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comparison fasplit.xml @ 3:086ddedd1bad draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fasplit commit 303002db06287fb25306020c4391626842f52162
author iuc
date Sun, 22 Sep 2024 07:24:45 +0000
parents 713741ee0185
children
comparison
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2:713741ee0185 3:086ddedd1bad
1 <tool id="fasplit" name="faSplit" version="@TOOL_VERSION@"> 1 <tool id="fasplit" name="faSplit" version="@TOOL_VERSION@" profile="22.05">
2 <description>Split a FASTA file</description> 2 <description>Split a FASTA file</description>
3 <macros>
4 <token name="@TOOL_VERSION@">469</token>
5 </macros>
3 <xrefs> 6 <xrefs>
4 <xref type="bio.tools">UCSC_Genome_Browser_Utilities</xref> 7 <xref type="bio.tools">UCSC_Genome_Browser_Utilities</xref>
5 </xrefs> 8 </xrefs>
6 <macros>
7 <token name="@TOOL_VERSION@">377</token>
8 </macros>
9 <requirements> 9 <requirements>
10 <requirement type="package" version="@TOOL_VERSION@">ucsc-fasplit</requirement> 10 <requirement type="package" version="@TOOL_VERSION@">ucsc-fasplit</requirement>
11 </requirements> 11 </requirements>
12 <command detect_errors="exit_code"><![CDATA[ 12 <command detect_errors="exit_code"><![CDATA[
13 mkdir out && 13 mkdir out &&
55 <element name="0" file="0.fa" /> 55 <element name="0" file="0.fa" />
56 <element name="1" file="1.fa" /> 56 <element name="1" file="1.fa" />
57 <element name="2" file="2.fa" /> 57 <element name="2" file="2.fa" />
58 <element name="3" file="3.fa" /> 58 <element name="3" file="3.fa" />
59 <element name="4" file="4.fa" /> 59 <element name="4" file="4.fa" />
60 </output_collection> 60 </output_collection>
61 </test> 61 </test>
62 <test> 62 <test>
63 <param name="input" ftype="fasta" value="CDS.fa"/> 63 <param name="input" ftype="fasta" value="CDS.fa"/>
64 <param name="split_type" value="byname"/> 64 <param name="split_type" value="byname"/>
65 <output_collection name="output_list" type="list"> 65 <output_collection name="output_list" type="list">
66 <element name="ENSCAFT00000022939_canisfamiliaris" file="ENSCAFT00000022939_canisfamiliaris.fa" /> 66 <element name="ENSCAFT00000022939_canisfamiliaris" file="ENSCAFT00000022939_canisfamiliaris.fa" />
67 <element name="ENSCAFT00000022963_canisfamiliaris" file="ENSCAFT00000022963_canisfamiliaris.fa" />
68 <element name="ENSCAFT00000025950_canisfamiliaris" file="ENSCAFT00000025950_canisfamiliaris.fa" />
69 <element name="ENSMUST00000026013_musmusculus" file="ENSMUST00000026013_musmusculus.fa" />
70 <element name="ENSMUST00000040820_musmusculus" file="ENSMUST00000040820_musmusculus.fa" />
71 <element name="ENSMUST00000041588_musmusculus" file="ENSMUST00000041588_musmusculus.fa" />
72 <element name="ENSMUST00000091291_musmusculus" file="ENSMUST00000091291_musmusculus.fa" />
73 <element name="ENSMUST00000100505_musmusculus" file="ENSMUST00000100505_musmusculus.fa" />
74 <element name="ENSMUST00000110806_musmusculus" file="ENSMUST00000110806_musmusculus.fa" />
75 <element name="ENSMUST00000153440_musmusculus" file="ENSMUST00000153440_musmusculus.fa" />
76 <element name="ENSMUST00000163344_musmusculus" file="ENSMUST00000163344_musmusculus.fa" />
77 <element name="ENSMUST00000168613_musmusculus" file="ENSMUST00000168613_musmusculus.fa" />
78 <element name="ENSMUST00000173143_musmusculus" file="ENSMUST00000173143_musmusculus.fa" />
67 <element name="ENSMUST00000207100_musmusculus" file="ENSMUST00000207100_musmusculus.fa" /> 79 <element name="ENSMUST00000207100_musmusculus" file="ENSMUST00000207100_musmusculus.fa" />
80 <element name="ENSMUST00000208839_musmusculus" file="ENSMUST00000208839_musmusculus.fa" />
81 <element name="ENSPTRT00000019089_pantroglodytes" file="ENSPTRT00000019089_pantroglodytes.fa" />
82 <element name="ENSPTRT00000034846_pantroglodytes" file="ENSPTRT00000034846_pantroglodytes.fa" />
83 <element name="ENSPTRT00000040520_pantroglodytes" file="ENSPTRT00000040520_pantroglodytes.fa" />
84 <element name="ENSPTRT00000040521_pantroglodytes" file="ENSPTRT00000040521_pantroglodytes.fa" />
85 <element name="ENSRNOT00000041155_rattusnorvegicus" file="ENSRNOT00000041155_rattusnorvegicus.fa" />
86 <element name="ENSRNOT00000044009_rattusnorvegicus" file="ENSRNOT00000044009_rattusnorvegicus.fa" />
87 <element name="ENSRNOT00000064726_rattusnorvegicus" file="ENSRNOT00000064726_rattusnorvegicus.fa" />
88 <element name="ENSRNOT00000066674_rattusnorvegicus" file="ENSRNOT00000066674_rattusnorvegicus.fa" />
89 <element name="ENSRNOT00000067448_rattusnorvegicus" file="ENSRNOT00000067448_rattusnorvegicus.fa" />
90 <element name="ENSSSCT00000008295_susscrofa" file="ENSSSCT00000008295_susscrofa.fa" />
91 <element name="ENSSSCT00000013404_susscrofa" file="ENSSSCT00000013404_susscrofa.fa" />
68 <element name="ENSSSCT00000014817_susscrofa" file="ENSSSCT00000014817_susscrofa.fa" /> 92 <element name="ENSSSCT00000014817_susscrofa" file="ENSSSCT00000014817_susscrofa.fa" />
69 <element name="ENSCAFT00000022963_canisfamiliaris" file="ENSCAFT00000022963_canisfamiliaris.fa" />
70 <element name="ENSMUST00000208839_musmusculus" file="ENSMUST00000208839_musmusculus.fa" />
71 <element name="ENSSSCT00000023183_susscrofa" file="ENSSSCT00000023183_susscrofa.fa" /> 93 <element name="ENSSSCT00000023183_susscrofa" file="ENSSSCT00000023183_susscrofa.fa" />
72 <element name="ENSCAFT00000025950_canisfamiliaris" file="ENSCAFT00000025950_canisfamiliaris.fa" />
73 <element name="ENSPTRT00000019089_pantroglodytes" file="ENSPTRT00000019089_pantroglodytes.fa" />
74 <element name="ENSSSCT00000032764_susscrofa" file="ENSSSCT00000032764_susscrofa.fa" /> 94 <element name="ENSSSCT00000032764_susscrofa" file="ENSSSCT00000032764_susscrofa.fa" />
75 <element name="ENSMUST00000026013_musmusculus" file="ENSMUST00000026013_musmusculus.fa" />
76 <element name="ENSPTRT00000034846_pantroglodytes" file="ENSPTRT00000034846_pantroglodytes.fa" />
77 <element name="ENSSSCT00000033745_susscrofa" file="ENSSSCT00000033745_susscrofa.fa" /> 95 <element name="ENSSSCT00000033745_susscrofa" file="ENSSSCT00000033745_susscrofa.fa" />
78 <element name="ENSMUST00000040820_musmusculus" file="ENSMUST00000040820_musmusculus.fa" />
79 <element name="ENSPTRT00000040520_pantroglodytes" file="ENSPTRT00000040520_pantroglodytes.fa" />
80 <element name="ENSSSCT00000035258_susscrofa" file="ENSSSCT00000035258_susscrofa.fa" /> 96 <element name="ENSSSCT00000035258_susscrofa" file="ENSSSCT00000035258_susscrofa.fa" />
81 <element name="ENSMUST00000041588_musmusculus" file="ENSMUST00000041588_musmusculus.fa" />
82 <element name="ENSPTRT00000040521_pantroglodytes" file="ENSPTRT00000040521_pantroglodytes.fa" />
83 <element name="ENST00000302850_homosapiens" file="ENST00000302850_homosapiens.fa" /> 97 <element name="ENST00000302850_homosapiens" file="ENST00000302850_homosapiens.fa" />
84 <element name="ENSMUST00000091291_musmusculus" file="ENSMUST00000091291_musmusculus.fa" />
85 <element name="ENSRNOT00000041155_rattusnorvegicus" file="ENSRNOT00000041155_rattusnorvegicus.fa" />
86 <element name="ENST00000338702_homosapiens" file="ENST00000338702_homosapiens.fa" /> 98 <element name="ENST00000338702_homosapiens" file="ENST00000338702_homosapiens.fa" />
87 <element name="ENSMUST00000100505_musmusculus" file="ENSMUST00000100505_musmusculus.fa" />
88 <element name="ENSRNOT00000044009_rattusnorvegicus" file="ENSRNOT00000044009_rattusnorvegicus.fa" />
89 <element name="ENST00000340611_homosapiens" file="ENST00000340611_homosapiens.fa" /> 99 <element name="ENST00000340611_homosapiens" file="ENST00000340611_homosapiens.fa" />
90 <element name="ENSMUST00000110806_musmusculus" file="ENSMUST00000110806_musmusculus.fa" />
91 <element name="ENSRNOT00000064726_rattusnorvegicus" file="ENSRNOT00000064726_rattusnorvegicus.fa" />
92 <element name="ENST00000341500_homosapiens" file="ENST00000341500_homosapiens.fa" /> 100 <element name="ENST00000341500_homosapiens" file="ENST00000341500_homosapiens.fa" />
93 <element name="ENSMUST00000153440_musmusculus" file="ENSMUST00000153440_musmusculus.fa" />
94 <element name="ENSRNOT00000066674_rattusnorvegicus" file="ENSRNOT00000066674_rattusnorvegicus.fa" />
95 <element name="ENST00000378069_homosapiens" file="ENST00000378069_homosapiens.fa" /> 101 <element name="ENST00000378069_homosapiens" file="ENST00000378069_homosapiens.fa" />
96 <element name="ENSMUST00000163344_musmusculus" file="ENSMUST00000163344_musmusculus.fa" />
97 <element name="ENSRNOT00000067448_rattusnorvegicus" file="ENSRNOT00000067448_rattusnorvegicus.fa" />
98 <element name="ENST00000421712_homosapiens" file="ENST00000421712_homosapiens.fa" /> 102 <element name="ENST00000421712_homosapiens" file="ENST00000421712_homosapiens.fa" />
99 <element name="ENSMUST00000168613_musmusculus" file="ENSMUST00000168613_musmusculus.fa" />
100 <element name="ENSSSCT00000008295_susscrofa" file="ENSSSCT00000008295_susscrofa.fa" />
101 <element name="ENST00000542639_homosapiens" file="ENST00000542639_homosapiens.fa" /> 103 <element name="ENST00000542639_homosapiens" file="ENST00000542639_homosapiens.fa" />
102 <element name="ENSMUST00000173143_musmusculus" file="ENSMUST00000173143_musmusculus.fa" />
103 <element name="ENSSSCT00000013404_susscrofa" file="ENSSSCT00000013404_susscrofa.fa" />
104 <element name="ENST00000600492_homosapiens" file="ENST00000600492_homosapiens.fa" /> 104 <element name="ENST00000600492_homosapiens" file="ENST00000600492_homosapiens.fa" />
105 </output_collection> 105 </output_collection>
106 </test> 106 </test>
107 </tests> 107 </tests>
108 <help><![CDATA[ 108 <help><![CDATA[
109 **What it does** 109 **What it does**
110 110
111 `faSplit`_ is a tool to split a single FASTA file into several files. 111 `faSplit`_ is a tool to split a single FASTA file into several files.
112 112
113 For implementation details see faSplit's `source code`_.
114
113 .. _faSplit: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/FOOTER.txt 115 .. _faSplit: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/FOOTER.txt
116 .. _source code: https://github.com/ucscGenomeBrowser/kent/blob/master/src/utils/faSplit/faSplit.c
114 ]]></help> 117 ]]></help>
115 <citations> 118 <citations>
119 <citation type="doi">10.1093/bib/bbs038</citation>
116 </citations> 120 </citations>
117 </tool> 121 </tool>