diff getfastaBed.xml @ 0:b8348686a0b9 draft

Imported from capsule None

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/getfastaBed.xml	Tue Nov 04 01:45:04 2014 -0500
@@ -0,0 +1,45 @@
+<tool id="bedtools_getfastabed" name="GetFastaBed" version="@WRAPPER_VERSION@.0">
+    <description></description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
+    <command>
+        bedtools getfasta
+        $name
+        $tab
+        $strand
+        $split
+        -fi $fasta 
+        -bed $inputA
+        -fo $output
+    </command>
+    <inputs>
+        <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file" />
+        <param format="fasta" name="fasta" type="data" label="Fasta file" />
+        <param name="name" type="boolean" checked="false" truevalue="-name" falsevalue="" label="Use the “name” column in the BED file for the FASTA headers in the output FASTA file" />
+        <param name="tab" type="boolean" checked="false" truevalue="-tab" falsevalue="" label="Report extract sequences in a tab-delimited format instead of in FASTA format" />
+        <param name="strand" type="boolean" checked="false" truevalue="-s" falsevalue="" label="Force strandedness" help="If the feature occupies the antisense strand, the sequence will be reverse complemented." />
+        <param name="split" type="boolean" checked="false" truevalue="-split" falsevalue="" label="Given BED12 input, extract and concatenate the sequences from the BED 'blocks' (e.g., exons)" />
+    </inputs>
+    <outputs>
+        <data format="fasta" name="output" />
+    </outputs>
+    <help>
+**What it does**
+
+bedtools getfasta will extract the sequence defined by the coordinates in a BED interval and create a new FASTA entry in the output file for each extracted sequence. By default, the FASTA header for each extracted sequence will be formatted as follows: “&lt;chrom>:&lt;start>-&lt;end>”.
+
+.. image:: $PATH_TO_IMAGES/getfasta-glyph.png
+
+.. class:: warningmark
+
+1. The headers in the input FASTA file must exactly match the chromosome column in the BED file.
+
+2. You can use the UNIX fold command to set the line width of the FASTA output. For example, fold -w 60 will make each line of the FASTA file have at most 60 nucleotides for easy viewing.
+
+@REFERENCES@
+    </help>
+    <expand macro="citations" />
+</tool>