Mercurial > repos > greg > extract_genomic_dna

comparison extract_genomic_dna.xml @ 23:23eaaaf7902e draft default tip

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author greg
date Sat, 05 Mar 2016 15:11:52 -0500
parents 2b565382e469
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22:2b565382e469 23:23eaaaf7902e
1 <tool id="Extract genomic DNA 1" name="Extract Genomic DNA" version="3.0.2"> 1 <tool id="Extract genomic DNA 1" name="Extract Genomic DNA" version="3.0.2">
2 <description>using coordinates from assembled/unassembled genomes</description> 2 <description>using coordinates from assembled/unassembled genomes</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="35x1">faToTwoBit</requirement>
4 <requirement type="package" version="0.7.1">bx-python</requirement> 5 <requirement type="package" version="0.7.1">bx-python</requirement>
5 <requirement type="package" version="35x1">faToTwoBit</requirement> 6 <!-- conda dependencies -->
7 <requirement type="package" version="324">ucsc-fatotwobit</requirement>
6 </requirements> 8 </requirements>
7 <command> 9 <command>
8 <![CDATA[ 10 <![CDATA[
9 #set genome = $input.metadata.dbkey 11 #set genome = $input.metadata.dbkey
10 #set datatype = $input.datatype 12 #set datatype = $input.datatype
99 </change_format> 101 </change_format>
100 </data> 102 </data>
101 </outputs> 103 </outputs>
102 <tests> 104 <tests>
103 <test> 105 <test>
104 <param name="input" value="1.bed" dbkey="hg17" ftype="bed" /> 106 <param name="input" value="mm9_input1.gff" dbkey="mm9" ftype="gff" />
105 <param name="interpret_features" value="yes"/> 107 <param name="interpret_features" value="no"/>
106 <param name="index_source" value="cached"/> 108 <param name="reference_genome_source" value="history"/>
109 <param name="reference_genome" value="mm9.fasta"/>
107 <param name="output_format" value="fasta"/> 110 <param name="output_format" value="fasta"/>
108 <param name="fasta_header_type" value="char_delimited"/> 111 <param name="fasta_header_type" value="char_delimited"/>
109 <param name="fasta_header_delimiter" value="underscore"/> 112 <param name="fasta_header_delimiter" value="tilde"/>
110 <output name="out_file1" file="extract_genomic_dna_out1.fasta" compare="contains" /> 113 <output name="output" file="extract_genomic_dna_out1.fasta" compare="contains" />
111 </test> 114 </test>
112 <test> 115 <test>
113 <param name="input" value="droPer1.bed" dbkey="droPer1" ftype="bed" /> 116 <param name="input" value="mm9_input1.gff" dbkey="mm9" ftype="gff" />
114 <param name="interpret_features" value="yes"/> 117 <param name="interpret_features" value="yes"/>
115 <param name="index_source" value="cached"/> 118 <param name="reference_genome_source" value="history"/>
116 <param name="output_format" value="fasta"/> 119 <param name="reference_genome" value="mm9.fasta"/>
117 <param name="fasta_header_type" value="char_delimited"/>
118 <param name="fasta_header_delimiter" value="underscore"/>
119 <output name="out_file1" file="extract_genomic_dna_out2.fasta" compare="contains" />
120 </test>
121 <test>
122 <param name="input" value="1.bed" dbkey="hg17" ftype="bed" />
123 <param name="interpret_features" value="yes"/>
124 <param name="index_source" value="cached"/>
125 <param name="output_format" value="interval"/>
126 <output name="out_file1" file="extract_genomic_dna_out3.interval" compare="contains" />
127 </test>
128 <!-- Test GFF file support. -->
129 <test>
130 <param name="input" value="gff_filter_by_attribute_out1.gff" dbkey="mm9" ftype="gff" />
131 <param name="interpret_features" value="no"/>
132 <param name="index_source" value="cached"/>
133 <param name="output_format" value="interval"/>
134 <output name="out_file1" file="extract_genomic_dna_out4.gff" compare="contains" />
135 </test>
136 <test>
137 <param name="input" value="gff_filter_by_attribute_out1.gff" dbkey="mm9" ftype="gff" />
138 <param name="interpret_features" value="no"/>
139 <param name="index_source" value="cached"/>
140 <param name="output_format" value="fasta"/>
141 <param name="fasta_header_type" value="char_delimited"/>
142 <param name="fasta_header_delimiter" value="underscore"/>
143 <output name="out_file1" file="extract_genomic_dna_out5.fasta" compare="contains" />
144 </test>
145 <!-- Test custom sequences support and GFF feature interpretation. -->
146 <test>
147 <param name="input" value="cufflinks_out1.gtf" dbkey="mm9" ftype="gff" />
148 <param name="interpret_features" value="no"/>
149 <param name="index_source" value="history"/>
150 <param name="ref_file" value="tophat_in1.fasta"/>
151 <param name="output_format" value="fasta"/>
152 <param name="fasta_header_type" value="char_delimited"/>
153 <param name="fasta_header_delimiter" value="underscore"/>
154 <output name="out_file1" file="extract_genomic_dna_out6.fasta" compare="contains" />
155 </test>
156 <test>
157 <param name="input" value="cufflinks_out1.gtf" dbkey="mm9" ftype="gff" />
158 <param name="interpret_features" value="yes"/>
159 <param name="index_source" value="history"/>
160 <param name="ref_file" value="tophat_in1.fasta"/>
161 <param name="output_format" value="fasta"/> 120 <param name="output_format" value="fasta"/>
162 <param name="fasta_header_type" value="bedtools_getfasta_default"/> 121 <param name="fasta_header_type" value="bedtools_getfasta_default"/>
163 <output name="out_file1" file="extract_genomic_dna_out7.fasta" compare="contains" /> 122 <output name="output" file="extract_genomic_dna_out2.fasta" compare="contains" />
123 </test>
124 <test>
125 <param name="input" value="mm9_input1.gff" dbkey="mm9" ftype="gff" />
126 <param name="interpret_features" value="no"/>
127 <param name="reference_genome_source" value="history"/>
128 <param name="reference_genome" value="mm9.fasta"/>
129 <param name="output_format" value="interval"/>
130 <output name="output" file="extract_genomic_dna_out3.gff" compare="contains" />
131 </test>
132 <test>
133 <param name="input" value="mm9_input1.gff" dbkey="mm9" ftype="gff" />
134 <param name="interpret_features" value="yes"/>
135 <param name="reference_genome_source" value="history"/>
136 <param name="reference_genome" value="mm9.fasta"/>
137 <param name="output_format" value="interval"/>
138 <output name="output" file="extract_genomic_dna_out4.gff" compare="contains" />
164 </test> 139 </test>
165 </tests> 140 </tests>
166 <help> 141 <help>
167 142
168 .. class:: warningmark 143 .. class:: warningmark