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68 lines
3.0 KiB
XML
68 lines
3.0 KiB
XML
<tool id="EMBOSS: extractseq35" name="extractseq" version="5.0.0">
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<description>Extract regions from a sequence</description>
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<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
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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> |