Mercurial > repos > dongjun > csem
comparison csem.xml @ 7:32dd04a63316
Uploaded
| author | dongjun |
|---|---|
| date | Mon, 12 Sep 2011 10:31:48 -0400 |
| parents | d58769ed6a44 |
| children |
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| 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 --> |