Mercurial > repos > iuc > emboss_needle
diff macros.xml @ 0:2f0dc62d0a19 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss commit 08f38b1f9b4241ba9037c64f732621efc628fd43
| author | iuc |
|---|---|
| date | Mon, 20 Jan 2025 16:22:05 +0000 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Mon Jan 20 16:22:05 2025 +0000 @@ -0,0 +1,159 @@ +<macros> + <token name="@PROFILE@">23.1</token> + <token name="@VERSION@">6.6.0</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@VERSION@">emboss</requirement> + <requirement type="package" version="5.26">perl</requirement> + </requirements> + </xml> + <xml name="bio_tools"> + <xrefs> + <xref type="bio.tools">emboss</xref> + </xrefs> + </xml> + <xml name="citations"> + <citations> + <citation type="doi">10.1016/S0168-9525(00)02024-2</citation> + <citation type="doi">10.1101/gr.5578007</citation> + <yield /> + </citations> + </xml> + + <xml name="scoring_matrix"> + <param argument="-datafile" type="select" optional="true" label="Scoring matrix" help="This is the scoring matrix used when comparing sequences. By default it is EBLOSUM62 (for proteins) or EDNAFULL (for nucleic sequences)"> + <option value="EBLOSUM30">EBLOSUM30</option> + <option value="EBLOSUM35">EBLOSUM35</option> + <option value="EBLOSUM40">EBLOSUM40</option> + <option value="EBLOSUM45">EBLOSUM45</option> + <option value="EBLOSUM50">EBLOSUM50</option> + <option value="EBLOSUM55">EBLOSUM55</option> + <option value="EBLOSUM60">EBLOSUM60</option> + <option value="EBLOSUM62">EBLOSUM62</option> + <option value="EBLOSUM62-12">EBLOSUM62-12</option> + <option value="EBLOSUM65">EBLOSUM65</option> + <option value="EBLOSUM70">EBLOSUM70</option> + <option value="EBLOSUM75">EBLOSUM75</option> + <option value="EBLOSUM80">EBLOSUM80</option> + <option value="EBLOSUM85">EBLOSUM85</option> + <option value="EBLOSUM90">EBLOSUM90</option> + <option value="EBLOSUMN">EBLOSUMN</option> + <option value="EDNAFULL">EDNAFULL</option> + <option value="EDNAMAT">EDNAMAT</option> + <option value="EDNASIMPLE">EDNASIMPLE</option> + <option value="ENUC.4.2">ENUC.4.2</option> + <option value="ENUC.4.4">ENUC.4.4</option> + <option value="EPAM10">EPAM10</option> + <option value="EPAM100">EPAM100</option> + <option value="EPAM110">EPAM110</option> + <option value="EPAM120">EPAM120</option> + <option value="EPAM130">EPAM130</option> + <option value="EPAM140">EPAM140</option> + <option value="EPAM150">EPAM150</option> + <option value="EPAM160">EPAM160</option> + <option value="EPAM170">EPAM170</option> + <option value="EPAM180">EPAM180</option> + <option value="EPAM190">EPAM190</option> + <option value="EPAM20">EPAM20</option> + <option value="EPAM200">EPAM200</option> + <option value="EPAM210">EPAM210</option> + <option value="EPAM220">EPAM220</option> + <option value="EPAM230">EPAM230</option> + <option value="EPAM240">EPAM240</option> + <option value="EPAM250">EPAM250</option> + <option value="EPAM260">EPAM260</option> + <option value="EPAM270">EPAM270</option> + <option value="EPAM280">EPAM280</option> + <option value="EPAM290">EPAM290</option> + <option value="EPAM30">EPAM30</option> + <option value="EPAM300">EPAM300</option> + <option value="EPAM310">EPAM310</option> + <option value="EPAM320">EPAM320</option> + <option value="EPAM330">EPAM330</option> + <option value="EPAM340">EPAM340</option> + <option value="EPAM350">EPAM350</option> + <option value="EPAM360">EPAM360</option> + <option value="EPAM370">EPAM370</option> + <option value="EPAM380">EPAM380</option> + <option value="EPAM390">EPAM390</option> + <option value="EPAM40">EPAM40</option> + <option value="EPAM400">EPAM400</option> + <option value="EPAM410">EPAM410</option> + <option value="EPAM420">EPAM420</option> + <option value="EPAM430">EPAM430</option> + <option value="EPAM440">EPAM440</option> + <option value="EPAM450">EPAM450</option> + <option value="EPAM460">EPAM460</option> + <option value="EPAM470">EPAM470</option> + <option value="EPAM480">EPAM480</option> + <option value="EPAM490">EPAM490</option> + <option value="EPAM50">EPAM50</option> + <option value="EPAM500">EPAM500</option> + <option value="EPAM60">EPAM60</option> + <option value="EPAM70">EPAM70</option> + <option value="EPAM80">EPAM80</option> + <option value="EPAM90">EPAM90</option> + <option value="SSSUB">SSSUB</option> + </param> + </xml> + + <xml name="param_brief"> + <param argument="-brief" type="select" label="Brief identity and similarity"> + <option value="yes">Yes</option> + <option value="no">No</option> + </param> + </xml> + + <xml name="gap_penalties"> + <param argument="-gapopen" type="float" value="10.0" min="1.0" max="100.0" label="Gap open penalty" /> + <param argument="-gapextend" type="float" value="0.5" min="0.0" max="10.0" label="Gap extension penalty" /> + </xml> + + <xml name="endgap_penalties"> + <conditional name="endgap"> + <param argument="-endweight" type="select" label="Apply end gap penalties?" help=""> + <option value="yes">yes</option> + <option value="no" selected="true">no</option> + </param> + <when value="yes"> + <param argument="-endopen" type="float" value="10.0" min="0.0" max="100.0" label="Penalty for creation of and end gap." help="The best value depends on the choice of comparison matrix. The default value assumes you are using the EBLOSUM62 matrix for protein sequences, and the EDNAFULL matrix for nucleotide sequences."/> + <param argument="-endextend" type="float" value="0.5" min="0.0" max="10.0" label="The end gap extensionpenalty" help="this penalty is added to the end gap penalty for each base or residue in the end gap."/> + </when> + <when value="no"/> + </conditional> + </xml> + + <xml name="choose_alignment_output_format"> + <param name="out_format1" type="select" label="Output alignment file format"> + <option value="srspair">SRS pair (p)</option> + <option value="simple">Simple (m)</option> + <option value="fasta">FASTA (m)</option> + <option value="msf">MSF (m)</option> + <option value="srs">SRS (m)</option> + <option value="pair">Pair (p)</option> + <option value="markx0">Markx0 (p)</option> + <option value="markx1">Markx1 (p)</option> + <option value="markx2">Markx2 (p)</option> + <option value="markx3">Markx3 (p)</option> + <option value="markx10">Markx10 (p)</option> + <option value="score">Score (p)</option> + </param> + </xml> + + <xml name="change_alignment_output_format"> + <change_format> + <when input="out_format1" value="fasta" format="fasta"/> + <when input="out_format1" value="score" format="score"/> + <when input="out_format1" value="pair" format="pair"/> + <when input="out_format1" value="srspair" format="srspair"/> + <when input="out_format1" value="simple" format="simple"/> + <when input="out_format1" value="srs" format="srs"/> + <when input="out_format1" value="msf" format="msf"/> + <when input="out_format1" value="markx0" format="markx0"/> + <when input="out_format1" value="markx1" format="markx1"/> + <when input="out_format1" value="markx2" format="markx2"/> + <when input="out_format1" value="markx3" format="markx3"/> + <when input="out_format1" value="markx10" format="markx10"/> + </change_format> + </xml> +</macros>