seqtk: seqtk_mergefa.xml annotate

annotate seqtk_mergefa.xml @ 19:36f4c569a594 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 35c8480f525d211d5e9996086c60b2c6d4f89146"

author	iuc
date	Tue, 10 Sep 2019 13:58:18 -0400
parents	069c8f0695ee
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_mergefa" name="seqtk_mergefa" 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>merge two 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>
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 mergefa
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d iuc parents: 7 diff changeset	11 -q $q
0 33ded39275c3 Uploaded iuc parents: diff changeset	12 $i
33ded39275c3 Uploaded iuc parents: diff changeset	13 $m
33ded39275c3 Uploaded iuc parents: diff changeset	14 $r
33ded39275c3 Uploaded iuc parents: diff changeset	15 $h
15 16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d iuc parents: 7 diff changeset	16 '$in_fa1'
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d iuc parents: 7 diff changeset	17 '$in_fa2'
19 36f4c569a594 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 35c8480f525d211d5e9996086c60b2c6d4f89146" iuc parents: 17 diff changeset	18 #echo "\| pigz -p ${GALAXY_SLOTS:-1} --no-name --no-time" if $in_fa1.is_of_type('fasta.gz', 'fastq.gz') else "" # > '$default'
15 16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d iuc parents: 7 diff changeset	19 ]]></command>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d iuc parents: 7 diff changeset	20 <inputs>
16 48a51c72f5e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit ad43df79dca3dc7c3511c6eb2ccf8589d2804eb2 iuc parents: 15 diff changeset	21 <param name="in_fa1" type="data" format="fasta,fastq,fasta.gz,fastq.gz" label="Input FASTA/Q file #1"/>
48a51c72f5e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit ad43df79dca3dc7c3511c6eb2ccf8589d2804eb2 iuc parents: 15 diff changeset	22 <param name="in_fa2" type="data" format="fasta,fastq,fasta.gz,fastq.gz" label="Input FASTA/Q file #2"/>
15 16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d iuc parents: 7 diff changeset	23 <param argument="-q" type="integer" value="0" label="Quality threshold"/>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d iuc parents: 7 diff changeset	24 <param argument="-i" type="boolean" truevalue="-i" falsevalue="" checked="false" label="Take intersection" />
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d iuc parents: 7 diff changeset	25 <param argument="-m" type="boolean" truevalue="-m" falsevalue="" checked="false" label="Convert to lowercase when one of the input base is N" />
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d iuc parents: 7 diff changeset	26 <param argument="-r" type="boolean" truevalue="-r" falsevalue="" checked="false" label="Pick a random allele from het" />
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d iuc parents: 7 diff changeset	27 <param argument="-h" type="boolean" truevalue="-h" falsevalue="" checked="false" label="Suppress hets in the input" />
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d iuc parents: 7 diff changeset	28 </inputs>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d iuc parents: 7 diff changeset	29 <outputs>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d iuc parents: 7 diff changeset	30 <data name="default" format_source="in_fa1" label="Merger of $in_fa1.name and $in_fa2.name"/>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d iuc parents: 7 diff changeset	31 </outputs>
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 <test>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d iuc parents: 7 diff changeset	34 <param name="in_fa1" value="seqtk_mergefa1.fa"/>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d iuc parents: 7 diff changeset	35 <param name="in_fa2" value="seqtk_mergefa2.fa"/>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d iuc parents: 7 diff changeset	36 <output name="default" file="seqtk_mergefa.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	37 </test>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d iuc parents: 7 diff changeset	38 <test>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d iuc parents: 7 diff changeset	39 <param name="in_fa1" value="seqtk_mergefa1.fa"/>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d iuc parents: 7 diff changeset	40 <param name="in_fa2" value="seqtk_mergefa2.fa"/>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d iuc parents: 7 diff changeset	41 <param name="m" value="True" />
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d iuc parents: 7 diff changeset	42 <output name="default" file="seqtk_mergefa2.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	43 </test>
16 48a51c72f5e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit ad43df79dca3dc7c3511c6eb2ccf8589d2804eb2 iuc parents: 15 diff changeset	44 <test>
48a51c72f5e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit ad43df79dca3dc7c3511c6eb2ccf8589d2804eb2 iuc parents: 15 diff changeset	45 <param name="in_fa1" value="seqtk_mergefa1.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	46 <param name="in_fa2" value="seqtk_mergefa2.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	47 <param name="m" value="True" />
48a51c72f5e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit ad43df79dca3dc7c3511c6eb2ccf8589d2804eb2 iuc parents: 15 diff changeset	48 <output name="default" file="seqtk_mergefa2.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	49 </test>
15 16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d iuc parents: 7 diff changeset	50 </tests>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d iuc parents: 7 diff changeset	51 <help><![CDATA[
0 33ded39275c3 Uploaded iuc parents: diff changeset	52 What it does
33ded39275c3 Uploaded iuc parents: diff changeset	53
33ded39275c3 Uploaded iuc parents: diff changeset	54 Merges two fasta files, using ambiguity codes
33ded39275c3 Uploaded iuc parents: diff changeset	55
33ded39275c3 Uploaded iuc parents: diff changeset	56 ::
33ded39275c3 Uploaded iuc parents: diff changeset	57
33ded39275c3 Uploaded iuc parents: diff changeset	58 # seq1.fa
33ded39275c3 Uploaded iuc parents: diff changeset	59 >test0
33ded39275c3 Uploaded iuc parents: diff changeset	60 ACTGACTGAAA
33ded39275c3 Uploaded iuc parents: diff changeset	61
33ded39275c3 Uploaded iuc parents: diff changeset	62 # seq2.fa
33ded39275c3 Uploaded iuc parents: diff changeset	63 >test0
33ded39275c3 Uploaded iuc parents: diff changeset	64 ACTGAMTGCGN
33ded39275c3 Uploaded iuc parents: diff changeset	65
33ded39275c3 Uploaded iuc parents: diff changeset	66 In the following the `-m` option has been set to highlight seqtk-mergefa's features.
33ded39275c3 Uploaded iuc parents: diff changeset	67
33ded39275c3 Uploaded iuc parents: diff changeset	68 ::
33ded39275c3 Uploaded iuc parents: diff changeset	69
33ded39275c3 Uploaded iuc parents: diff changeset	70 >test0
33ded39275c3 Uploaded iuc parents: diff changeset	71 ACTGACTGxxa
33ded39275c3 Uploaded iuc parents: diff changeset	72
33ded39275c3 Uploaded iuc parents: diff changeset	73 @ATTRIBUTION@
15 16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d iuc parents: 7 diff changeset	74 ]]></help>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d iuc parents: 7 diff changeset	75 <expand macro="citation" />
0 33ded39275c3 Uploaded iuc parents: diff changeset	76 </tool>

Mercurial > repos > iuc > seqtk

annotate seqtk_mergefa.xml @ 19:36f4c569a594 draft