Mercurial > repos > devteam > emboss_5
diff emboss_trimest.xml @ 10:d49956b87f7e draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
author | iuc |
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date | Wed, 08 Feb 2017 12:42:22 -0500 |
parents | |
children | 8992d258e42f |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/emboss_trimest.xml Wed Feb 08 12:42:22 2017 -0500 @@ -0,0 +1,85 @@ +<tool id="EMBOSS: trimest102" name="trimest" version="5.0.0.1"> + <description>Trim poly-A tails off EST sequences</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <code file="emboss_format_corrector.py" /> + <command>trimest -sequence '$input1' -outseq '$out_file1' -minlength $minlength -mismatches $mismatches -reverse $reverse -tolower $tolower -fiveprime $fiveprime -osformat2 $out_format1 + -auto</command> + <inputs> + <param name="input1" type="data" format="fasta" label="Sequences" /> + <param name="minlength" type="integer" value="4" label="Minimum length that a poly-A (or poly-T) tail must have before it is removed" /> + <param name="mismatches" type="integer" value="1" label="Number of fewer mismatched non-A bases in a poly-A tail" /> + <param name="reverse" type="select" label="Change the sequence to the forward sense when it is written out"> + <option value="yes">Yes</option> + <option value="no">No</option> + </param> + <param name="tolower" type="select" label="Mask poly-A by converting to lowercase"> + <option value="no">No</option> + <option value="yes">Yes</option> + </param> + <param name="fiveprime" type="select" label="Inspect 5' end of the sequence for poly-T tails"> + <option value="yes">Yes</option> + <option value="no">No</option> + </param> + <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> + <option value="clustal">Clustal (m)</option> + <option value="codata">CODATA (m)</option> + <option value="embl">EMBL (m)</option> + <option value="fitch">Fitch (m)</option> + <option value="gcg">Wisconsin Package GCG 9.x and 10.x (s)</option> + <option value="genbank">GENBANK (m)</option> + <option value="gff">GFF (m)</option> + <option value="hennig86">Hennig86 (m)</option> + <option value="ig">Intelligenetics (m)</option> + <option value="jackknifer">Jackknifer (m)</option> + <option value="jackknifernon">Jackknifernon (m)</option> + <option value="mega">Mega (m)</option> + <option value="meganon">Meganon (m)</option> + <option value="msf">Wisconsin Package GCG's MSF (m)</option> + <option value="pir">NBRF (PIR) (m)</option> + <option value="ncbi">NCBI style FASTA (m)</option> + <option value="nexus">Nexus/PAUP (m)</option> + <option value="nexusnon">Nexusnon/PAUPnon (m)</option> + <option value="phylip">PHYLIP interleaved (m)</option> + <option value="phylipnon">PHYLIP non-interleaved (m)</option> + <option value="selex">SELEX (m)</option> + <option value="staden">Staden (s)</option> + <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 name="out_file1" format="fasta" /> + </outputs> + <tests> + <test> + <param name="input1" value="2.fasta"/> + <param name="minlength" value="4"/> + <param name="mismatches" value="1"/> + <param name="reverse" value="yes"/> + <param name="tolower" value="no"/> + <param name="fiveprime" value="yes"/> + <param name="out_format1" value="fasta"/> + <output name="out_file1" file="emboss_trimest_out.fasta"/> + </test> + </tests> + <help> +.. class:: warningmark + +The input dataset needs to be sequences. + +----- + + You can view the original documentation here_. + + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/trimest.html + </help> + <expand macro="citations" /> +</tool>