annotate fimo2bed.xml @ 11:b7f1d9f8f3bc

Uploaded
author xuebing
date Sat, 10 Mar 2012 07:59:27 -0500
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
11
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
1 <tool id="fimo2bed" name="fimo-to-bed">
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
2 <description>convert FIMO output to BED</description>
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
3 <command interpreter="python">fimo2bed.py $input $rc > $output</command>
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
4 <inputs>
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
5 <param name="input" format="txt" type="data" label="FIMO output file"/>
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
6 <param name="rc" label="Check if the sequences are reverse complement" type="boolean" truevalue="rc" falsevalue="none" checked="False"/>
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
7 </inputs>
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
8 <outputs>
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
9 <data format="bed" name="output" />
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
10 </outputs>
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
11 <help>
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
12
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
13 Only works if your original FIMO input fasta sequences have ids like::
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
14
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
15 mm9_chr15_99358448_99360448_-
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
16
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
17
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
18 </help>
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
19 </tool>