annotate mytools/fastqdump.xml @ 5:84e2c77a6abd

Uploaded
author xuebing
date Fri, 16 Mar 2012 14:01:16 -0400
parents 39217fa39ff2
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
39217fa39ff2 Uploaded
xuebing
parents:
diff changeset
1 <tool id="fastqdump" name="fastq-dump">
39217fa39ff2 Uploaded
xuebing
parents:
diff changeset
2 <description>convert SRA to FASTQ</description>
39217fa39ff2 Uploaded
xuebing
parents:
diff changeset
3 <command>/Users/xuebing/tools/sratoolkit.2.1.9-mac32/fastq-dump -A $input -M $minReadLen -Z > $out_file1 </command>
39217fa39ff2 Uploaded
xuebing
parents:
diff changeset
4 <inputs>
39217fa39ff2 Uploaded
xuebing
parents:
diff changeset
5 <param name="input" format="sra" type="data" label="Original file (SRA)"/>
39217fa39ff2 Uploaded
xuebing
parents:
diff changeset
6 <param name="minReadLen" size="10" type="integer" value="10" label="minimum read length to output"/>
39217fa39ff2 Uploaded
xuebing
parents:
diff changeset
7 </inputs>
39217fa39ff2 Uploaded
xuebing
parents:
diff changeset
8 <outputs>
39217fa39ff2 Uploaded
xuebing
parents:
diff changeset
9 <data format="fastq" name="out_file1" />
39217fa39ff2 Uploaded
xuebing
parents:
diff changeset
10 </outputs>
39217fa39ff2 Uploaded
xuebing
parents:
diff changeset
11 <help>
39217fa39ff2 Uploaded
xuebing
parents:
diff changeset
12
39217fa39ff2 Uploaded
xuebing
parents:
diff changeset
13 **What it does**
39217fa39ff2 Uploaded
xuebing
parents:
diff changeset
14
39217fa39ff2 Uploaded
xuebing
parents:
diff changeset
15 This is a wrapper of the fastq-dump tool from sra-toolkit. See http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software
39217fa39ff2 Uploaded
xuebing
parents:
diff changeset
16
39217fa39ff2 Uploaded
xuebing
parents:
diff changeset
17 </help>
39217fa39ff2 Uploaded
xuebing
parents:
diff changeset
18 </tool>