seqtk: seqtk_listhet.xml annotate

annotate seqtk_listhet.xml @ 20:8f26884c60b6 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"

author	iuc
date	Wed, 01 Sep 2021 08:36:24 +0000
parents	069c8f0695ee
children	f2a792351212

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_listhet" name="seqtk_listhet" 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 the position of each het</description>
20 8f26884c60b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7" iuc parents: 17 diff changeset	4 <expand macro="bio_tools"/>
15 16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d iuc parents: 7 diff changeset	5 <macros>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d iuc parents: 7 diff changeset	6 <import>macros.xml</import>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d iuc parents: 7 diff changeset	7 </macros>
17 069c8f0695ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 83ecfe7d9bbf03c91f27ba18776352a1ebf8cf6f iuc parents: 16 diff changeset	8 <expand macro="requirements">
069c8f0695ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 83ecfe7d9bbf03c91f27ba18776352a1ebf8cf6f iuc parents: 16 diff changeset	9 <requirement type="package" version="@AWK_VERSION@">gawk</requirement>
069c8f0695ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 83ecfe7d9bbf03c91f27ba18776352a1ebf8cf6f iuc parents: 16 diff changeset	10 </expand>
15 16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d iuc parents: 7 diff changeset	11 <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	12 <command><![CDATA[
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d iuc parents: 7 diff changeset	13 seqtk listhet
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d iuc parents: 7 diff changeset	14 '$in_file' \| awk 'BEGIN{print "#chr\tposition\tbase"}1'
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d iuc parents: 7 diff changeset	15 > '$default'
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d iuc parents: 7 diff changeset	16 ]]></command>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d iuc parents: 7 diff changeset	17 <inputs>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d iuc parents: 7 diff changeset	18 <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	19 </inputs>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d iuc parents: 7 diff changeset	20 <outputs>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d iuc parents: 7 diff changeset	21 <data name="default" format="tabular" label="Positions of heterozygous bases in $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	22 </outputs>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d iuc parents: 7 diff changeset	23 <tests>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d iuc parents: 7 diff changeset	24 <test>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d iuc parents: 7 diff changeset	25 <param name="in_file" value="seqtk_listhet.fa"/>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d iuc parents: 7 diff changeset	26 <output name="default" file="seqtk_listhet.out" ftype="tabular"/>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d iuc parents: 7 diff changeset	27 </test>
16 48a51c72f5e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit ad43df79dca3dc7c3511c6eb2ccf8589d2804eb2 iuc parents: 15 diff changeset	28 <test>
48a51c72f5e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit ad43df79dca3dc7c3511c6eb2ccf8589d2804eb2 iuc parents: 15 diff changeset	29 <param name="in_file" value="seqtk_listhet.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	30 <output name="default" file="seqtk_listhet.out" ftype="tabular"/>
48a51c72f5e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit ad43df79dca3dc7c3511c6eb2ccf8589d2804eb2 iuc parents: 15 diff changeset	31 </test>
15 16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d iuc parents: 7 diff changeset	32 </tests>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d iuc parents: 7 diff changeset	33 <help><![CDATA[
0 33ded39275c3 Uploaded iuc parents: diff changeset	34 What it does
33ded39275c3 Uploaded iuc parents: diff changeset	35
33ded39275c3 Uploaded iuc parents: diff changeset	36 Lists regions of heterozygosity.
33ded39275c3 Uploaded iuc parents: diff changeset	37
33ded39275c3 Uploaded iuc parents: diff changeset	38 ::
33ded39275c3 Uploaded iuc parents: diff changeset	39
33ded39275c3 Uploaded iuc parents: diff changeset	40 >ambig
33ded39275c3 Uploaded iuc parents: diff changeset	41 ACGTMRWSYKVHDBN
33ded39275c3 Uploaded iuc parents: diff changeset	42
33ded39275c3 Uploaded iuc parents: diff changeset	43 The seqtk suite recognises MRWSYK:
33ded39275c3 Uploaded iuc parents: diff changeset	44
33ded39275c3 Uploaded iuc parents: diff changeset	45 ::
33ded39275c3 Uploaded iuc parents: diff changeset	46
33ded39275c3 Uploaded iuc parents: diff changeset	47 #chr position base
33ded39275c3 Uploaded iuc parents: diff changeset	48 ambig 5 M
33ded39275c3 Uploaded iuc parents: diff changeset	49 ambig 6 R
33ded39275c3 Uploaded iuc parents: diff changeset	50 ambig 7 W
33ded39275c3 Uploaded iuc parents: diff changeset	51 ambig 8 S
33ded39275c3 Uploaded iuc parents: diff changeset	52 ambig 9 Y
33ded39275c3 Uploaded iuc parents: diff changeset	53 ambig 10 K
33ded39275c3 Uploaded iuc parents: diff changeset	54
33ded39275c3 Uploaded iuc parents: diff changeset	55
33ded39275c3 Uploaded iuc parents: diff changeset	56 @ATTRIBUTION@
15 16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d iuc parents: 7 diff changeset	57 ]]></help>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d iuc parents: 7 diff changeset	58 <expand macro="citation" />
0 33ded39275c3 Uploaded iuc parents: diff changeset	59 </tool>

Mercurial > repos > iuc > seqtk

annotate seqtk_listhet.xml @ 20:8f26884c60b6 draft