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comparison sorting.xml @ 3:ebd03dc31ed4 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 32693b6ea0a12cd77294fdc3cae53863cba4a8f6
author iuc
date Wed, 26 Aug 2015 08:11:49 -0400
parents 24e4f42410e5
children e8401372796a
comparison
equal deleted inserted replaced
2:90759bd72d2e 3:ebd03dc31ed4
1 <tool id="vsearch_sorting" name="VSearch sorting" version="@VERSION@.0"> 1 <tool id="vsearch_sorting" name="VSearch sorting" version="@VERSION@.1">
2 <description></description> 2 <description></description>
3 <macros> 3 <macros>
4 <import>vsearch_macros.xml</import> 4 <import>vsearch_macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
20 #if $sorting_mode.maxsize: 20 #if $sorting_mode.maxsize:
21 --maxsize $sorting_mode.maxsize 21 --maxsize $sorting_mode.maxsize
22 #end if 22 #end if
23 #end if 23 #end if
24 --output $outfile 24 --output $outfile
25 #if $sizeout: 25 #if $relabel:
26 --sizeout $sizeout 26 --relabel "$relabel"
27 #end if 27 #end if
28 $sizeout
28 #if $topn: 29 #if $topn:
29 --topn $topn 30 --topn $topn
30 #end if 31 #end if
31 32
32 ]]> 33 ]]>
47 <param name="maxsize" type="integer" value="" optional="True" label="Maximum abundance" 48 <param name="maxsize" type="integer" value="" optional="True" label="Maximum abundance"
48 help="(--maxsize)"/> 49 help="(--maxsize)"/>
49 </when> 50 </when>
50 </conditional> 51 </conditional>
51 <expand macro="topn" /> 52 <expand macro="topn" />
53 <param name="relabel" type="text" value=""
54 label="Relabel with this prefix string after sorting" help="(--relabel)"/>
52 <param name="sizeout" type="boolean" truevalue="--sizeout" falsevalue="" checked="False" 55 <param name="sizeout" type="boolean" truevalue="--sizeout" falsevalue="" checked="False"
53 label="Add abundance annotation to output" help="(--sizeout)"/> 56 label="Add abundance annotation to output" help="(--sizeout)"/>
54 </inputs> 57 </inputs>
55 <outputs> 58 <outputs>
56 <data name="outfile" format="fasta" label="${tool.name} on ${on_string}" /> 59 <data name="outfile" format="fasta" label="${tool.name} on ${on_string}" />
63 </test> 66 </test>
64 <test> 67 <test>
65 <param name="sorting_mode_select" value="sortbylength"/> 68 <param name="sorting_mode_select" value="sortbylength"/>
66 <param name="infile" value="db.fasta" ftype="fasta" /> 69 <param name="infile" value="db.fasta" ftype="fasta" />
67 <output name="outfile" file="sorting_result2.fasta" ftype="fasta" /> 70 <output name="outfile" file="sorting_result2.fasta" ftype="fasta" />
71 </test>
72 <test>
73 <param name="sorting_mode_select" value="sortbylength"/>
74 <param name="infile" value="db.fasta" ftype="fasta" />
75 <param name="relabel" value="TEST" />
76 <output name="outfile" file="sorting_result3.fasta" ftype="fasta" />
77 </test>
78 <test>
79 <param name="sorting_mode_select" value="sortbylength"/>
80 <param name="infile" value="db.fasta" ftype="fasta" />
81 <param name="sizeout" value="--sizeout" />
82 <output name="outfile" file="sorting_result4.fasta" ftype="fasta" />
83 </test>
84 <test>
85 <param name="sorting_mode_select" value="sortbylength"/>
86 <param name="infile" value="db.fasta" ftype="fasta" />
87 <param name="relabel" value="With spaces" />
88 <output name="outfile" file="sorting_result5.fasta" ftype="fasta" />
68 </test> 89 </test>
69 </tests> 90 </tests>
70 <help> 91 <help>
71 <![CDATA[ 92 <![CDATA[
72 **What it does** 93 **What it does**