diff getfastaBed.xml @ 1:82aac94b06c3 draft

Uploaded

--- a/getfastaBed.xml	Tue Nov 04 01:45:04 2014 -0500
+++ b/getfastaBed.xml	Thu Jan 08 14:25:51 2015 -0500
@@ -6,30 +6,59 @@
     <expand macro="requirements" />
     <expand macro="stdio" />
     <command>
+<![CDATA[
         bedtools getfasta
         $name
         $tab
         $strand
         $split
         -fi $fasta 
-        -bed $inputA
+        -bed $input
         -fo $output
+]]>
     </command>
     <inputs>
-        <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file" />
+        <param format="bed,vcf,gff,gff3" name="input" 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)" />
+        <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"
+            help="(-name)" />
+        <param name="tab" type="boolean" checked="false" truevalue="-tab" falsevalue=""
+            label="Report extract sequences in a tab-delimited format instead of in FASTA format"
+            help="(-tab)" />
+        <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. (-s)" />
+        <expand macro="split" />
     </inputs>
     <outputs>
-        <data format="fasta" name="output" />
+        <data format="fasta" name="output">
+            <change_format>
+                <when input="tab" value="-tab" format="tabular" />
+            </change_format>
+        </data>
     </outputs>
+    <tests>
+        <test>
+            <param name="input" value="nucBed1.bed" ftype="bed" />
+            <param name="fasta" value="nucBed1.fasta" ftype="fasta" />
+            <param name="tab" value="False" />
+            <param name="split" value="False" />
+            <output name="output" file="getfastaBed_result1.bed" ftype="fasta" />
+        </test>
+        <test>
+            <param name="input" value="nucBed1.bed" ftype="bed" />
+            <param name="fasta" value="nucBed1.fasta" ftype="fasta" />
+            <param name="tab" value="True" />
+            <param name="split" value="False" />
+            <output name="output" file="getfastaBed_result2.tabular" ftype="tabular" />
+        </test>
+    </tests>
     <help>
+<![CDATA[
 **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>”.
+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: “>chrom>:&lt;start>-&lt;end>”.
 
 .. image:: $PATH_TO_IMAGES/getfasta-glyph.png
 
@@ -40,6 +69,7 @@
 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>