Mercurial > repos > iuc > seqtk

annotate seqtk_mutfa.xml @ 2:f73729b62b51 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 2249d643284ee782d882cd200729a86a2c6bb744
author iuc
date Fri, 01 Jan 2016 14:49:42 -0500
parents e0a0fd938de4
children bc7d99f46a5d
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_mutfa" name="seqtk_mutfa" version="@WRAPPER_VERSION@.0">
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
3 <description>point mutate FASTA at specified positions</description>
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 mutfa
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
10 $in_file $in_snp
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
11 > $default]]></command>
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
12 <inputs>
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
13 <expand macro="in_faq"/>
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
14 <param name="in_snp" type="data" format="tabular" label="Input SNP file"/>
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
15 </inputs>
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
16 <outputs>
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
17 <data format_source="in_file" hidden="false" name="default" label="Mutated $in_file.name"/>
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
18 </outputs>
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
19 <tests>
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
20 <test>
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
21 <param name="in_file" value="seqtk_mutfa.fa"/>
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
22 <param name="in_snp" value="seqtk_mutfa.snp"/>
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
23 <output name="default" file="seqtk_mutfa.out" ftype="fasta"/>
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
24 </test>
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
25 </tests>
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
26 <help><![CDATA[
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
27 **What it does**
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
28
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
29 the SNP inputs consist of 4 columns: chromosome, 1-based-pos, any, base-changed-to.
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
30
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
31 ::
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
32
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
33 # Input fasta
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
34 >test0
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
35 ACTGACTGAA
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
36
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
37 # Input SNP file
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
38 test0 1 . G
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
39 test0 4 . A
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
40
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
41 This will effect the desired mutations in the output file
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
42
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
43 ::
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
44
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
45 # Output result
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
46 >test0
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
47 GCTAACTGAA
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
48
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
49 @ATTRIBUTION@
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
50 ]]></help>
2
f73729b62b51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 2249d643284ee782d882cd200729a86a2c6bb744
iuc
parents: 0
diff changeset
51 <expand macro="citation" />
0
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
52 </tool>