/var/lib/mobyle/programs/showalign.xml is in mobyle-programs 5.1.2-1.
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<!-- XML Authors: Corinne Maufrais and Nicolas Joly, -->
<!-- 'Biological Software and Databases' Group, Institut Pasteur, Paris. -->
<!-- Distributed under LGPLv2 License. Please refer to the COPYING.LIB document. -->
<program>
<head>
<name>showalign</name>
<package>
<name>EMBOSS</name>
<version>6.3.1</version>
<doc>
<title>EMBOSS</title>
<description>
<text lang="en">European Molecular Biology Open Software Suite</text>
</description>
<authors>Rice,P. Longden,I. and Bleasby, A.</authors>
<reference>EMBOSS: The European Molecular Biology Open Software Suite (2000) Rice,P. Longden,I. and Bleasby, A. Trends in Genetics 16, (6) pp276--277</reference>
<sourcelink>http://emboss.sourceforge.net/download</sourcelink>
<homepagelink>http://emboss.sourceforge.net</homepagelink>
</doc>
</package>
<doc>
<title>showalign</title>
<description>
<text lang="en">Display a multiple sequence alignment in pretty format</text>
</description>
<doclink>http://bioweb2.pasteur.fr/docs/EMBOSS/showalign.html</doclink>
<doclink>http://emboss.sourceforge.net/docs/themes</doclink>
</doc>
<category>alignment:multiple:display</category>
<command>showalign</command>
</head>
<parameters>
<paragraph>
<name>e_input</name>
<prompt lang="en">Input section</prompt>
<parameters>
<parameter issimple="1" ismandatory="1">
<name>e_sequence</name>
<prompt lang="en">sequence option</prompt>
<type>
<datatype>
<class>Alignment</class>
</datatype>
<dataFormat>FASTA</dataFormat>
<dataFormat>MSF</dataFormat>
<dataFormat>PAIR</dataFormat>
<dataFormat>MARKX0</dataFormat>
<dataFormat>MARKX1</dataFormat>
<dataFormat>MARKX2</dataFormat>
<dataFormat>MARKX3</dataFormat>
<dataFormat>MARKX10</dataFormat>
<dataFormat>SRS</dataFormat>
<dataFormat>SRSPAIR</dataFormat>
<dataFormat>SCORE</dataFormat>
<dataFormat>UNKNOWN</dataFormat>
<dataFormat>MULTIPLE</dataFormat>
<dataFormat>SIMPLE</dataFormat>
<dataFormat>MATCH</dataFormat>
<card>1,n</card>
</type>
<format>
<code proglang="python">("", " -sequence=" + str(value))[value is not None]</code>
</format>
<argpos>1</argpos>
<comment>
<text lang="en">The sequence alignment to be displayed.</text>
</comment>
</parameter>
<parameter>
<name>e_matrix</name>
<prompt lang="en">Similarity scoring matrix file</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>mobyle_null</value>
</vdef>
<vlist>
<velem undef="1">
<value>mobyle_null</value>
<label></label>
</velem>
<velem>
<value>EBLOSUM30</value>
<label>Eblosum30</label>
</velem>
<velem>
<value>EBLOSUM35</value>
<label>Eblosum35</label>
</velem>
<velem>
<value>EBLOSUM40</value>
<label>Eblosum40</label>
</velem>
<velem>
<value>EBLOSUM45</value>
<label>Eblosum45</label>
</velem>
<velem>
<value>EBLOSUM50</value>
<label>Eblosum50</label>
</velem>
<velem>
<value>EBLOSUM55</value>
<label>Eblosum55</label>
</velem>
<velem>
<value>EBLOSUM60</value>
<label>Eblosum60</label>
</velem>
<velem>
<value>EBLOSUM62</value>
<label>Eblosum62</label>
</velem>
<velem>
<value>EBLOSUM62-12</value>
<label>Eblosum62-12</label>
</velem>
<velem>
<value>EBLOSUM65</value>
<label>Eblosum65</label>
</velem>
<velem>
<value>EBLOSUM70</value>
<label>Eblosum70</label>
</velem>
<velem>
<value>EBLOSUM75</value>
<label>Eblosum75</label>
</velem>
<velem>
<value>EBLOSUM80</value>
<label>Eblosum80</label>
</velem>
<velem>
<value>EBLOSUM85</value>
<label>Eblosum85</label>
</velem>
<velem>
<value>EBLOSUM90</value>
<label>Eblosum90</label>
</velem>
<velem>
<value>EBLOSUMN</value>
<label>Eblosumn</label>
</velem>
<velem>
<value>EDNAFULL</value>
<label>Ednafull</label>
</velem>
<velem>
<value>EDNAMAT</value>
<label>Ednamat</label>
</velem>
<velem>
<value>EDNASIMPLE</value>
<label>Ednasimple</label>
</velem>
<velem>
<value>EPAM10</value>
<label>Epam10</label>
</velem>
<velem>
<value>EPAM100</value>
<label>Epam100</label>
</velem>
<velem>
<value>EPAM110</value>
<label>Epam110</label>
</velem>
<velem>
<value>EPAM120</value>
<label>Epam120</label>
</velem>
<velem>
<value>EPAM130</value>
<label>Epam130</label>
</velem>
<velem>
<value>EPAM140</value>
<label>Epam140</label>
</velem>
<velem>
<value>EPAM150</value>
<label>Epam150</label>
</velem>
<velem>
<value>EPAM160</value>
<label>Epam160</label>
</velem>
<velem>
<value>EPAM170</value>
<label>Epam170</label>
</velem>
<velem>
<value>EPAM180</value>
<label>Epam180</label>
</velem>
<velem>
<value>EPAM190</value>
<label>Epam190</label>
</velem>
<velem>
<value>EPAM20</value>
<label>Epam20</label>
</velem>
<velem>
<value>EPAM200</value>
<label>Epam200</label>
</velem>
<velem>
<value>EPAM210</value>
<label>Epam210</label>
</velem>
<velem>
<value>EPAM220</value>
<label>Epam220</label>
</velem>
<velem>
<value>EPAM230</value>
<label>Epam230</label>
</velem>
<velem>
<value>EPAM240</value>
<label>Epam240</label>
</velem>
<velem>
<value>EPAM250</value>
<label>Epam250</label>
</velem>
<velem>
<value>EPAM260</value>
<label>Epam260</label>
</velem>
<velem>
<value>EPAM270</value>
<label>Epam270</label>
</velem>
<velem>
<value>EPAM280</value>
<label>Epam280</label>
</velem>
<velem>
<value>EPAM290</value>
<label>Epam290</label>
</velem>
<velem>
<value>EPAM30</value>
<label>Epam30</label>
</velem>
<velem>
<value>EPAM300</value>
<label>Epam300</label>
</velem>
<velem>
<value>EPAM310</value>
<label>Epam310</label>
</velem>
<velem>
<value>EPAM320</value>
<label>Epam320</label>
</velem>
<velem>
<value>EPAM330</value>
<label>Epam330</label>
</velem>
<velem>
<value>EPAM340</value>
<label>Epam340</label>
</velem>
<velem>
<value>EPAM350</value>
<label>Epam350</label>
</velem>
<velem>
<value>EPAM360</value>
<label>Epam360</label>
</velem>
<velem>
<value>EPAM370</value>
<label>Epam370</label>
</velem>
<velem>
<value>EPAM380</value>
<label>Epam380</label>
</velem>
<velem>
<value>EPAM390</value>
<label>Epam390</label>
</velem>
<velem>
<value>EPAM40</value>
<label>Epam40</label>
</velem>
<velem>
<value>EPAM400</value>
<label>Epam400</label>
</velem>
<velem>
<value>EPAM410</value>
<label>Epam410</label>
</velem>
<velem>
<value>EPAM420</value>
<label>Epam420</label>
</velem>
<velem>
<value>EPAM430</value>
<label>Epam430</label>
</velem>
<velem>
<value>EPAM440</value>
<label>Epam440</label>
</velem>
<velem>
<value>EPAM450</value>
<label>Epam450</label>
</velem>
<velem>
<value>EPAM460</value>
<label>Epam460</label>
</velem>
<velem>
<value>EPAM470</value>
<label>Epam470</label>
</velem>
<velem>
<value>EPAM480</value>
<label>Epam480</label>
</velem>
<velem>
<value>EPAM490</value>
<label>Epam490</label>
</velem>
<velem>
<value>EPAM50</value>
<label>Epam50</label>
</velem>
<velem>
<value>EPAM500</value>
<label>Epam500</label>
</velem>
<velem>
<value>EPAM60</value>
<label>Epam60</label>
</velem>
<velem>
<value>EPAM70</value>
<label>Epam70</label>
</velem>
<velem>
<value>EPAM80</value>
<label>Epam80</label>
</velem>
<velem>
<value>EPAM90</value>
<label>Epam90</label>
</velem>
<velem>
<value>SSSUB</value>
<label>Sssub</label>
</velem>
</vlist>
<format>
<code proglang="python">("", " -matrix=" + str(value))[value is not None and value!=vdef]</code>
</format>
<argpos>2</argpos>
<comment>
<text lang="en">This is the scoring matrix file used when comparing sequences. By default it is the file 'EBLOSUM62' (for proteins) or the file 'EDNAFULL' (for nucleic sequences). These files are found in the 'data' directory of the EMBOSS installation.</text>
</comment>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>e_additional</name>
<prompt lang="en">Additional section</prompt>
<parameters>
<parameter>
<name>e_refseq</name>
<prompt lang="en">The number or the name of the reference sequence</prompt>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="python">("", " -refseq=" + str(value))[value is not None and value!=vdef]</code>
</format>
<argpos>3</argpos>
<comment>
<text lang="en">If you give the number in the alignment or the name of a sequence, it will be taken to be the reference sequence. The reference sequence is always shown in full and is the one against which all the other sequences are compared. If this is set to 0 then the consensus sequence will be used as the reference sequence. By default the consensus sequence is used as the reference sequence.</text>
</comment>
</parameter>
<parameter>
<name>e_bottom</name>
<prompt lang="en">Display the reference sequence at the bottom</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="python">(" -nobottom", "")[ bool(value) ]</code>
</format>
<argpos>4</argpos>
<comment>
<text lang="en">If this is true then the reference sequence is displayed at the bottom of the alignment instead of the top.</text>
</comment>
</parameter>
<parameter>
<name>e_show</name>
<prompt lang="en">What to show</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>N</value>
</vdef>
<vlist>
<velem>
<value>A</value>
<label>All of the sequences</label>
</velem>
<velem>
<value>I</value>
<label>Identities between the sequences</label>
</velem>
<velem>
<value>N</value>
<label>Non-identities between the sequences</label>
</velem>
<velem>
<value>S</value>
<label>Similarities between the sequences</label>
</velem>
<velem>
<value>D</value>
<label>Dissimilarities between the sequences</label>
</velem>
</vlist>
<format>
<code proglang="python">("", " -show=" + str(value))[value is not None and value!=vdef]</code>
</format>
<argpos>5</argpos>
</parameter>
<parameter>
<name>e_order</name>
<prompt lang="en">Output order of the sequences</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>I</value>
</vdef>
<vlist>
<velem>
<value>I</value>
<label>Input order - no change</label>
</velem>
<velem>
<value>A</value>
<label>Alphabetical order of the names</label>
</velem>
<velem>
<value>S</value>
<label>Similarity to the reference sequence</label>
</velem>
</vlist>
<format>
<code proglang="python">("", " -order=" + str(value))[value is not None and value!=vdef]</code>
</format>
<argpos>6</argpos>
</parameter>
<parameter>
<name>e_similarcase</name>
<prompt lang="en">Show similar residues in lower-case</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="python">(" -nosimilarcase", "")[ bool(value) ]</code>
</format>
<argpos>7</argpos>
<comment>
<text lang="en">If this is set True, then when -show is set to 'Similarities' or 'Non-identities' and a residue is similar but not identical to the reference sequence residue, it will be changed to lower-case. If -show is set to 'All' then non-identical, non-similar residues will be changed to lower-case. If this is False then no change to the case of the residues is made on the basis of their similarity to the reference sequence.</text>
</comment>
</parameter>
<parameter>
<name>e_consensus</name>
<prompt lang="en">Display the consensus line</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="python">(" -noconsensus", "")[ bool(value) ]</code>
</format>
<argpos>8</argpos>
<comment>
<text lang="en">If this is true then the consensus line is displayed.</text>
</comment>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>e_advanced</name>
<prompt lang="en">Advanced section</prompt>
<parameters>
<parameter>
<name>e_uppercase</name>
<prompt lang="en">Regions to put in uppercase (eg: 4-57,78-94)</prompt>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<format>
<code proglang="python">("", " -uppercase=" + str(value))[value is not None]</code>
</format>
<argpos>9</argpos>
<comment>
<text lang="en">Regions to put in uppercase.
If this is left blank, then the sequence case is left alone.
A set of regions is specified by a set of pairs of positions.
The positions are integers.
They are separated by any non-digit, non-alpha character.
Examples of region specifications are:
24-45, 56-78
1:45, 67=99;765..888
1,5,8,10,23,45,57,99</text>
</comment>
</parameter>
<parameter>
<name>e_number</name>
<prompt lang="en">Number the sequences</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="python">(" -nonumber", "")[ bool(value) ]</code>
</format>
<argpos>10</argpos>
<comment>
<text lang="en">If this option is true then a line giving the positions in the alignment is displayed every 10 characters above the alignment.</text>
</comment>
</parameter>
<parameter>
<name>e_ruler</name>
<prompt lang="en">Display ruler</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="python">(" -noruler", "")[ bool(value) ]</code>
</format>
<argpos>11</argpos>
<comment>
<text lang="en">If this option is true then a ruler line marking every 5th and 10th character in the alignment is displayed.</text>
</comment>
</parameter>
<parameter>
<name>e_width</name>
<prompt lang="en">Width of sequence to display (value greater than or equal to 1)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>60</value>
</vdef>
<format>
<code proglang="python">("", " -width=" + str(value))[value is not None and value!=vdef]</code>
</format>
<ctrl>
<message>
<text lang="en">Value greater than or equal to 1 is required</text>
</message>
<code proglang="python">value >= 1</code>
</ctrl>
<argpos>12</argpos>
</parameter>
<parameter>
<name>e_margin</name>
<prompt lang="en">Length of margin for sequence names (value greater than or equal to -1)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>-1</value>
</vdef>
<format>
<code proglang="python">("", " -margin=" + str(value))[value is not None and value!=vdef]</code>
</format>
<ctrl>
<message>
<text lang="en">Value greater than or equal to -1 is required</text>
</message>
<code proglang="python">value >= -1</code>
</ctrl>
<argpos>13</argpos>
<comment>
<text lang="en">This sets the length of the left-hand margin for sequence names. If the margin is set at 0 then no margin and no names are displayed. If the margin is set to a value that is less than the length of a sequence name then the sequence name is displayed truncated to the length of the margin. If the margin is set to -1 then the minimum margin width that will allow all the sequence names to be displayed in full plus a space at the end of the name will automatically be selected.</text>
</comment>
</parameter>
<parameter>
<name>e_html</name>
<prompt lang="en">Use html formatting</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="python">("", " -html")[ bool(value) ]</code>
</format>
<argpos>14</argpos>
</parameter>
<parameter>
<name>e_highlight</name>
<prompt lang="en">Regions to colour in html (eg: 4-57 red 78-94 green)</prompt>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<format>
<code proglang="python">("", " -highlight=" + str(value))[value is not None]</code>
</format>
<argpos>15</argpos>
<comment>
<text lang="en">Regions to colour if formatting for HTML.
If this is left blank, then the sequence is left alone.
A set of regions is specified by a set of pairs of positions.
The positions are integers.
They are followed by any valid HTML font colour.
Examples of region specifications are:
24-45 blue 56-78 orange
1-100 green 120-156 red
A file of ranges to colour (one range per line) can be specified as '@filename'.</text>
</comment>
</parameter>
<parameter>
<name>e_plurality</name>
<prompt lang="en">Plurality check % for consensus (value from 0.0 to 100.0)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<vdef>
<value>50.0</value>
</vdef>
<format>
<code proglang="python">("", " -plurality=" + str(value))[value is not None and value!=vdef]</code>
</format>
<ctrl>
<message>
<text lang="en">Value greater than or equal to 0.0 is required</text>
</message>
<code proglang="python">value >= 0.0</code>
</ctrl>
<ctrl>
<message>
<text lang="en">Value less than or equal to 100.0 is required</text>
</message>
<code proglang="python">value <= 100.0</code>
</ctrl>
<argpos>16</argpos>
<comment>
<text lang="en">Set a cut-off for the % of positive scoring matches below which there is no consensus. The default plurality is taken as 50% of the total weight of all the sequences in the alignment.</text>
</comment>
</parameter>
<parameter>
<name>e_setcase</name>
<prompt lang="en">Threshold above which the consensus is given in uppercase</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<format>
<code proglang="python">("", " -setcase=" + str(value))[value is not None]</code>
</format>
<argpos>17</argpos>
<comment>
<text lang="en">Sets the threshold for the scores of the positive matches above which the consensus is in upper-case and below which the consensus is in lower-case. By default this is set to be half of the (weight-adjusted) number of sequences in the alignment.</text>
</comment>
</parameter>
<parameter>
<name>e_identity</name>
<prompt lang="en">Required % of identities at a position for consensus (value from 0.0 to 100.0)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<vdef>
<value>0.0</value>
</vdef>
<format>
<code proglang="python">("", " -identity=" + str(value))[value is not None and value!=vdef]</code>
</format>
<ctrl>
<message>
<text lang="en">Value greater than or equal to 0.0 is required</text>
</message>
<code proglang="python">value >= 0.0</code>
</ctrl>
<ctrl>
<message>
<text lang="en">Value less than or equal to 100.0 is required</text>
</message>
<code proglang="python">value <= 100.0</code>
</ctrl>
<argpos>18</argpos>
<comment>
<text lang="en">Provides the facility of setting the required number of identities at a position for it to give a consensus. Therefore, if this is set to 100% only columns of identities contribute to the consensus.</text>
</comment>
</parameter>
<parameter>
<name>e_gaps</name>
<prompt lang="en">Use gap characters in consensus</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="python">(" -nogaps", "")[ bool(value) ]</code>
</format>
<argpos>19</argpos>
<comment>
<text lang="en">If this option is true then gap characters can appear in the consensus. The alternative is 'N' for nucleotide, or 'X' for protein</text>
</comment>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>e_output</name>
<prompt lang="en">Output section</prompt>
<parameters>
<parameter>
<name>e_outfile</name>
<prompt lang="en">Name of the output file (e_outfile)</prompt>
<type>
<datatype>
<class>Filename</class>
</datatype>
</type>
<vdef>
<value>showalign.e_outfile</value>
</vdef>
<format>
<code proglang="python">("" , " -outfile=" + str(value))[value is not None]</code>
</format>
<argpos>20</argpos>
</parameter>
<parameter isout="1">
<name>e_outfile_out</name>
<prompt lang="en">outfile_out option</prompt>
<type>
<datatype>
<class>ShowalignReport</class>
<superclass>Report</superclass>
</datatype>
</type>
<filenames>
<code proglang="python">e_outfile</code>
</filenames>
</parameter>
</parameters>
</paragraph>
<parameter ishidden="1">
<name>auto</name>
<prompt lang="en">Turn off any prompting</prompt>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<format>
<code proglang="python">" -auto -stdout"</code>
</format>
<argpos>21</argpos>
</parameter>
</parameters>
</program>
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