<?xml version="1.0" encoding="ISO-8859-1" ?>
<!DOCTYPE pise SYSTEM "PARSER/pise.dtd" [
<!ENTITY emboss_init SYSTEM "XMLDIR/emboss.xml">
]>

<pise>

<head>
<title>FINDKM</title>
<description>Find Km and Vmax for an enzyme reaction by a Hanes/Woolf plot (EMBOSS)</description>
<category>enzyme kinetics</category>
<doclink>http://bioweb.pasteur.fr/docs/EMBOSS/findkm.html</doclink>
</head>

<command>findkm</command>

<parameters>

&emboss_init;


<parameter type="Paragraph">
<paragraph>
<name>input</name>
	<prompt>Input section</prompt>

<parameters>
	<parameter type="InFile" ismandatory="1" issimple="1" ishidden="0">
	<name>infile</name>
	<attributes>
		<prompt>Enter name of file containing data (-infile)</prompt>
		<format>
			<language>perl</language>
			<code>" -infile=$value"</code>
		</format>
		<group>1</group>
	</attributes>
	</parameter>

	</parameters>
</paragraph>
</parameter>


<parameter type="Paragraph">
<paragraph>
<name>advanced</name>
	<prompt>Advanced section</prompt>

<parameters>
	<parameter type="Switch" ismandatory="0" issimple="0" ishidden="0">
	<name>plot</name>
	<attributes>
		<prompt>S/V vs S (-plot)</prompt>
		<vdef>
			<value>1</value>
		</vdef>
		<format>
			<language>perl</language>
			<code>($value)? "" : " -noplot"</code>
		</format>
		<group>2</group>
	</attributes>
	</parameter>

	</parameters>
</paragraph>
</parameter>


<parameter type="Paragraph">
<paragraph>
<name>output</name>
	<prompt>Output section</prompt>

<parameters>
	<parameter type="OutFile" ismandatory="1" issimple="1" ishidden="0">
	<name>outfile</name>
	<attributes>
		<prompt>outfile (-outfile)</prompt>
		<vdef><value>outfile.out</value></vdef>
		<format>
			<language>perl</language>
			<code>" -outfile=$value"</code>
		</format>
		<group>3</group>
	</attributes>
	</parameter>

	<parameter type="Excl" ismandatory="0" issimple="0" ishidden="0">
	<name>graphlb</name>
	<attributes>
		<prompt>graphlb (-graphlb)</prompt>
			<vlist>
				<value>x11</value>
				<label>x11</label>
				<value>hp7470</value>
				<label>hp7470</label>
				<value>postscript</value>
				<label>postscript</label>
				<value>cps</value>
				<label>cps</label>
				<value>hp7580</value>
				<label>hp7580</label>
				<value>null</value>
				<label>null</label>
				<value>data</value>
				<label>data</label>
				<value>colourps</value>
				<label>colourps</label>
				<value>text</value>
				<label>text</label>
				<value>none</value>
				<label>none</label>
				<value>tek4107t</value>
				<label>tek4107t</label>
				<value>tekt</value>
				<label>tekt</label>
				<value>xwindows</value>
				<label>xwindows</label>
				<value>hpgl</value>
				<label>hpgl</label>
				<value>xterm</value>
				<label>xterm</label>
				<value>meta</value>
				<label>meta</label>
				<value>ps</value>
				<label>ps</label>
				<value>tek</value>
				<label>tek</label>
				<value>png</value>
				<label>png</label>
				<value>tektronics</value>
				<label>tektronics</label>
			</vlist>
		<vdef><value>postscript</value></vdef>
		<format>
			<language>perl</language>
			<code>($value)? " -graphlb=$value" : ""</code>
		</format>
		<group>4</group>
	</attributes>
	</parameter>

	</parameters>
</paragraph>
</parameter>

<parameter type="String" ishidden="1">
<name>auto</name>
<attributes>
	<format>
		<language>perl</language>
		<code>" -auto -stdout"</code>
	</format>
	<group>5</group>
</attributes>
</parameter>
<parameter type="String" ishidden="1">
<name>psouput</name>
<attributes>
	<precond>
		<language>perl</language>
		<code>$graphlb eq "postscript" || $graphlb eq "ps" || $graphlb eq "colourps"  || $graphlb eq "cps" || $graphlb eq "png"</code>
	</precond>
	<format>
		<language>perl</language>
		<code>" -goutfile=findkm"</code>
	</format>
	<group>100</group>
</attributes>
</parameter>
<parameter type="Results">
<name>psresults</name>
<attributes>
	<precond>
		<language>perl</language>
		<code>$graphlb eq "postscript" || $graphlb eq "ps" || $graphlb eq "colourps" || $graphlb eq "cps"</code>
	</precond>
	<filenames>*.ps</filenames>
</attributes>
</parameter>
<parameter type="Results">
<name>metaresults</name>
<attributes>
	<precond>
		<language>perl</language>
		<code>$graphlb eq "meta"</code>
	</precond>
	<filenames>*.meta</filenames>
</attributes>
</parameter>
<parameter type="Results">
<name>dataresults</name>
<attributes>
	<precond>
		<language>perl</language>
		<code>$graphlb eq "data"</code>
	</precond>
	<filenames>*.dat</filenames>
</attributes>
</parameter>
<parameter type="Results">
<name>pngresults</name>
<attributes>
	<precond>
		<language>perl</language>
		<code>$graphlb eq "png"</code>
	</precond>
	<filenames>*.png *.2 *.3</filenames>
</attributes>
</parameter>

</parameters>
</pise>
