Mercurial > repos > devteam > emboss_5
diff emboss_est2genome.xml @ 11:0e2484b6829b draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
| author | iuc |
|---|---|
| date | Mon, 30 Jan 2017 13:27:40 -0500 |
| parents | 9b98d3d903c6 |
| children | 27c43fb015f0 |
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--- a/emboss_est2genome.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_est2genome.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,71 +1,47 @@ -<tool id="EMBOSS: est2genome32" name="est2genome" version="5.0.0"> - <description>Align EST and genomic DNA sequences</description> - <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command>est2genome -estsequence $input1 -genomesequence $input2 -outfile $out_file1 -match $match -mismatch $mismatch -gappenalty $gappenalty -intronpenalty $intronpenalty -splicepenalty - $splicepenalty -minscore $minscore -reverse $reverse -splice $splice -mode $mode -best $best -shuffle $shuffle -seed $seed -align $align -width $width -auto</command> - <inputs> - <param format="fasta" name="input1" type="data"> - <label>EST sequence(s)</label> - </param> - <param format="data" name="input2" type="data"> - <label>Genomic sequence</label> - </param> - <param name="match" type="text" value="1"> - <label>Score for matching two bases</label> - </param> - <param name="mismatch" type="text" value="1"> - <label>Cost for mismatching two bases</label> - </param> - <param name="gappenalty" type="text" value="2"> - <label>Cost for deleting a single base in either sequence, excluding introns</label> - </param> - <param name="intronpenalty" type="text" value="40"> - <label>Cost for an intron, independent of length</label> - </param> - <param name="splicepenalty" type="text" value="20"> - <label>Cost for an intron, independent of length and starting/ending on donor-acceptor sites</label> - </param> - <param name="minscore" type="text" value="30"> - <label>Exclude alignments with scores below this threshold score</label> - </param> - <param name="reverse" type="select"> - <label>Reverse the orientation of the EST sequence</label> - <option value="no">No</option> - <option value="yes">Yes</option> - </param> - <param name="splice" type="select"> - <label>Use donor and acceptor splice sites</label> - <option value="yes">Yes</option> - <option value="no">No</option> - </param> - <param name="mode" type="select"> - <label>Comparison mode</label> - <option value="both">Both strands</option> - <option value="forward">Forward strand only</option> - <option value="reverse">Reverse strand only</option> - </param> - <param name="best" type="select"> - <label>Only best comparisons</label> - <option value="yes">Yes</option> - <option value="no">No</option> - </param> - <param name="shuffle" type="text" value="0"> - <label>Shuffle</label> - </param> - <param name="seed" type="text" value="20825"> - <label>Random number seed</label> - </param> - <param name="align" type="select"> - <label>Show the alignment</label> - <option value="no">No</option> - <option value="yes">Yes</option> - </param> - <param name="width" type="text" value="50"> - <label>Alignment width</label> - </param> - </inputs> - <outputs> - <data format="est2genome" name="out_file1" /> +<tool id="EMBOSS: est2genome32" name="est2genome" version="5.0.0.1"> + <description>Align EST and genomic DNA sequences</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <command>est2genome -estsequence '$input1' -genomesequence '$input2' -outfile '$out_file1' -match $match -mismatch $mismatch -gappenalty $gappenalty -intronpenalty $intronpenalty -splicepenalty + $splicepenalty -minscore $minscore -reverse $reverse -splice $splice -mode $mode -best $best -shuffle $shuffle -seed $seed -align $align -width $width -auto</command> + <inputs> + <param name="input1" type="data" format="fasta" label="EST sequence(s)" /> + <param name="input2" type="data" format="data" label="Genomic sequence" /> + <param name="match" type="integer" value="1" label="Score for matching two bases" /> + <param name="mismatch" type="integer" value="1" label="Cost for mismatching two bases" /> + <param name="gappenalty" type="integer" value="2" label="Cost for deleting a single base in either sequence, excluding introns" /> + <param name="intronpenalty" type="integer" value="40" label="Cost for an intron, independent of length" /> + <param name="splicepenalty" type="integer" value="20" label="Cost for an intron, independent of length and starting/ending on donor-acceptor sites" /> + <param name="minscore" type="integer" value="30" label="Exclude alignments with scores below this threshold score" /> + <param name="reverse" type="select" label="Reverse the orientation of the EST sequence"> + <option value="no">No</option> + <option value="yes">Yes</option> + </param> + <param name="splice" type="select" label="Use donor and acceptor splice sites"> + <option value="yes">Yes</option> + <option value="no">No</option> + </param> + <param name="mode" type="select" label="Comparison mode"> + <option value="both">Both strands</option> + <option value="forward">Forward strand only</option> + <option value="reverse">Reverse strand only</option> + </param> + <param name="best" type="select" label="Only best comparisons"> + <option value="yes">Yes</option> + <option value="no">No</option> + </param> + <param name="shuffle" type="integer" value="0" label="Shuffle" /> + <param name="seed" type="integer" value="20825" label="Random number seed" /> + <param name="align" type="select" label="Show the alignment"> + <option value="no">No</option> + <option value="yes">Yes</option> + </param> + <param name="width" type="integer" value="50" label="Alignment width" /> + </inputs> + <outputs> + <data name="out_file1" format="est2genome" /> </outputs> <tests> <test> @@ -88,7 +64,7 @@ <param name="width" value="50"/> <output name="out_file1" file="emboss_est2genome_out.est2genome"/> </test> - </tests> + </tests> <help> .. class:: warningmark @@ -97,15 +73,8 @@ ----- You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/est2genome.html - ------- - -**Citation** -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/est2genome.html </help> + <expand macro="citations" /> </tool>