diff fimo_gff_to_gff.xml @ 0:48d424adfaef draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fimo_gff_to_gff.xml	Thu Mar 03 21:16:32 2016 -0500
@@ -0,0 +1,52 @@
+<tool id="fimo_gff_to_gff" name="Fimo Gff to Gff" version="1.0.0">
+    <description></description>
+    <requirements>
+        <requirement type="package" version="5.18.1">perl</requirement>
+    </requirements>
+    <command>
+        <![CDATA[
+            mkdir -p output &&
+            perl $__tool_directory__/fimo_gff_to_gff.pl "$input" output
+        ]]>
+    </command>
+    <inputs>
+        <param name="input" type="data" format="tabular" label="FIMO (almost) Gff input" />
+    </inputs>
+    <outputs>
+        <collection name="motifs" type="list" label="Motifs: ${tool.name} on ${on_string}">
+            <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="output" ext="gff" visible="false" />
+        </collection>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="input.tabular" ftype="tabular" />
+            <output_collection name="motifs" type="list">
+                <element name="MOTIF1" file="motif1.gff" ftype="gff"/>
+            </output_collection>
+        </test>
+    </tests>
+    <help>
+
+.. class:: warningmark
+
+This tool requires FASTA headers that use the default bedtools getfasta header format of
+**chrom:start-stop(strand)** or **chrom:start-stop** in which case strand is set as '+'
+per the bedtools standard.
+
+**What it does**
+
+Converts FIMO tabular (almost GFF) files to true genomic coordinates in valid GFF format.  A
+collection of datasets is produced consisting of one dataset per motif discovered in the input.
+
+    </help>
+    <citations>
+        <citation type="bibtex">
+            @unpublished{None,
+            author = {Lai, William},
+            title = {None},
+            year = {None},
+            eprint = {None},
+            url = {http://www.huck.psu.edu/content/research/independent-centers-excellence/center-for-eukaryotic-gene-regulation}
+        }</citation>
+    </citations>
+</tool>