Mercurial > repos > iuc > seqtk

annotate seqtk_subseq.xml @ 18:1d63dbcecb10 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 50a0bd6d783a69e7303363a31130134767493e66"
author iuc
date Fri, 06 Sep 2019 09:09:35 -0400
parents 069c8f0695ee
children 8f26884c60b6
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
33ded39275c3 Uploaded
iuc
parents:
diff changeset
1 <?xml version="1.0"?>
17
069c8f0695ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 83ecfe7d9bbf03c91f27ba18776352a1ebf8cf6f
iuc
parents: 16
diff changeset
2 <tool id="seqtk_subseq" name="seqtk_subseq" version="@TOOL_VERSION@.1">
15
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
3 <description>extract subsequences from FASTA/Q files</description>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
4 <macros>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
5 <import>macros.xml</import>
17
069c8f0695ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 83ecfe7d9bbf03c91f27ba18776352a1ebf8cf6f
iuc
parents: 16
diff changeset
6 <requirement type="package" version="@AWK_VERSION@">gawk</requirement>
15
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
7 </macros>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
8 <expand macro="requirements"/>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
9 <expand macro="stdio"/>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
10 <command><![CDATA[
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
11 seqtk subseq
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
12 $t
0
33ded39275c3 Uploaded
iuc
parents:
diff changeset
13 -l $l
15
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
14 '$in_file'
0
33ded39275c3 Uploaded
iuc
parents:
diff changeset
15 #if $source.type == 'bed':
15
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
16 '$in_bed'
0
33ded39275c3 Uploaded
iuc
parents:
diff changeset
17 #else
15
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
18 '$name_list'
0
33ded39275c3 Uploaded
iuc
parents:
diff changeset
19 #end if
33ded39275c3 Uploaded
iuc
parents:
diff changeset
20 #if $t == '-t':
15
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
21 | awk 'BEGIN{print "chr\tunknown\tseq"}1'
0
33ded39275c3 Uploaded
iuc
parents:
diff changeset
22 #end if
16
48a51c72f5e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit ad43df79dca3dc7c3511c6eb2ccf8589d2804eb2
iuc
parents: 15
diff changeset
23 @CONDITIONAL_GZIP_OUT@
15
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
24 ]]></command>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
25 <inputs>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
26 <expand macro="in_faq"/>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
27 <conditional name="source">
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
28 <param name="type" type="select" label="Select source of sequence choices">
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
29 <option value="bed">BED</option>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
30 <option value="name">FASTA/Q ID list</option>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
31 </param>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
32 <when value="bed">
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
33 <param name="in_bed" type="data" format="bed" label="Input BED file"/>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
34 </when>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
35 <when value="name">
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
36 <param name="name_list" type="data" format="txt" label="Input ID list"/>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
37 </when>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
38 </conditional>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
39 <param argument="-t" type="boolean" truevalue="-t" falsevalue="" label="TAB delimited output" />
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
40 <param argument="-l" type="integer" value="0" label="Sequence line length" />
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
41 </inputs>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
42 <outputs>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
43 <data name="default" format_source="in_file" label="Selected sequences from $in_file.name">
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
44 <change_format>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
45 <when input="t" value="-t" format="tabular"/>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
46 </change_format>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
47 </data>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
48 </outputs>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
49 <tests>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
50 <test>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
51 <param name="in_file" value="seqtk_subseq.fa"/>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
52 <param name="type" value="name"/>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
53 <param name="t" value="False" />
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
54 <param name="name_list" value="seqtk_subseq_list.txt"/>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
55 <output name="default" file="seqtk_subseq.out" ftype="fasta"/>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
56 </test>
16
48a51c72f5e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit ad43df79dca3dc7c3511c6eb2ccf8589d2804eb2
iuc
parents: 15
diff changeset
57 <test>
48a51c72f5e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit ad43df79dca3dc7c3511c6eb2ccf8589d2804eb2
iuc
parents: 15
diff changeset
58 <param name="in_file" value="seqtk_subseq.fa.gz" ftype="fasta.gz"/>
48a51c72f5e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit ad43df79dca3dc7c3511c6eb2ccf8589d2804eb2
iuc
parents: 15
diff changeset
59 <param name="type" value="name"/>
48a51c72f5e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit ad43df79dca3dc7c3511c6eb2ccf8589d2804eb2
iuc
parents: 15
diff changeset
60 <param name="t" value="False" />
48a51c72f5e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit ad43df79dca3dc7c3511c6eb2ccf8589d2804eb2
iuc
parents: 15
diff changeset
61 <param name="name_list" value="seqtk_subseq_list.txt"/>
48a51c72f5e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit ad43df79dca3dc7c3511c6eb2ccf8589d2804eb2
iuc
parents: 15
diff changeset
62 <output name="default" file="seqtk_subseq.out.gz" ftype="fasta.gz"/>
48a51c72f5e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit ad43df79dca3dc7c3511c6eb2ccf8589d2804eb2
iuc
parents: 15
diff changeset
63 </test>
15
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
64 </tests>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
65 <help><![CDATA[
0
33ded39275c3 Uploaded
iuc
parents:
diff changeset
66 **What it does**
33ded39275c3 Uploaded
iuc
parents:
diff changeset
67
33ded39275c3 Uploaded
iuc
parents:
diff changeset
68 Given a list of newline separated IDs from a fasta file, this will extract those named fasta sequences from the input file.
33ded39275c3 Uploaded
iuc
parents:
diff changeset
69
33ded39275c3 Uploaded
iuc
parents:
diff changeset
70 ::
33ded39275c3 Uploaded
iuc
parents:
diff changeset
71
33ded39275c3 Uploaded
iuc
parents:
diff changeset
72 # Input ID list
33ded39275c3 Uploaded
iuc
parents:
diff changeset
73 seq1
33ded39275c3 Uploaded
iuc
parents:
diff changeset
74
33ded39275c3 Uploaded
iuc
parents:
diff changeset
75 # Input fasta
33ded39275c3 Uploaded
iuc
parents:
diff changeset
76 >seq1
33ded39275c3 Uploaded
iuc
parents:
diff changeset
77 ACGTMRWSYK
33ded39275c3 Uploaded
iuc
parents:
diff changeset
78 >seq2
33ded39275c3 Uploaded
iuc
parents:
diff changeset
79 RWSYKACGTM
33ded39275c3 Uploaded
iuc
parents:
diff changeset
80
33ded39275c3 Uploaded
iuc
parents:
diff changeset
81 results in
33ded39275c3 Uploaded
iuc
parents:
diff changeset
82
33ded39275c3 Uploaded
iuc
parents:
diff changeset
83 ::
33ded39275c3 Uploaded
iuc
parents:
diff changeset
84
33ded39275c3 Uploaded
iuc
parents:
diff changeset
85 # Output result
33ded39275c3 Uploaded
iuc
parents:
diff changeset
86 >seq1
33ded39275c3 Uploaded
iuc
parents:
diff changeset
87 ACGTMRWSYK
33ded39275c3 Uploaded
iuc
parents:
diff changeset
88
33ded39275c3 Uploaded
iuc
parents:
diff changeset
89 @ATTRIBUTION@
15
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
90 ]]></help>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
91 <expand macro="citation" />
0
33ded39275c3 Uploaded
iuc
parents:
diff changeset
92 </tool>