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Daniel Blankenberg
250da4e41f
negative strand. When extracting alignments corresponding to intervals, the alignments are now output according to the strand specified in the interval file. New test data is forthcoming.
36 lines
1.6 KiB
XML
36 lines
1.6 KiB
XML
<tool id="Interval_Maf_Merged_Fasta1" name="Extract Interval blocks">
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<description>from locally cached alignments</description>
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<command interpreter="python2.4">interval_maf_to_merged_fasta.py $dbkey $species $mafSource $input1 $out_file1 $input1_chromCol $input1_startCol $input1_endCol $input1_strandCol -</command>
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<inputs>
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<page>
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<param format="interval" name="input1" type="data" label="Interval File"/>
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<!-- <param name="unkown_gap_char" type="select">
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<label>Character for missing data</label>
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<option value="-">-</option>
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<option value="?">?</option>
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</param> -->
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</page>
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<page>
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<param name="mafSource" label="Choose MAF source" type="select" dynamic_options="get_available_data( input1.dbkey )"/>
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</page>
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<page>
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<param name="species" label="Choose desired species" type="select" display="checkboxes" multiple="True" dynamic_options="get_available_species( mafSource )"/>
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</page>
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</inputs>
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<outputs>
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<data format="fasta" name="out_file1" />
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</outputs>
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<!-- <tests>
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<test>
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<param name="input1" value="gene_bed.dat"/>
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<param name="mafSource" value="8_WAY_MULTIZ_hg17"/>
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<param name="species" value="canFam1,hg17,mm5,panTro1,rn3"/>
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<output name="out_file1" file="gene_bed_maf_to_fasta_out.dat" />
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</test>
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</tests> -->
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<help>
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This tool takes an interval file and creates a FASTA file which contains merged alignments of user specified species which correspond to the supplied regions using locally cached alignments.
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</help>
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<code file="interval_maf_to_merged_fasta_code.py"/>
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</tool>
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