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comparison blastXmlToPsl.xml @ 2:30f2068e8738 draft

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planemo upload commit cdddf587d82288414cfffd0ce6e312b4bf45a842-dirty
author yating-l
date Thu, 28 Jun 2018 12:32:41 -0400
parents ed804cd92001
children 2be225b8c6cc
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1:8239e68ff79c 2:30f2068e8738
1 <tool id="blastXmlToPsl" name="blastXmlToPsl" version="0.1.0"> 1 <tool id="blastXmlToPsl" name="blastXmlToPsl" version="1.1">
2 <requirements> 2 <requirements>
3 </requirements> 3 </requirements>
4 <stdio> 4 <stdio>
5 <exit_code range="1:" /> 5 <exit_code range="1:" />
6 </stdio> 6 </stdio>
7 <command><![CDATA[ 7 <command><![CDATA[
8 $__tool_directory__/blastXmlToPsl -convertToNucCoords $input $output 8 $__tool_directory__/blastXmlToPsl $input $output
9 #if $convertToNucCoords == "true"
10 -convertToNucCoords
11 #end if
9 ]]></command> 12 ]]></command>
10 <inputs> 13 <inputs>
11 <param type="data" name="input" format="xml" /> 14 <param type="data" name="input" format="xml" />
15 <param type="boolean" name="convertToNucCoords" checked="true" label="only support for TBLASTN restuls. Convert protein to nucleic alignments to nucleic
16 to nucleic coordinates"/>
12 </inputs> 17 </inputs>
13 <outputs> 18 <outputs>
14 <data format="psl" name="output" /> 19 <data format="psl" name="output" />
15 </outputs> 20 </outputs>
21 <tests>
22 <test>
23 <param name="input" value="tblastn_Dbia3_ci.xml" />
24 <param name="convertToNucCoords" value="true" />
25 <output name="output" value="tblastn_Dbia3_ci.psl" />
26 </test>
27 <test>
28 <param name="input" value="blastn_mRNA_seq.xml" />
29 <param name="convertToNucCoords" value="false" />
30 <output name="output" value="blastn_mRNA_seq.psl" />
31 </test>
32 </tests>
16 <help><![CDATA[ 33 <help><![CDATA[
17 blastXmlToPsl - convert blast XML output to PSLs 34 blastXmlToPsl - convert blast XML output to PSLs
18 35
19 usage: 36 usage:
20 blastXmlToPsl [options] blastXml psl 37 blastXmlToPsl [options] blastXml psl
56 -forcePsiBlast - treat as output of PSI-BLAST. blast-2.2.16 and maybe 73 -forcePsiBlast - treat as output of PSI-BLAST. blast-2.2.16 and maybe
57 others indentify psiblast as blastp. 74 others indentify psiblast as blastp.
58 75
59 Output only results of last round from PSI BLAST 76 Output only results of last round from PSI BLAST
60 ]]></help> 77 ]]></help>
78 <citations>
79 <citation type="bibtex">
80 @article{Kent01062002,
81 author = {Kent, W. James and Sugnet, Charles W. and Furey, Terrence S. and Roskin, Krishna M. and Pringle, Tom H. and Zahler, Alan M. and Haussler, and David},
82 title = {The Human Genome Browser at UCSC},
83 volume = {12},
84 number = {6},
85 pages = {996-1006},
86 year = {2002},
87 doi = {10.1101/gr.229102},
88 URL = {http://genome.cshlp.org/content/12/6/996.abstract},
89 eprint = {http://genome.cshlp.org/content/12/6/996.full.pdf+html},
90 journal = {Genome Research}
91 }
92 </citation>
93 </citations>
61 </tool> 94 </tool>