Mercurial > repos > devteam > emboss_5
diff emboss_extractfeat.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 |
line wrap: on
line diff
--- a/emboss_extractfeat.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_extractfeat.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,58 +1,38 @@ -<tool id="EMBOSS: extractfeat34" name="extractfeat" version="5.0.0"> - <!-- tool tested with documentation, functional test not designed due to empty files resulting from test input sequences --> - <description>Extract features from a sequence</description> - <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command>extractfeat -sequence $input1 -outseq $out_file1 -before $before -after $after -source "$source" -type "$type" -sense $sense -minscore $minscore -maxscore $maxscore -tag "$tag" -value - "$value" -join $join -featinname $featinname -describe "$describe" -osformat2 $out_format1 -auto</command> - <inputs> - <param format="data" name="input1" type="data"> - <label>Sequences</label> - </param> - <param name="before" type="text" value="0"> - <label>Number of bases or residues before the feature to include in the extracted sequence</label> - </param> - <param name="after" type="text" value="0"> - <label>Number of bases or residues after the feature to include in the extracted sequence</label> - </param> - <param name="source" type="text" value="*"> - <label>Feature source</label> - </param> - <param name="type" type="text" value="*"> - <label>Feature type</label> - </param> - <param name="sense" type="select"> - <label>Feature sense</label> - <option value="0">Any sense</option> - <option value="1">Forward sense</option> - <option value="-1">Reverse sense</option> - </param> - <param name="minscore" type="text" value="0.0"> - <label>Minimum score</label> - </param> - <param name="maxscore" type="text" value="0.0"> - <label>Maximum score</label> - </param> - <param name="tag" type="text" value="*"> - <label>Feature tags</label> - </param> - <param name="value" type="text" value="*"> - <label>Tag values</label> - </param> - <param name="join" type="select"> - <label>Join features</label> - <option value="no">No</option> - <option value="yes">Yes</option> - </param> - <param name="featinname" type="select"> - <label>Put feature type in sequence name</label> - <option value="no">No</option> - <option value="yes">Yes</option> - </param> - <param name="describe" type="text" value=""> - <label>Specify one or more tag names that should be added to the output sequence Description text</label> - </param> - <param name="out_format1" type="select"> - <label>Output Sequence File Format</label> +<tool id="EMBOSS: extractfeat34" name="extractfeat" version="5.0.0.1"> + <!-- tool tested with documentation, functional test not designed due to empty files resulting from test input sequences --> + <description>Extract features from a sequence</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <code file="emboss_format_corrector.py" /> + <command>extractfeat -sequence '$input1' -outseq '$out_file1' -before $before -after $after -source '$source' -type '$type' -sense $sense -minscore $minscore -maxscore $maxscore -tag '$tag' -value + '$value' -join $join -featinname $featinname -describe '$describe' -osformat2 $out_format1 -auto</command> + <inputs> + <param name="input1" type="data" format="data" label="Sequences" /> + <param name="before" type="integer" value="0" label="Number of bases or residues before the feature to include in the extracted sequence" /> + <param name="after" type="integer" value="0" label="Number of bases or residues after the feature to include in the extracted sequence" /> + <param name="source" type="text" value="*" label="Feature source" /> + <param name="type" type="text" value="*" label="Feature type" /> + <param name="sense" type="select" label="Feature sense"> + <option value="0">Any sense</option> + <option value="1">Forward sense</option> + <option value="-1">Reverse sense</option> + </param> + <param name="minscore" type="float" value="0.0" label="Minimum score" /> + <param name="maxscore" type="float" value="0.0" label="Maximum score" /> + <param name="tag" type="text" value="*" label="Feature tags" /> + <param name="value" type="text" value="*" label="Tag values" /> + <param name="join" type="select" label="Join features"> + <option value="no">No</option> + <option value="yes">Yes</option> + </param> + <param name="featinname" type="select" label="Put feature type in sequence name"> + <option value="no">No</option> + <option value="yes">Yes</option> + </param> + <param name="describe" type="text" value="" label="Specify one or more tag names that should be added to the output sequence Description text" /> + <param name="out_format1" type="select" label="Output sequence file format"> <option value="fasta">FASTA (m)</option> <option value="acedb">ACeDB (m)</option> <option value="asn1">ASN.1 (m)</option> @@ -81,24 +61,16 @@ <option value="strider">DNA strider (m)</option> <option value="swiss">SwisProt entry (m)</option> <option value="text">Plain sequence (s)</option> - <option value="treecon">Treecon (m)</option> - </param> - </inputs> - <outputs> - <data format="fasta" name="out_file1" /> - </outputs> - <code file="emboss_format_corrector.py" /> + <option value="treecon">Treecon (m)</option> + </param> + </inputs> + <outputs> + <data name="out_file1" format="fasta" /> + </outputs> <help> You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/extractfeat.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/extractfeat.html </help> -</tool> \ No newline at end of file + <expand macro="citations" /> +</tool>