</option>
|
||||
<option value="motif">Motif</option>
|
||||
<option value="regions">Regions</option>
|
||||
<option value="seqtable">SeqTable</option>
|
||||
<option value="simple">SRS Simple</option>
|
||||
<option value="srs">SRS</option>
|
||||
<option value="table">Table</option>
|
||||
</param>
|
||||
</inputs>
|
||||
<outputs>
|
||||
<data format="garnier" name="out_file1" />
|
||||
</outputs>
|
||||
<tests>
|
||||
<test>
|
||||
<param name="input1" value="2.fasta"/>
|
||||
<param name="idc" value="0"/>
|
||||
<param name="out_format1" value="excel"/>
|
||||
<output name="out_file1" file="emboss_garnier_out.tabular"/>
|
||||
</test>
|
||||
</tests>
|
||||
<code file="emboss_format_corrector.py" />
|
||||
<help>
|
||||
You can view the original documentation here_.
|
||||
|
||||
.. _here: http://emboss.sourceforge.net/apps/release/4.0/emboss/apps/garnier.html
|
||||
</help>
|
||||
</tool>
|
||||
@@ -0,0 +1,23 @@
|
||||
<tool id="EMBOSS_geecee41" name="geecee">
|
||||
<description>Calculates fractional GC content of nucleic acid sequences</description>
|
||||
<command>geecee -sequence $input1 -outfile $out_file1 -auto</command>
|
||||
<inputs>
|
||||
<param format="data" name="input1" type="data">
|
||||
<label>Sequences</label>
|
||||
</param>
|
||||
</inputs>
|
||||
<outputs>
|
||||
<data format="geecee" name="out_file1" />
|
||||
</outputs>
|
||||
<tests>
|
||||
<test>
|
||||
<param name="input1" value="2.fasta"/>
|
||||
<output name="out_file1" file="emboss_geecee_out.geecee"/>
|
||||
</test>
|
||||
</tests>
|
||||
<help>
|
||||
You can view the original documentation here_.
|
||||
|
||||
.. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/geecee.html
|
||||
</help>
|
||||
</tool>
|
||||
Reference in New Issue
Block a user