seqtk: seqtk_comp.xml annotate

annotate seqtk_comp.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_comp" name="seqtk_comp" 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>get the nucleotide composition of FASTA/Q</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 comp
0 33ded39275c3 Uploaded iuc parents: diff changeset	14 #if $in_bed:
15 16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d iuc parents: 7 diff changeset	15 -r '$in_bed'
0 33ded39275c3 Uploaded iuc parents: diff changeset	16 #end if
15 16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d iuc parents: 7 diff changeset	17 '$in_file' \| awk 'BEGIN{print "#chr\tlength\t#A\t#C\t#G\t#T\t#2\t#3\t#4\t#CpG\t#tv\t#ts\t#CpG-ts"}1'
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d iuc parents: 7 diff changeset	18 > '$default'
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>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d iuc parents: 7 diff changeset	21 <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	22 <param name="in_bed" type="data" format="bed" optional="true" label="BED file"/>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d iuc parents: 7 diff changeset	23 </inputs>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d iuc parents: 7 diff changeset	24 <outputs>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d iuc parents: 7 diff changeset	25 <data name="default" format="tabular" label="Nucleotide composition of $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	26 </outputs>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d iuc parents: 7 diff changeset	27 <tests>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d iuc parents: 7 diff changeset	28 <test>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d iuc parents: 7 diff changeset	29 <param name="in_file" value="seqtk_comp.fa" ftype="fasta"/>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d iuc parents: 7 diff changeset	30 <output name="default" file="seqtk_comp.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	31 </test>
16 48a51c72f5e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit ad43df79dca3dc7c3511c6eb2ccf8589d2804eb2 iuc parents: 15 diff changeset	32 <test>
48a51c72f5e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit ad43df79dca3dc7c3511c6eb2ccf8589d2804eb2 iuc parents: 15 diff changeset	33 <param name="in_file" value="seqtk_comp.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	34 <output name="default" file="seqtk_comp.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	35 </test>
15 16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d iuc parents: 7 diff changeset	36 </tests>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d iuc parents: 7 diff changeset	37 <help><![CDATA[
0 33ded39275c3 Uploaded iuc parents: diff changeset	38 What it does
33ded39275c3 Uploaded iuc parents: diff changeset	39
33ded39275c3 Uploaded iuc parents: diff changeset	40 Reports composition of fasta/fastq sequences. For an example sequence like
33ded39275c3 Uploaded iuc parents: diff changeset	41
33ded39275c3 Uploaded iuc parents: diff changeset	42 ::
33ded39275c3 Uploaded iuc parents: diff changeset	43 >test0
33ded39275c3 Uploaded iuc parents: diff changeset	44 ACTGACTGAA
33ded39275c3 Uploaded iuc parents: diff changeset	45 >ambig_ref
33ded39275c3 Uploaded iuc parents: diff changeset	46 ACGTCGTGTTVHDBN
33ded39275c3 Uploaded iuc parents: diff changeset	47
33ded39275c3 Uploaded iuc parents: diff changeset	48 The seqtk tool will report:
33ded39275c3 Uploaded iuc parents: diff changeset	49
33ded39275c3 Uploaded iuc parents: diff changeset	50 ::
33ded39275c3 Uploaded iuc parents: diff changeset	51
33ded39275c3 Uploaded iuc parents: diff changeset	52 #chr length #A #C #G #T #2 #3 #4 #CpG #tv #ts #CpG-ts
33ded39275c3 Uploaded iuc parents: diff changeset	53 test0 11 4 2 2 2 0 0 1 0 0 0 0
33ded39275c3 Uploaded iuc parents: diff changeset	54 ambig_ref 15 1 2 3 4 0 4 1 4 0 0 0
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_comp.xml @ 20:8f26884c60b6 draft