Mercurial > repos > greg > extract_genomic_dna

comparison extract_genomic_dna.xml @ 6:3d40351fc9ac draft

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author greg
date Thu, 14 Jan 2016 10:51:45 -0500
parents cc1879e0b0ae
children 338e991cdd1f
comparison
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5:ee00b3c68801 6:3d40351fc9ac
3 <requirements> 3 <requirements>
4 <requirement type="package" version="35x1">faToTwoBit</requirement> 4 <requirement type="package" version="35x1">faToTwoBit</requirement>
5 </requirements> 5 </requirements>
6 <command> 6 <command>
7 <![CDATA[ 7 <![CDATA[
8 #set input_format = $input.ext
9 #set genome = $input.metadata.dbkey 8 #set genome = $input.metadata.dbkey
10 #set datatype = $input.datatype 9 #set datatype = $input.datatype
11 mkdir -p output_dir && 10 mkdir -p output_dir &&
12 python $__tool_directory__/extract_genomic_dna.py 11 python $__tool_directory__/extract_genomic_dna.py
13 --input_format $input_format
14 --input "$input" 12 --input "$input"
15 --genome "$genome" 13 --genome "$genome"
16 #if str($input_format) == "gff": 14 #if isinstance($datatype, $__app__.datatypes_registry.get_datatype_by_extension('gff').__class__):
15 --input_format "gff"
16 --columns "1,4,5,7"
17 --interpret_features $interpret_features 17 --interpret_features $interpret_features
18 #end if
19 #if isinstance($datatype, $__app__.datatypes_registry.get_datatype_by_extension('gff').__class__):
20 --columns "1,4,5,7"
21 #else: 18 #else:
19 --input_format "interval"
22 --columns "${input.metadata.chromCol},${input.metadata.startCol},${input.metadata.endCol},${input.metadata.strandCol},${input.metadata.nameCol}" 20 --columns "${input.metadata.chromCol},${input.metadata.startCol},${input.metadata.endCol},${input.metadata.strandCol},${input.metadata.nameCol}"
23 #end if 21 #end if
24 --reference_genome_source $reference_genome_cond.reference_genome_source 22 --reference_genome_source $reference_genome_cond.reference_genome_source
25 #if str($reference_genome_cond.reference_genome_source) == "cached" 23 #if str($reference_genome_cond.reference_genome_source) == "cached"
26 --reference_genome $reference_genome_cond.reference_genome.fields.path 24 --reference_genome $reference_genome_cond.reference_genome.fields.path
77 <test> 75 <test>
78 <param name="input" value="1.bed" dbkey="hg17" ftype="bed" /> 76 <param name="input" value="1.bed" dbkey="hg17" ftype="bed" />
79 <param name="interpret_features" value="yes"/> 77 <param name="interpret_features" value="yes"/>
80 <param name="index_source" value="cached"/> 78 <param name="index_source" value="cached"/>
81 <param name="out_format" value="fasta"/> 79 <param name="out_format" value="fasta"/>
82 <output name="out_file1"> 80 <output name="out_file1" file="extract_genomic_dna_out1.fasta">
83 <assert_contents> 81 <assert_contents>
84 <!-- First few lines... --> 82 <!-- First few lines... -->
85 <has_text text=">hg17_chr1_147962192_147962580_- CCDS989.1_cds_0_0_chr1_147962193_r" /> 83 <has_text text=">hg17_chr1_147962192_147962580_- CCDS989.1_cds_0_0_chr1_147962193_r" />
86 <has_text text="ACTTGATCCTGCTCCCTCGGTGTCTGCATTGACTCCTCATGCTGGGACTG" /> 84 <has_text text="ACTTGATCCTGCTCCCTCGGTGTCTGCATTGACTCCTCATGCTGGGACTG" />
87 <has_text text="GACCCGTCAACCCCCCTGCTCGCTGCTCACGTACCTTCATCACTTTTAGT" /> 85 <has_text text="GACCCGTCAACCCCCCTGCTCGCTGCTCACGTACCTTCATCACTTTTAGT" />
98 <test> 96 <test>
99 <param name="input" value="droPer1.bed" dbkey="droPer1" ftype="bed" /> 97 <param name="input" value="droPer1.bed" dbkey="droPer1" ftype="bed" />
100 <param name="interpret_features" value="yes"/> 98 <param name="interpret_features" value="yes"/>
101 <param name="index_source" value="cached"/> 99 <param name="index_source" value="cached"/>
102 <param name="out_format" value="fasta"/> 100 <param name="out_format" value="fasta"/>
103 <output name="out_file1" file="extract_genomic_dna_out2.fasta" /> 101 <output name="out_file1" file="extract_genomic_dna_out2.fasta" compare="contains"/>
104 </test> 102 </test>
105 <test> 103 <test>
106 <param name="input" value="1.bed" dbkey="hg17" ftype="bed" /> 104 <param name="input" value="1.bed" dbkey="hg17" ftype="bed" />
107 <param name="interpret_features" value="yes"/> 105 <param name="interpret_features" value="yes"/>
108 <param name="index_source" value="cached"/> 106 <param name="index_source" value="cached"/>
113 <test> 111 <test>
114 <param name="input" value="gff_filter_by_attribute_out1.gff" dbkey="mm9" ftype="gff" /> 112 <param name="input" value="gff_filter_by_attribute_out1.gff" dbkey="mm9" ftype="gff" />
115 <param name="interpret_features" value="no"/> 113 <param name="interpret_features" value="no"/>
116 <param name="index_source" value="cached"/> 114 <param name="index_source" value="cached"/>
117 <param name="out_format" value="interval"/> 115 <param name="out_format" value="interval"/>
118 <output name="out_file1" file="extract_genomic_dna_out4.gff" /> 116 <output name="out_file1" file="extract_genomic_dna_out4.gff" compare="contains"/>
119 </test> 117 </test>
120 <test> 118 <test>
121 <param name="input" value="gff_filter_by_attribute_out1.gff" dbkey="mm9" ftype="gff" /> 119 <param name="input" value="gff_filter_by_attribute_out1.gff" dbkey="mm9" ftype="gff" />
122 <param name="interpret_features" value="no"/> 120 <param name="interpret_features" value="no"/>
123 <param name="out_format" value="fasta"/> 121 <param name="out_format" value="fasta"/>
124 <param name="index_source" value="cached"/> 122 <param name="index_source" value="cached"/>
125 <output name="out_file1" file="extract_genomic_dna_out5.fasta" /> 123 <output name="out_file1" file="extract_genomic_dna_out5.fasta" compare="contains"/>
126 </test> 124 </test>
127 <!-- Test custom sequences support and GFF feature interpretation. --> 125 <!-- Test custom sequences support and GFF feature interpretation. -->
128 <test> 126 <test>
129 <param name="input" value="cufflinks_out1.gtf" dbkey="mm9" ftype="gff" /> 127 <param name="input" value="cufflinks_out1.gtf" dbkey="mm9" ftype="gff" />
130 <param name="interpret_features" value="no"/> 128 <param name="interpret_features" value="no"/>
131 <param name="index_source" value="history"/> 129 <param name="index_source" value="history"/>
132 <param name="ref_file" value="tophat_in1.fasta"/> 130 <param name="ref_file" value="tophat_in1.fasta"/>
133 <param name="out_format" value="fasta"/> 131 <param name="out_format" value="fasta"/>
134 <output name="out_file1" file="extract_genomic_dna_out6.fasta" /> 132 <output name="out_file1" file="extract_genomic_dna_out6.fasta" compare="contains"/>
135 </test> 133 </test>
136 <test> 134 <test>
137 <param name="input" value="cufflinks_out1.gtf" dbkey="mm9" ftype="gff" /> 135 <param name="input" value="cufflinks_out1.gtf" dbkey="mm9" ftype="gff" />
138 <param name="interpret_features" value="yes"/> 136 <param name="interpret_features" value="yes"/>
139 <param name="index_source" value="history"/> 137 <param name="index_source" value="history"/>
140 <param name="ref_file" value="tophat_in1.fasta"/> 138 <param name="ref_file" value="tophat_in1.fasta"/>
141 <param name="out_format" value="fasta"/> 139 <param name="out_format" value="fasta"/>
142 <output name="out_file1" file="extract_genomic_dna_out7.fasta" /> 140 <output name="out_file1" file="extract_genomic_dna_out7.fasta" compare="contains"/>
143 </test> 141 </test>
144 </tests> 142 </tests>
145 <help> 143 <help>
146 144
147 .. class:: warningmark 145 .. class:: warningmark