Mercurial > repos > iuc > seqtk

annotate seqtk_subseq.xml @ 4:ecf1c30da3a2 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 ad43df79dca3dc7c3511c6eb2ccf8589d2804eb2
author iuc
date Wed, 17 Oct 2018 05:59:21 -0400
parents bc7d99f46a5d
children a09586d5149a
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_subseq" name="seqtk_subseq" version="@WRAPPER_VERSION@.0">
3
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 2
diff changeset
3 <description>extract subsequences from FASTA/Q files</description>
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 2
diff changeset
4 <macros>
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 2
diff changeset
5 <import>macros.xml</import>
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 2
diff changeset
6 </macros>
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 2
diff changeset
7 <expand macro="requirements"/>
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 2
diff changeset
8 <expand macro="stdio"/>
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 2
diff changeset
9 <command><![CDATA[
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 2
diff changeset
10 seqtk subseq
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 2
diff changeset
11 $t
0
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
12 -l $l
3
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 2
diff changeset
13 '$in_file'
0
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
14 #if $source.type == 'bed':
3
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 2
diff changeset
15 '$in_bed'
0
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
16 #else
3
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 2
diff changeset
17 '$name_list'
0
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
18 #end if
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
19 #if $t == '-t':
3
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 2
diff changeset
20 | awk 'BEGIN{print "chr\tunknown\tseq"}1'
0
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
21 #end if
4
ecf1c30da3a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit ad43df79dca3dc7c3511c6eb2ccf8589d2804eb2
iuc
parents: 3
diff changeset
22 @CONDITIONAL_GZIP_OUT@
3
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 2
diff changeset
23 ]]></command>
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 2
diff changeset
24 <inputs>
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 2
diff changeset
25 <expand macro="in_faq"/>
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 2
diff changeset
26 <conditional name="source">
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 2
diff changeset
27 <param name="type" type="select" label="Select source of sequence choices">
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 2
diff changeset
28 <option value="bed">BED</option>
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 2
diff changeset
29 <option value="name">FASTA/Q ID list</option>
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 2
diff changeset
30 </param>
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 2
diff changeset
31 <when value="bed">
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 2
diff changeset
32 <param name="in_bed" type="data" format="bed" label="Input BED file"/>
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 2
diff changeset
33 </when>
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 2
diff changeset
34 <when value="name">
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 2
diff changeset
35 <param name="name_list" type="data" format="txt" label="Input ID list"/>
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 2
diff changeset
36 </when>
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 2
diff changeset
37 </conditional>
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 2
diff changeset
38 <param argument="-t" type="boolean" truevalue="-t" falsevalue="" label="TAB delimited output" />
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 2
diff changeset
39 <param argument="-l" type="integer" value="0" label="Sequence line length" />
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 2
diff changeset
40 </inputs>
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 2
diff changeset
41 <outputs>
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 2
diff changeset
42 <data name="default" format_source="in_file" label="Selected sequences from $in_file.name">
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 2
diff changeset
43 <change_format>
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 2
diff changeset
44 <when input="t" value="-t" format="tabular"/>
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 2
diff changeset
45 </change_format>
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 2
diff changeset
46 </data>
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 2
diff changeset
47 </outputs>
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 2
diff changeset
48 <tests>
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 2
diff changeset
49 <test>
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 2
diff changeset
50 <param name="in_file" value="seqtk_subseq.fa"/>
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 2
diff changeset
51 <param name="type" value="name"/>
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 2
diff changeset
52 <param name="t" value="False" />
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 2
diff changeset
53 <param name="name_list" value="seqtk_subseq_list.txt"/>
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 2
diff changeset
54 <output name="default" file="seqtk_subseq.out" ftype="fasta"/>
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 2
diff changeset
55 </test>
4
ecf1c30da3a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit ad43df79dca3dc7c3511c6eb2ccf8589d2804eb2
iuc
parents: 3
diff changeset
56 <test>
ecf1c30da3a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit ad43df79dca3dc7c3511c6eb2ccf8589d2804eb2
iuc
parents: 3
diff changeset
57 <param name="in_file" value="seqtk_subseq.fa.gz" ftype="fasta.gz"/>
ecf1c30da3a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit ad43df79dca3dc7c3511c6eb2ccf8589d2804eb2
iuc
parents: 3
diff changeset
58 <param name="type" value="name"/>
ecf1c30da3a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit ad43df79dca3dc7c3511c6eb2ccf8589d2804eb2
iuc
parents: 3
diff changeset
59 <param name="t" value="False" />
ecf1c30da3a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit ad43df79dca3dc7c3511c6eb2ccf8589d2804eb2
iuc
parents: 3
diff changeset
60 <param name="name_list" value="seqtk_subseq_list.txt"/>
ecf1c30da3a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit ad43df79dca3dc7c3511c6eb2ccf8589d2804eb2
iuc
parents: 3
diff changeset
61 <output name="default" file="seqtk_subseq.out.gz" ftype="fasta.gz"/>
ecf1c30da3a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit ad43df79dca3dc7c3511c6eb2ccf8589d2804eb2
iuc
parents: 3
diff changeset
62 </test>
3
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 2
diff changeset
63 </tests>
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 2
diff changeset
64 <help><![CDATA[
0
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
65 **What it does**
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
66
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
67 Given a list of newline separated IDs from a fasta file, this will extract those named fasta sequences from the input file.
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
68
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
69 ::
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
70
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
71 # Input ID list
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
72 seq1
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
73
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
74 # Input fasta
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
75 >seq1
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
76 ACGTMRWSYK
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
77 >seq2
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
78 RWSYKACGTM
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
79
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
80 results in
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
81
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
82 ::
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
83
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
84 # Output result
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
85 >seq1
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
86 ACGTMRWSYK
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
87
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
88 @ATTRIBUTION@
3
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 2
diff changeset
89 ]]></help>
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 2
diff changeset
90 <expand macro="citation" />
0
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
91 </tool>