Mercurial > repos > dongjun > csem

comparison csem.xml @ 7:32dd04a63316

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author dongjun
date Mon, 12 Sep 2011 10:31:48 -0400
parents d58769ed6a44
children
comparison
equal deleted inserted replaced
6:d58769ed6a44 7:32dd04a63316
48 <options from_data_table="bowtie_indexes"> 48 <options from_data_table="bowtie_indexes">
49 <filter type="sort_by" column="2" /> 49 <filter type="sort_by" column="2" />
50 <validator type="no_options" message="No indexes are available" /> 50 <validator type="no_options" message="No indexes are available" />
51 </options> 51 </options>
52 </param> 52 </param>
53 <param name="InfileFormat" type="select" label="Select file format to process" help="Bowtie accepts FASTA or FASTQ file formats."> 53 <conditional name="InputParams">
54 <option value="fasta">FASTA</option> 54 <param name="InfileFormat" type="select" label="Select file format to process" help="Bowtie accepts FASTA or FASTQ file formats.">
55 <option value="fastq">FASTQ</option> 55 <option value="fasta">FASTA</option>
56 </param> 56 <option value="fastq">FASTQ</option>
57 <conditional name="InfileFormat"> 57 </param>
58 <when value="fasta"> 58 <when value="fasta">
59 <param name="Input" type="data" format="fasta" label="FASTA file"/> 59 <param name="Input" type="data" format="fasta" label="FASTA file"/>
60 </when> 60 </when>
61 <when value="fastq"> 61 <when value="fastq">
62 <param name="Input" type="data" format="fastq,fastqsanger,fastqillumina,fastqsolexa" label="FASTQ file"/> 62 <param name="Input" type="data" format="fastq,fastqsanger,fastqillumina,fastqsolexa" label="FASTQ file"/>
68 <option value="table">table</option> 68 <option value="table">table</option>
69 </param> 69 </param>
70 <param name="pseudoTag" type="select" label="Generate pseudo-tags?" help="See section 'Pseudo-tags' in the help below for more details."> 70 <param name="pseudoTag" type="select" label="Generate pseudo-tags?" help="See section 'Pseudo-tags' in the help below for more details.">
71 <option value="N">NO</option> 71 <option value="N">NO</option>
72 <option value="Y">YES</option> 72 <option value="Y">YES</option>
73 </param>
74 <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'.">
75 <option value="preSet">Commonly used</option>
76 <option value="full">Full parameter list</option>
77 </param> 73 </param>
78 <conditional name="bSettingsType"> 74 <conditional name="bowtieParams">
75 <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'.">
76 <option value="preSet">Commonly used</option>
77 <option value="full">Full parameter list</option>
78 </param>
79 <when value="preSet" /> 79 <when value="preSet" />
80 <when value="full"> 80 <when value="full">
81 <param name="Mismatch" type="integer" value="2" label="Maximum number of mismatches permitted (-v)" help="May be 0, 1, 2, or 3." /> 81 <param name="Mismatch" type="integer" value="2" label="Maximum number of mismatches permitted (-v)" help="May be 0, 1, 2, or 3." />
82 <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." /> 82 <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." />
83 </when> <!-- full --> 83 </when> <!-- full -->
84 </conditional> <!-- bowtieParams --> 84 </conditional> <!-- bowtieParams -->
85 <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'."> 85 <conditional name="csemParams">
86 <option value="preSet">Commonly used</option> 86 <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'.">
87 <option value="full">Full parameter list</option> 87 <option value="preSet">Commonly used</option>
88 </param> 88 <option value="full">Full parameter list</option>
89 <conditional name="cSettingsType"> 89 </param>
90 <when value="preSet" /> 90 <when value="preSet" />
91 <when value="full"> 91 <when value="full">
92 <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." /> 92 <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." />
93 <param name="nIteration" type="integer" value="200" label="Number of iterations for the multi-read allocator" help="200 is appropriate for most cases." /> 93 <param name="nIteration" type="integer" value="200" label="Number of iterations for the multi-read allocator" help="200 is appropriate for most cases." />
94 </when> <!-- full --> 94 </when> <!-- full -->