Mercurial > repos > greg > extract_genomic_dna

comparison extract_genomic_dna.xml @ 18:ec35e8d25958 draft

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author greg
date Thu, 03 Mar 2016 14:52:47 -0500
parents 1a10864abc1f
children b212210c1808
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17:24c055f48065 18:ec35e8d25958
26 #else: 26 #else:
27 --reference_genome $reference_genome_cond.reference_genome 27 --reference_genome $reference_genome_cond.reference_genome
28 #end if 28 #end if
29 --output_format $output_format_cond.output_format 29 --output_format $output_format_cond.output_format
30 #if str($output_format_cond.output_format) == "fasta": 30 #if str($output_format_cond.output_format) == "fasta":
31 --description_field_delimiter $output_format_cond.description_field_delimiter 31 --fasta_header_type $output_format_cond.fasta_header_type_cond.fasta_header_type
32 #if str($output_format_cond.fasta_header_type_cond.fasta_header_type) == "char_delimited":
33 --fasta_header_delimiter $output_format_cond.fasta_header_type_cond.fasta_header_delimiter
34 #end if
32 #end if 35 #end if
33 --output $output 36 --output $output
34 ]]> 37 ]]>
35 </command> 38 </command>
36 <inputs> 39 <inputs>
67 <param name="output_format" type="select" label="Select output format"> 70 <param name="output_format" type="select" label="Select output format">
68 <option value="fasta" selected="True">fasta</option> 71 <option value="fasta" selected="True">fasta</option>
69 <option value="interval">interval</option> 72 <option value="interval">interval</option>
70 </param> 73 </param>
71 <when value="fasta"> 74 <when value="fasta">
72 <param name="description_field_delimiter" type="select" label="Select description field delimiter" help="Character delimiter for words in description line"> 75 <conditional name="fasta_header_type_cond">
73 <option value="underscore" selected="True">underscore (_)</option> 76 <param name="fasta_header_type" type="select" label="Select fasta header format">
74 <option value="semicolon">semicolon (;)</option> 77 <option value="bedtools_getfasta_default" selected="True">bedtools getfasta default</option>
75 <option value="comma">comma (,)</option> 78 <option value="char_delimited">character delimited field values</option>
76 <option value="tilda">tilda (~)</option> 79 </param>
77 <option value="vetical_bar">vertical bar (|)</option> 80 <when value="bedtools_getfasta_default"/>
78 </param> 81 <when value="char_delimited">
82 <param name="fasta_header_delimiter" type="select" label="Select fasta header field delimiter">
83 <option value="underscore" selected="True">underscore (_)</option>
84 <option value="semicolon">semicolon (;)</option>
85 <option value="comma">comma (,)</option>
86 <option value="tilda">tilda (~)</option>
87 <option value="vetical_bar">vertical bar (|)</option>
88 </param>
89 </when>
90 </conditional>
79 </when> 91 </when>
80 <when value="interval"/> 92 <when value="interval"/>
81 </conditional> 93 </conditional>
82 </inputs> 94 </inputs>
83 <outputs> 95 <outputs>
91 <test> 103 <test>
92 <param name="input" value="1.bed" dbkey="hg17" ftype="bed" /> 104 <param name="input" value="1.bed" dbkey="hg17" ftype="bed" />
93 <param name="interpret_features" value="yes"/> 105 <param name="interpret_features" value="yes"/>
94 <param name="index_source" value="cached"/> 106 <param name="index_source" value="cached"/>
95 <param name="out_format" value="fasta"/> 107 <param name="out_format" value="fasta"/>
96 <param name="description_field_delimiter" value="underscore"/> 108 <param name="fasta_header_type" value="char_delimited"/>
109 <param name="fasta_header_delimiter" value="underscore"/>
97 <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" />
98 </test> 111 </test>
99 <test> 112 <test>
100 <param name="input" value="droPer1.bed" dbkey="droPer1" ftype="bed" /> 113 <param name="input" value="droPer1.bed" dbkey="droPer1" ftype="bed" />
101 <param name="interpret_features" value="yes"/> 114 <param name="interpret_features" value="yes"/>
102 <param name="index_source" value="cached"/> 115 <param name="index_source" value="cached"/>
103 <param name="out_format" value="fasta"/> 116 <param name="out_format" value="fasta"/>
104 <param name="description_field_delimiter" value="underscore"/> 117 <param name="fasta_header_type" value="char_delimited"/>
118 <param name="fasta_header_delimiter" value="underscore"/>
105 <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" />
106 </test> 120 </test>
107 <test> 121 <test>
108 <param name="input" value="1.bed" dbkey="hg17" ftype="bed" /> 122 <param name="input" value="1.bed" dbkey="hg17" ftype="bed" />
109 <param name="interpret_features" value="yes"/> 123 <param name="interpret_features" value="yes"/>
122 <test> 136 <test>
123 <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" />
124 <param name="interpret_features" value="no"/> 138 <param name="interpret_features" value="no"/>
125 <param name="index_source" value="cached"/> 139 <param name="index_source" value="cached"/>
126 <param name="out_format" value="fasta"/> 140 <param name="out_format" value="fasta"/>
127 <param name="description_field_delimiter" value="underscore"/> 141 <param name="fasta_header_type" value="char_delimited"/>
142 <param name="fasta_header_delimiter" value="underscore"/>
128 <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" />
129 </test> 144 </test>
130 <!-- Test custom sequences support and GFF feature interpretation. --> 145 <!-- Test custom sequences support and GFF feature interpretation. -->
131 <test> 146 <test>
132 <param name="input" value="cufflinks_out1.gtf" dbkey="mm9" ftype="gff" /> 147 <param name="input" value="cufflinks_out1.gtf" dbkey="mm9" ftype="gff" />
133 <param name="interpret_features" value="no"/> 148 <param name="interpret_features" value="no"/>
134 <param name="index_source" value="history"/> 149 <param name="index_source" value="history"/>
135 <param name="ref_file" value="tophat_in1.fasta"/> 150 <param name="ref_file" value="tophat_in1.fasta"/>
136 <param name="out_format" value="fasta"/> 151 <param name="out_format" value="fasta"/>
137 <param name="description_field_delimiter" value="underscore"/> 152 <param name="fasta_header_type" value="char_delimited"/>
153 <param name="fasta_header_delimiter" value="underscore"/>
138 <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" />
139 </test> 155 </test>
140 <test> 156 <test>
141 <param name="input" value="cufflinks_out1.gtf" dbkey="mm9" ftype="gff" /> 157 <param name="input" value="cufflinks_out1.gtf" dbkey="mm9" ftype="gff" />
142 <param name="interpret_features" value="yes"/> 158 <param name="interpret_features" value="yes"/>
143 <param name="index_source" value="history"/> 159 <param name="index_source" value="history"/>
144 <param name="ref_file" value="tophat_in1.fasta"/> 160 <param name="ref_file" value="tophat_in1.fasta"/>
145 <param name="out_format" value="fasta"/> 161 <param name="out_format" value="fasta"/>
146 <param name="description_field_delimiter" value="underscore"/> 162 <param name="fasta_header_type" value="bedtools_getfasta_default"/>
147 <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" />
148 </test> 164 </test>
149 </tests> 165 </tests>
150 <help> 166 <help>
151 167
168 ----- 184 -----
169 185
170 **What it does** 186 **What it does**
171 187
172 This tool uses coordinate, strand, and build information to fetch genomic DNAs in FASTA or interval format. 188 This tool uses coordinate, strand, and build information to fetch genomic DNAs in FASTA or interval format.
173 If the output format is FASTA, the character delimiter can be selected for the fields in the description. 189 If the output format is FASTA, the header format can be specified.
174 For example, selecting an underscore will produce a description like this: 190
175 191 Selecting the **bedtools getfasta default** option produces a FASTA heder formatted like the default header
176 >gi_31563518_ref_NP_852610.1 192 produced the the bedtools getfasta tool, and the "force strandedness" option is assumed. If the input data
193 includes a strand column and the strand is '+' or '-', it is included in the header. If the input data includes
194 a strand column and the value of strand is anything but '+' or '-', a '.' is included in the header. If the
195 input data does not include a strand column, a '.' is included in the header.
196
197 An example FASTA header produced by selecting this option is:
198
199 &gt;chr7:127475281-127475310(+)
200
201 Selecing the **character delimited field values** option allows selection of a character delimiter that is used
202 when generating the FASTA header with fields genome, chrom, start, end, strand (name) delimited by the
203 selected character. For example, selecting an underscore will produce a FASTA header like this:
204
205 &gt;mm9_53_550_+ test_chromosome
177 206
178 while selecting a vertical bar will produce a description like this: 207 while selecting a vertical bar will produce a description like this:
179 208
180 >gi|31563518|ref|NP_852610.1 209 &gt;mm9|53|550|+ test_chromosome
181 210
182 If strand is not defined, the default value is "+". 211 If strand is not defined, the default value is "+".
183 212
184 ----- 213 -----
185 214