annotate seqtk_sample.xml @ 1:61718851f199 draft

Uploaded
author iuc
date Thu, 05 Feb 2015 12:00:43 -0500
parents e0a0fd938de4
children f73729b62b51
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
1 <?xml version="1.0"?>
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
2 <tool id="seqtk_sample" name="seqtk_sample" version="@WRAPPER_VERSION@.0">
1
61718851f199 Uploaded
iuc
parents: 0
diff changeset
3 <description>random subsample of fasta or fastq sequences</description>
0
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
4 <macros>
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
5 <import>macros.xml</import>
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
6 </macros>
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
7 <expand macro="requirements"/>
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
8 <expand macro="stdio"/>
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
9 <command><![CDATA[seqtk sample -s $s
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
10 $in_file
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
11 $subsample_size
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
12 > $default]]></command>
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
13 <inputs>
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
14 <expand macro="in_faq" />
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
15 <param label="RNG seed" help="(-s)" name="s" type="integer" value="4"/>
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
16 <param label="Subsample (decimal fraction or number)" name="subsample_size" type="integer" value="100"/>
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
17 </inputs>
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
18 <outputs>
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
19 <data format_source="in_file" hidden="false" name="default" label="Subsample of reads from $in_file.name"/>
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
20 </outputs>
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
21 <tests>
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
22 <test>
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
23 <param name="in_file" value="seqtk_sample.fa"/>
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
24 <param name="subsample_size" value="4"/>
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
25 <param name="s" value="4"/>
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
26 <output name="default" file="seqtk_sample.out" ftype="fasta"/>
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
27 </test>
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
28 </tests>
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
29 <help><![CDATA[
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
30 **What it does**
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
31
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
32 Takes a random subsample of fasta or fastq sequences. The RNG is seedable to allow for reproducible results, and defaults to `4 <http://xkcd.com/221/>`__.
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
33
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
34 The subsample size can be a decimal fraction <=1, where 1 implies 100% of the reads should be used. If a number >1 is provided, that many reads will be taken from the dataset.
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
35
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
36 @ATTRIBUTION@
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
37 ]]></help>
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
38 </tool>