seqtk: seqtk_hety.xml annotate

annotate seqtk_hety.xml @ 8:3da72230c066 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 690c73637e3b8be3a52fe3afc8ba6436c4bab46f"

author	iuc
date	Thu, 14 Oct 2021 09:22:39 +0000
parents	a09586d5149a
children	4b494533146a

rev	line source
0 e0a0fd938de4 Uploaded iuc parents: diff changeset	1 <?xml version="1.0"?>
5 a09586d5149a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 83ecfe7d9bbf03c91f27ba18776352a1ebf8cf6f iuc parents: 4 diff changeset	2 <tool id="seqtk_hety" name="seqtk_hety" version="@TOOL_VERSION@.1">
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>regional heterozygosity</description>
8 3da72230c066 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 690c73637e3b8be3a52fe3afc8ba6436c4bab46f" iuc parents: 5 diff changeset	4 <expand macro="bio_tools"/>
3 bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d iuc parents: 2 diff changeset	5 <macros>
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d iuc parents: 2 diff changeset	6 <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	7 </macros>
5 a09586d5149a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 83ecfe7d9bbf03c91f27ba18776352a1ebf8cf6f iuc parents: 4 diff changeset	8 <expand macro="requirements">
a09586d5149a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 83ecfe7d9bbf03c91f27ba18776352a1ebf8cf6f iuc parents: 4 diff changeset	9 <requirement type="package" version="@AWK_VERSION@">gawk</requirement>
a09586d5149a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 83ecfe7d9bbf03c91f27ba18776352a1ebf8cf6f iuc parents: 4 diff changeset	10 </expand>
3 bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d iuc parents: 2 diff changeset	11 <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	12 <command><![CDATA[
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d iuc parents: 2 diff changeset	13 seqtk hety
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d iuc parents: 2 diff changeset	14 -w $w
0 e0a0fd938de4 Uploaded iuc parents: diff changeset	15 -t $t
e0a0fd938de4 Uploaded iuc parents: diff changeset	16 $m
3 bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d iuc parents: 2 diff changeset	17 '$in_file' \| awk 'BEGIN{print "#chr\tstart\tend\tA\tB\tnum_het"}1'
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d iuc parents: 2 diff changeset	18 > '$default'
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d iuc parents: 2 diff changeset	19 ]]></command>
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d iuc parents: 2 diff changeset	20 <inputs>
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d iuc parents: 2 diff changeset	21 <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	22 <param argument="-w" type="integer" value="50000" label="Window size" />
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d iuc parents: 2 diff changeset	23 <param argument="-t" type="integer" value="5" label="# start positions in a window" />
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d iuc parents: 2 diff changeset	24 <param argument="-m" type="boolean" truevalue="-m" falsevalue="" checked="false" label="Treat lowercases as masked" />
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d iuc parents: 2 diff changeset	25 </inputs>
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d iuc parents: 2 diff changeset	26 <outputs>
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d iuc parents: 2 diff changeset	27 <data name="default" format="tabular" label="Heterozygous regions in $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	28 </outputs>
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d iuc parents: 2 diff changeset	29 <tests>
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d iuc parents: 2 diff changeset	30 <test>
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d iuc parents: 2 diff changeset	31 <param name="in_file" value="seqtk_hety.fa"/>
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="w" value="8"/>
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d iuc parents: 2 diff changeset	33 <output name="default" file="seqtk_hety.out" ftype="tabular"/>
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d iuc parents: 2 diff changeset	34 </test>
4 ecf1c30da3a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit ad43df79dca3dc7c3511c6eb2ccf8589d2804eb2 iuc parents: 3 diff changeset	35 <test>
ecf1c30da3a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit ad43df79dca3dc7c3511c6eb2ccf8589d2804eb2 iuc parents: 3 diff changeset	36 <param name="in_file" value="seqtk_hety.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	37 <param name="w" value="8"/>
ecf1c30da3a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit ad43df79dca3dc7c3511c6eb2ccf8589d2804eb2 iuc parents: 3 diff changeset	38 <output name="default" file="seqtk_hety.out" ftype="tabular"/>
ecf1c30da3a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit ad43df79dca3dc7c3511c6eb2ccf8589d2804eb2 iuc parents: 3 diff changeset	39 </test>
3 bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d iuc parents: 2 diff changeset	40 </tests>
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d iuc parents: 2 diff changeset	41 <help><![CDATA[
0 e0a0fd938de4 Uploaded iuc parents: diff changeset	42 What it does
e0a0fd938de4 Uploaded iuc parents: diff changeset	43
e0a0fd938de4 Uploaded iuc parents: diff changeset	44 Reports on heterozygosity over a region
e0a0fd938de4 Uploaded iuc parents: diff changeset	45
e0a0fd938de4 Uploaded iuc parents: diff changeset	46 ::
e0a0fd938de4 Uploaded iuc parents: diff changeset	47
e0a0fd938de4 Uploaded iuc parents: diff changeset	48 >het_region
e0a0fd938de4 Uploaded iuc parents: diff changeset	49 ACTTTACATCGAGCMMMMMMMACAGTACTG
e0a0fd938de4 Uploaded iuc parents: diff changeset	50
e0a0fd938de4 Uploaded iuc parents: diff changeset	51 As can be seen in the following output:
e0a0fd938de4 Uploaded iuc parents: diff changeset	52
e0a0fd938de4 Uploaded iuc parents: diff changeset	53 ::
e0a0fd938de4 Uploaded iuc parents: diff changeset	54
e0a0fd938de4 Uploaded iuc parents: diff changeset	55 #chr start end A B num_het
e0a0fd938de4 Uploaded iuc parents: diff changeset	56 het_region 0 8 0.00 8 0
e0a0fd938de4 Uploaded iuc parents: diff changeset	57 het_region 8 9 0.00 8 0
e0a0fd938de4 Uploaded iuc parents: diff changeset	58 het_region 9 10 0.00 8 0
e0a0fd938de4 Uploaded iuc parents: diff changeset	59 het_region 10 11 0.00 8 0
e0a0fd938de4 Uploaded iuc parents: diff changeset	60 het_region 11 12 0.00 8 0
e0a0fd938de4 Uploaded iuc parents: diff changeset	61 het_region 12 13 0.00 8 0
e0a0fd938de4 Uploaded iuc parents: diff changeset	62 het_region 13 14 0.00 8 0
e0a0fd938de4 Uploaded iuc parents: diff changeset	63 het_region 14 15 1.00 8 1
e0a0fd938de4 Uploaded iuc parents: diff changeset	64 het_region 15 16 2.00 8 2
e0a0fd938de4 Uploaded iuc parents: diff changeset	65 het_region 16 17 3.00 8 3
e0a0fd938de4 Uploaded iuc parents: diff changeset	66 het_region 17 18 4.00 8 4
e0a0fd938de4 Uploaded iuc parents: diff changeset	67 het_region 18 19 5.00 8 5
e0a0fd938de4 Uploaded iuc parents: diff changeset	68 het_region 19 20 6.00 8 6
e0a0fd938de4 Uploaded iuc parents: diff changeset	69 het_region 20 21 7.00 8 7
e0a0fd938de4 Uploaded iuc parents: diff changeset	70 het_region 21 22 7.00 8 7
e0a0fd938de4 Uploaded iuc parents: diff changeset	71 het_region 22 23 6.00 8 6
e0a0fd938de4 Uploaded iuc parents: diff changeset	72 het_region 23 24 5.00 8 5
e0a0fd938de4 Uploaded iuc parents: diff changeset	73 het_region 24 25 4.00 8 4
e0a0fd938de4 Uploaded iuc parents: diff changeset	74 het_region 25 26 3.00 8 3
e0a0fd938de4 Uploaded iuc parents: diff changeset	75 het_region 26 27 2.00 8 2
e0a0fd938de4 Uploaded iuc parents: diff changeset	76 het_region 27 28 1.00 8 1
e0a0fd938de4 Uploaded iuc parents: diff changeset	77 het_region 28 29 0.00 8 0
e0a0fd938de4 Uploaded iuc parents: diff changeset	78 het_region 29 30 0.00 1 0
e0a0fd938de4 Uploaded iuc parents: diff changeset	79
e0a0fd938de4 Uploaded iuc parents: diff changeset	80 If you know what A and B are measures of, please `submit an issue <https://github.com/galaxyproject/tools-iuc/issues>`__ and it will be corrected
e0a0fd938de4 Uploaded iuc parents: diff changeset	81
e0a0fd938de4 Uploaded iuc parents: diff changeset	82 @ATTRIBUTION@
3 bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d iuc parents: 2 diff changeset	83 ]]></help>
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d iuc parents: 2 diff changeset	84 <expand macro="citation" />
0 e0a0fd938de4 Uploaded iuc parents: diff changeset	85 </tool>

Mercurial > repos > iuc > seqtk

annotate seqtk_hety.xml @ 8:3da72230c066 draft