Mercurial > repos > greg > extract_genomic_dna

comparison extract_genomic_dna.xml @ 22:2b565382e469 draft

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author greg
date Fri, 04 Mar 2016 07:58:39 -0500
parents 5e839bb29ba9
children 23eaaaf7902e
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21:2a80b722679c 22:2b565382e469
81 <when value="char_delimited"> 81 <when value="char_delimited">
82 <param name="fasta_header_delimiter" type="select" label="Select fasta header field delimiter"> 82 <param name="fasta_header_delimiter" type="select" label="Select fasta header field delimiter">
83 <option value="underscore" selected="True">underscore (_)</option> 83 <option value="underscore" selected="True">underscore (_)</option>
84 <option value="semicolon">semicolon (;)</option> 84 <option value="semicolon">semicolon (;)</option>
85 <option value="comma">comma (,)</option> 85 <option value="comma">comma (,)</option>
86 <option value="tilda">tilda (~)</option> 86 <option value="tilde">tilde (~)</option>
87 <option value="vetical_bar">vertical bar (|)</option> 87 <option value="vertical_bar">vertical bar (|)</option>
88 </param> 88 </param>
89 </when> 89 </when>
90 </conditional> 90 </conditional>
91 </when> 91 </when>
92 <when value="interval"/> 92 <when value="interval"/>
102 <tests> 102 <tests>
103 <test> 103 <test>
104 <param name="input" value="1.bed" dbkey="hg17" ftype="bed" /> 104 <param name="input" value="1.bed" dbkey="hg17" ftype="bed" />
105 <param name="interpret_features" value="yes"/> 105 <param name="interpret_features" value="yes"/>
106 <param name="index_source" value="cached"/> 106 <param name="index_source" value="cached"/>
107 <param name="out_format" value="fasta"/> 107 <param name="output_format" value="fasta"/>
108 <param name="fasta_header_type" value="char_delimited"/> 108 <param name="fasta_header_type" value="char_delimited"/>
109 <param name="fasta_header_delimiter" value="underscore"/> 109 <param name="fasta_header_delimiter" value="underscore"/>
110 <output name="out_file1" file="extract_genomic_dna_out1.fasta" compare="contains" /> 110 <output name="out_file1" file="extract_genomic_dna_out1.fasta" compare="contains" />
111 </test> 111 </test>
112 <test> 112 <test>
113 <param name="input" value="droPer1.bed" dbkey="droPer1" ftype="bed" /> 113 <param name="input" value="droPer1.bed" dbkey="droPer1" ftype="bed" />
114 <param name="interpret_features" value="yes"/> 114 <param name="interpret_features" value="yes"/>
115 <param name="index_source" value="cached"/> 115 <param name="index_source" value="cached"/>
116 <param name="out_format" value="fasta"/> 116 <param name="output_format" value="fasta"/>
117 <param name="fasta_header_type" value="char_delimited"/> 117 <param name="fasta_header_type" value="char_delimited"/>
118 <param name="fasta_header_delimiter" value="underscore"/> 118 <param name="fasta_header_delimiter" value="underscore"/>
119 <output name="out_file1" file="extract_genomic_dna_out2.fasta" compare="contains" /> 119 <output name="out_file1" file="extract_genomic_dna_out2.fasta" compare="contains" />
120 </test> 120 </test>
121 <test> 121 <test>
122 <param name="input" value="1.bed" dbkey="hg17" ftype="bed" /> 122 <param name="input" value="1.bed" dbkey="hg17" ftype="bed" />
123 <param name="interpret_features" value="yes"/> 123 <param name="interpret_features" value="yes"/>
124 <param name="index_source" value="cached"/> 124 <param name="index_source" value="cached"/>
125 <param name="out_format" value="interval"/> 125 <param name="output_format" value="interval"/>
126 <output name="out_file1" file="extract_genomic_dna_out3.interval" compare="contains" /> 126 <output name="out_file1" file="extract_genomic_dna_out3.interval" compare="contains" />
127 </test> 127 </test>
128 <!-- Test GFF file support. --> 128 <!-- Test GFF file support. -->
129 <test> 129 <test>
130 <param name="input" value="gff_filter_by_attribute_out1.gff" dbkey="mm9" ftype="gff" /> 130 <param name="input" value="gff_filter_by_attribute_out1.gff" dbkey="mm9" ftype="gff" />
131 <param name="interpret_features" value="no"/> 131 <param name="interpret_features" value="no"/>
132 <param name="index_source" value="cached"/> 132 <param name="index_source" value="cached"/>
133 <param name="out_format" value="interval"/> 133 <param name="output_format" value="interval"/>
134 <output name="out_file1" file="extract_genomic_dna_out4.gff" compare="contains" /> 134 <output name="out_file1" file="extract_genomic_dna_out4.gff" compare="contains" />
135 </test> 135 </test>
136 <test> 136 <test>
137 <param name="input" value="gff_filter_by_attribute_out1.gff" dbkey="mm9" ftype="gff" /> 137 <param name="input" value="gff_filter_by_attribute_out1.gff" dbkey="mm9" ftype="gff" />
138 <param name="interpret_features" value="no"/> 138 <param name="interpret_features" value="no"/>
139 <param name="index_source" value="cached"/> 139 <param name="index_source" value="cached"/>
140 <param name="out_format" value="fasta"/> 140 <param name="output_format" value="fasta"/>
141 <param name="fasta_header_type" value="char_delimited"/> 141 <param name="fasta_header_type" value="char_delimited"/>
142 <param name="fasta_header_delimiter" value="underscore"/> 142 <param name="fasta_header_delimiter" value="underscore"/>
143 <output name="out_file1" file="extract_genomic_dna_out5.fasta" compare="contains" /> 143 <output name="out_file1" file="extract_genomic_dna_out5.fasta" compare="contains" />
144 </test> 144 </test>
145 <!-- Test custom sequences support and GFF feature interpretation. --> 145 <!-- Test custom sequences support and GFF feature interpretation. -->
146 <test> 146 <test>
147 <param name="input" value="cufflinks_out1.gtf" dbkey="mm9" ftype="gff" /> 147 <param name="input" value="cufflinks_out1.gtf" dbkey="mm9" ftype="gff" />
148 <param name="interpret_features" value="no"/> 148 <param name="interpret_features" value="no"/>
149 <param name="index_source" value="history"/> 149 <param name="index_source" value="history"/>
150 <param name="ref_file" value="tophat_in1.fasta"/> 150 <param name="ref_file" value="tophat_in1.fasta"/>
151 <param name="out_format" value="fasta"/> 151 <param name="output_format" value="fasta"/>
152 <param name="fasta_header_type" value="char_delimited"/> 152 <param name="fasta_header_type" value="char_delimited"/>
153 <param name="fasta_header_delimiter" value="underscore"/> 153 <param name="fasta_header_delimiter" value="underscore"/>
154 <output name="out_file1" file="extract_genomic_dna_out6.fasta" compare="contains" /> 154 <output name="out_file1" file="extract_genomic_dna_out6.fasta" compare="contains" />
155 </test> 155 </test>
156 <test> 156 <test>
157 <param name="input" value="cufflinks_out1.gtf" dbkey="mm9" ftype="gff" /> 157 <param name="input" value="cufflinks_out1.gtf" dbkey="mm9" ftype="gff" />
158 <param name="interpret_features" value="yes"/> 158 <param name="interpret_features" value="yes"/>
159 <param name="index_source" value="history"/> 159 <param name="index_source" value="history"/>
160 <param name="ref_file" value="tophat_in1.fasta"/> 160 <param name="ref_file" value="tophat_in1.fasta"/>
161 <param name="out_format" value="fasta"/> 161 <param name="output_format" value="fasta"/>
162 <param name="fasta_header_type" value="bedtools_getfasta_default"/> 162 <param name="fasta_header_type" value="bedtools_getfasta_default"/>
163 <output name="out_file1" file="extract_genomic_dna_out7.fasta" compare="contains" /> 163 <output name="out_file1" file="extract_genomic_dna_out7.fasta" compare="contains" />
164 </test> 164 </test>
165 </tests> 165 </tests>
166 <help> 166 <help>
218 218
219 chr7 127475281 127475310 NM_000230 0 + 219 chr7 127475281 127475310 NM_000230 0 +
220 chr7 127485994 127486166 NM_000230 0 + 220 chr7 127485994 127486166 NM_000230 0 +
221 chr7 127486011 127486166 D49487 0 + 221 chr7 127486011 127486166 D49487 0 +
222 222
223 Extracting sequences with **FASTA** output data type and **Description Field Delimiter** set to the underscore character returns:: 223 Extracting sequences with **FASTA** output data type, **character delimited field values** as header format and **header field delimiter** set to the underscore character returns::
224 224
225 &gt;hg17_chr7_127475281_127475310_+ NM_000230 225 &gt;hg17_chr7_127475281_127475310_+ NM_000230
226 GTAGGAATCGCAGCGCCAGCGGTTGCAAG 226 GTAGGAATCGCAGCGCCAGCGGTTGCAAG
227 &gt;hg17_chr7_127485994_127486166_+ NM_000230 227 &gt;hg17_chr7_127485994_127486166_+ NM_000230
228 GCCCAAGAAGCCCATCCTGGGAAGGAAAATGCATTGGGGAACCCTGTGCG 228 GCCCAAGAAGCCCATCCTGGGAAGGAAAATGCATTGGGGAACCCTGTGCG
243 243
244 </help> 244 </help>
245 <citations> 245 <citations>
246 <citation type="bibtex"> 246 <citation type="bibtex">
247 @unpublished{None, 247 @unpublished{None,
248 author = {Guru Ananda, Greg Von Kuster}, 248 author = {Guru Ananda,Greg Von Kuster},
249 title = {None}, 249 title = {None},
250 year = {None}, 250 year = {None},
251 eprint = {None}, 251 eprint = {None},
252 url = {http://www.bx.psu.edu/~anton/labSite/} 252 url = {http://www.bx.psu.edu/~anton/labSite/}
253 }</citation> 253 }</citation>