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comparison seqtk_seq.xml @ 3:bc7d99f46a5d 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 13:27:11 -0400
parents f73729b62b51
children ecf1c30da3a2
comparison
equal deleted inserted replaced
2:f73729b62b51 3:bc7d99f46a5d
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="seqtk_seq" name="seqtk_seq" version="@WRAPPER_VERSION@.0"> 2 <tool id="seqtk_seq" name="seqtk_seq" version="@WRAPPER_VERSION@.2">
3 <description>common transformation of FASTA/Q</description> 3 <description>common transformation 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 seq -q $q 9 <command><![CDATA[
10 seqtk seq -q $q
10 -X $X 11 -X $X
11 #if $n and $n != "None" and $n is not None and $n != "": 12 #if $n:
12 -n "$n" 13 -n '$n'
13 #end if 14 #end if
14 -l $l 15 -l $l
15 -Q $Q 16 -Q $Q
16 -s $s 17 -s $s
17 -f $f 18 -f $f
18 #if $M and $M != "None" and $M is not None and $M != "": 19 #if $M:
19 -M "$M" 20 -M '$M'
20 #end if 21 #end if
21 -L $L 22 -L $L
22 $c 23 $c
23 $r 24 $r
24 $A 25 $A
25 $C 26 $C
26 $N 27 $N
27 $x1 28 $x1
28 $x2 29 $x2
29 #if $in_file.ext == "fastqillumina" 30 #if $in_file.is_of_type('fastqillumina')
30 -V 31 -V
31 #end if 32 #end if
32 33 '$in_file'
33 $in_file 34 > '$default'
34 > $default]]></command> 35 ]]></command>
35 <inputs> 36 <inputs>
36 <expand macro="in_faq"/> 37 <expand macro="in_faq"/>
37 <param label="mask bases with quality lower than INT" help="(-q)" name="q" type="integer" value="0"/> 38 <param argument="-q" type="integer" value="0" label="Mask bases with quality lower than INT" />
38 <param label="mask bases with quality higher than INT" help="(-X)" name="X" type="integer" value="255"/> 39 <param argument="-X" type="integer" value="255" label="Mask bases with quality higher than INT" />
39 <param area="false" default="0" label="masked bases converted to CHAR; 0 for lowercase" help="(-n)" name="n" type="text"/> 40 <param argument="-n" type="text" value="0" label="Masked bases converted to CHAR; 0 for lowercase" />
40 <param label="number of residues per line; 0 for 2^32-1" help="(-l)" name="l" type="integer" value="0"/> 41 <param argument="-l" type="integer" value="0" label="Number of residues per line; 0 for 2^32-1" />
41 <param label="quality shift: ASCII-INT gives base quality" help="(-Q)" name="Q" type="integer" value="33"/> 42 <param argument="-Q" type="integer" value="33" label="Quality shift: ASCII-INT gives base quality" />
42 <param label="random seed" help="effective with -f (-s)" name="s" type="integer" value="11"/> 43 <param argument="-s" type="integer" value="11" label="Random seed" help="Effective with -f" />
43 <param label="sample fraction of sequences" help="(-f)" name="f" type="float" value="1"/> 44 <param argument="-f" type="float" value="1" label="Sample fraction of sequences" />
44 <param area="false" default="null" label="mask regions in BED or name list FILE" help="(-M)" name="M" type="text"/> 45 <param argument="-M" type="data" format="bed,txt" optional="true" label="Mask regions in BED or name list file" />
45 <param label="drop sequences with length shorter than INT" help="(-L)" name="L" type="integer" value="0"/> 46 <param argument="-L" type="integer" value="0" label="Drop sequences with length shorter than INT" />
46 <param checked="false" label="mask complement region" help="effective with -M (-c)" name="c" type="boolean" falsevalue="" truevalue="-c"/> 47 <param argument="-c" type="boolean" truevalue="-c" falsevalue="" checked="false" label="Mask complement region" help="Effective with -M" />
47 <param checked="false" label="reverse complement" help="(-r)" name="r" type="boolean" falsevalue="" truevalue="-r"/> 48 <param argument="-r" type="boolean" truevalue="-r" falsevalue="" checked="false" label="Reverse complement" />
48 <param checked="false" label="force FASTA output (discard quality)" help="(-A)" name="A" type="boolean" falsevalue="" truevalue="-A"/> 49 <param argument="-A" type="boolean" truevalue="-A" falsevalue="" checked="false" label="Force FASTA output (discard quality)" />
49 <param checked="false" label="drop comments at the header lines" help="(-C)" name="C" type="boolean" falsevalue="" truevalue="-C"/> 50 <param argument="-C" type="boolean" truevalue="-C" falsevalue="" checked="false" label="Drop comments at the header lines" />
50 <param checked="false" label="drop sequences containing ambiguous bases" help="(-N)" name="N" type="boolean" falsevalue="" truevalue="-N"/> 51 <param argument="-N" type="boolean" truevalue="-N" falsevalue="" checked="false" label="Drop sequences containing ambiguous bases" />
51 <param checked="false" label="output the 2n-1 reads only" help="(-1)" name="x1" type="boolean" falsevalue="" truevalue="-1"/> 52 <param name="x1" argument="-1" type="boolean" truevalue="-1" falsevalue="" checked="false" label="Output the 2n-1 reads only" />
52 <param checked="false" label="output the 2n reads only" help="(-2)" name="x2" type="boolean" falsevalue="" truevalue="-2"/> 53 <param name="x2" argument="-2" type="boolean" truevalue="-2" falsevalue="" checked="false" label="Output the 2n reads only" />
53 </inputs> 54 </inputs>
54 <outputs> 55 <outputs>
55 <data format_source="in_file" hidden="false" name="default"/> 56 <data name="default" format_source="in_file" />
56 </outputs> 57 </outputs>
57 <tests> 58 <tests>
58 <test> 59 <!-- This is a sorry excuse for a test for a tool which does way more
59 <!-- This is a sorry excuse for a test for a tool which does way more 60 than it should, but upstream decided to put a TON of functionality
60 than it should, but upstream decided to put a TON of functionality 61 into a single tool rather than using the single responsibility
61 into a single tool rather than using the single responsibility 62 principle. -->
62 principle. --> 63 <test>
63 <param name="in_file" value="seqtk_seq.fa"/> 64 <param name="in_file" value="seqtk_seq.fa"/>
64 <param name="r" value="True"/> 65 <param name="r" value="True"/>
65 <param name="n" value=""/> 66 <param name="n" value=""/>
66 <param name="M" value=""/> 67 <output name="default" file="seqtk_seq_revcom.fa" ftype="fasta"/>
67 <output name="default" file="seqtk_seq_revcom.fa" ftype="fasta"/> 68 </test>
68 </test> 69 </tests>
69 </tests> 70 <help><![CDATA[
70 <help><![CDATA[
71 **What it does** 71 **What it does**
72 72
73 Various utilities for transforming FASTA/Q data 73 Various utilities for transforming FASTA/Q data
74 74
75 @ATTRIBUTION@ 75 @ATTRIBUTION@
76 ]]></help> 76 ]]></help>
77 <expand macro="citation" /> 77 <expand macro="citation" />
78 </tool> 78 </tool>