seqtk: seqtk_mutfa.xml annotate

annotate seqtk_mutfa.xml @ 17:069c8f0695ee draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 83ecfe7d9bbf03c91f27ba18776352a1ebf8cf6f

author	iuc
date	Fri, 11 Jan 2019 05:14:48 -0500
parents	48a51c72f5e7
children	8f26884c60b6

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_mutfa" name="seqtk_mutfa" 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>point mutate FASTA at specified positions</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>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d iuc parents: 7 diff changeset	6 </macros>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d iuc parents: 7 diff changeset	7 <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	8 <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	9 <command><![CDATA[
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d iuc parents: 7 diff changeset	10 seqtk mutfa
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d iuc parents: 7 diff changeset	11 '$in_file'
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d iuc parents: 7 diff changeset	12 '$in_snp'
16 48a51c72f5e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit ad43df79dca3dc7c3511c6eb2ccf8589d2804eb2 iuc parents: 15 diff changeset	13 @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	14 ]]></command>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d iuc parents: 7 diff changeset	15 <inputs>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d iuc parents: 7 diff changeset	16 <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	17 <param name="in_snp" type="data" format="tabular" label="Input SNP file"/>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d iuc parents: 7 diff changeset	18 </inputs>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d iuc parents: 7 diff changeset	19 <outputs>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d iuc parents: 7 diff changeset	20 <data name="default" format_source="in_file" label="Mutated $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	21 </outputs>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d iuc parents: 7 diff changeset	22 <tests>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d iuc parents: 7 diff changeset	23 <test>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d iuc parents: 7 diff changeset	24 <param name="in_file" value="seqtk_mutfa.fa"/>
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_snp" value="seqtk_mutfa.snp"/>
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_mutfa.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	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_mutfa.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 <param name="in_snp" value="seqtk_mutfa.snp"/>
48a51c72f5e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit ad43df79dca3dc7c3511c6eb2ccf8589d2804eb2 iuc parents: 15 diff changeset	31 <output name="default" file="seqtk_mutfa.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	32 </test>
15 16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d iuc parents: 7 diff changeset	33 </tests>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d iuc parents: 7 diff changeset	34 <help><![CDATA[
0 33ded39275c3 Uploaded iuc parents: diff changeset	35 What it does
33ded39275c3 Uploaded iuc parents: diff changeset	36
33ded39275c3 Uploaded iuc parents: diff changeset	37 the SNP inputs consist of 4 columns: chromosome, 1-based-pos, any, base-changed-to.
33ded39275c3 Uploaded iuc parents: diff changeset	38
33ded39275c3 Uploaded iuc parents: diff changeset	39 ::
33ded39275c3 Uploaded iuc parents: diff changeset	40
33ded39275c3 Uploaded iuc parents: diff changeset	41 # Input fasta
33ded39275c3 Uploaded iuc parents: diff changeset	42 >test0
33ded39275c3 Uploaded iuc parents: diff changeset	43 ACTGACTGAA
33ded39275c3 Uploaded iuc parents: diff changeset	44
33ded39275c3 Uploaded iuc parents: diff changeset	45 # Input SNP file
33ded39275c3 Uploaded iuc parents: diff changeset	46 test0 1 . G
33ded39275c3 Uploaded iuc parents: diff changeset	47 test0 4 . A
33ded39275c3 Uploaded iuc parents: diff changeset	48
33ded39275c3 Uploaded iuc parents: diff changeset	49 This will effect the desired mutations in the output file
33ded39275c3 Uploaded iuc parents: diff changeset	50
33ded39275c3 Uploaded iuc parents: diff changeset	51 ::
33ded39275c3 Uploaded iuc parents: diff changeset	52
33ded39275c3 Uploaded iuc parents: diff changeset	53 # Output result
33ded39275c3 Uploaded iuc parents: diff changeset	54 >test0
33ded39275c3 Uploaded iuc parents: diff changeset	55 GCTAACTGAA
33ded39275c3 Uploaded iuc parents: diff changeset	56
33ded39275c3 Uploaded iuc parents: diff changeset	57 @ATTRIBUTION@
15 16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d iuc parents: 7 diff changeset	58 ]]></help>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d iuc parents: 7 diff changeset	59 <expand macro="citation" />
0 33ded39275c3 Uploaded iuc parents: diff changeset	60 </tool>

Mercurial > repos > iuc > seqtk

annotate seqtk_mutfa.xml @ 17:069c8f0695ee draft