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comparison seqtk_comp.xml @ 15:16f2535c08bf draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
author iuc
date Mon, 05 Jun 2017 13:26:30 -0400
parents 55e75a28fde7
children 48a51c72f5e7
comparison
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14:bdc5ba2a7486 15:16f2535c08bf
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="seqtk_comp" name="seqtk_comp" version="@WRAPPER_VERSION@.0"> 2 <tool id="seqtk_comp" name="seqtk_comp" version="@WRAPPER_VERSION@.0">
3 <description>get the nucleotide composition of FASTA/Q</description> 3 <description>get the nucleotide composition of FASTA/Q</description>
4 <macros> 4 <macros>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements"/> 7 <expand macro="requirements"/>
8 <expand macro="stdio"/> 8 <expand macro="stdio"/>
9 <command><![CDATA[seqtk comp 9 <command><![CDATA[
10 seqtk comp
10 #if $in_bed: 11 #if $in_bed:
11 -r $in_bed 12 -r '$in_bed'
12 #end if 13 #end if
13 14 '$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'
14 $in_file | awk 'BEGIN{print "#chr\tlength\t#A\t#C\t#G\t#T\t#2\t#3\t#4\t#CpG\t#tv\t#ts\t#CpG-ts"}1' 15 > '$default'
15 16 ]]></command>
16 > $default]]></command> 17 <inputs>
17 <inputs> 18 <expand macro="in_faq"/>
18 <expand macro="in_faq"/> 19 <param name="in_bed" type="data" format="bed" optional="true" label="BED file"/>
19 <param name="in_bed" optional="True" type="data" format="bed" label="bed file"/> 20 </inputs>
20 </inputs> 21 <outputs>
21 <outputs> 22 <data name="default" format="tabular" label="Nucleotide composition of $in_file.name"/>
22 <data format="tabular" hidden="false" name="default" label="Nucleotide composition of $in_file.name"/> 23 </outputs>
23 </outputs> 24 <tests>
24 <tests> 25 <test>
25 <test> 26 <param name="in_file" value="seqtk_comp.fa" ftype="fasta"/>
26 <param name="in_file" value="seqtk_comp.fa" ftype="fasta"/> 27 <output name="default" file="seqtk_comp.out" ftype="tabular"/>
27 <output name="default" file="seqtk_comp.out" ftype="tabular"/> 28 </test>
28 </test> 29 </tests>
29 </tests> 30 <help><![CDATA[
30 <help><![CDATA[
31 **What it does** 31 **What it does**
32 32
33 Reports composition of fasta/fastq sequences. For an example sequence like 33 Reports composition of fasta/fastq sequences. For an example sequence like
34 34
35 :: 35 ::
44 44
45 #chr length #A #C #G #T #2 #3 #4 #CpG #tv #ts #CpG-ts 45 #chr length #A #C #G #T #2 #3 #4 #CpG #tv #ts #CpG-ts
46 test0 11 4 2 2 2 0 0 1 0 0 0 0 46 test0 11 4 2 2 2 0 0 1 0 0 0 0
47 ambig_ref 15 1 2 3 4 0 4 1 4 0 0 0 47 ambig_ref 15 1 2 3 4 0 4 1 4 0 0 0
48 48
49
50 @ATTRIBUTION@ 49 @ATTRIBUTION@
51 ]]></help> 50 ]]></help>
52 <expand macro="citation" /> 51 <expand macro="citation" />
53 </tool> 52 </tool>