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modified:
csem.xml |
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| diff -r d58769ed6a44 -r 32dd04a63316 csem.xml --- a/csem.xml Mon Sep 12 10:15:59 2011 -0400 +++ b/csem.xml Mon Sep 12 10:31:48 2011 -0400 |
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| @@ -50,11 +50,11 @@ <validator type="no_options" message="No indexes are available" /> </options> </param> - <param name="InfileFormat" type="select" label="Select file format to process" help="Bowtie accepts FASTA or FASTQ file formats."> - <option value="fasta">FASTA</option> - <option value="fastq">FASTQ</option> - </param> - <conditional name="InfileFormat"> + <conditional name="InputParams"> + <param name="InfileFormat" type="select" label="Select file format to process" help="Bowtie accepts FASTA or FASTQ file formats."> + <option value="fasta">FASTA</option> + <option value="fastq">FASTQ</option> + </param> <when value="fasta"> <param name="Input" type="data" format="fasta" label="FASTA file"/> </when> @@ -70,23 +70,23 @@ <param name="pseudoTag" type="select" label="Generate pseudo-tags?" help="See section 'Pseudo-tags' in the help below for more details."> <option value="N">NO</option> <option value="Y">YES</option> - </param> - <param name="bSettingsType" type="select" label="Bowtie settings to use" help="For most mapping applications, use the 'Commonly used' settings. If you want full control, use 'Full parameter list'."> - <option value="preSet">Commonly used</option> - <option value="full">Full parameter list</option> </param> - <conditional name="bSettingsType"> + <conditional name="bowtieParams"> + <param name="bSettingsType" type="select" label="Bowtie settings to use" help="For most mapping applications, use the 'Commonly used' settings. If you want full control, use 'Full parameter list'."> + <option value="preSet">Commonly used</option> + <option value="full">Full parameter list</option> + </param> <when value="preSet" /> <when value="full"> <param name="Mismatch" type="integer" value="2" label="Maximum number of mismatches permitted (-v)" help="May be 0, 1, 2, or 3." /> <param name="SuppressAlign" type="integer" value="99" label="Suppress all alignments for a read if more than n reportable alignments exist (-m)" help="99 is appropriate for most cases. Use -1 for no limit." /> </when> <!-- full --> - </conditional> <!-- bowtieParams --> - <param name="cSettingsType" type="select" label="CSEM settings to use" help="For most multi-read allocation applications, use the 'Commonly used' settings. If you want full control, use 'Full parameter list'."> - <option value="preSet">Commonly used</option> - <option value="full">Full parameter list</option> - </param> - <conditional name="cSettingsType"> + </conditional> <!-- bowtieParams --> + <conditional name="csemParams"> + <param name="cSettingsType" type="select" label="CSEM settings to use" help="For most multi-read allocation applications, use the 'Commonly used' settings. If you want full control, use 'Full parameter list'."> + <option value="preSet">Commonly used</option> + <option value="full">Full parameter list</option> + </param> <when value="preSet" /> <when value="full"> <param name="windowSize" type="integer" value="101" label="Window size for the multi-read allocator" help="Set window size to some odd number close to the half of average fragment length." /> |