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comparison BlastAlign.xml @ 5:0d2da4c020dc draft

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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit df6ba874c5e5f0cde12c9253b5c192e4a35f2280
author abims-sbr
date Thu, 18 Jan 2018 08:13:26 -0500
parents 9eb5bb56bf41
children e0bea88bb09f
comparison
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4:9eb5bb56bf41 5:0d2da4c020dc
1 <tool name="BlastAlign" id="blastalign" version="2.0"> 1 <tool name="BlastAlign" id="blastalign" version="2.1">
2 2
3 <description> 3 <description>
4 Align the nucleic acid sequences using BLASTN 4 Align the nucleic acid sequences using BLASTN
5 </description> 5 </description>
6 6
53 53
54 <param name="fasta_out" type="boolean" checked="true" label="Do you want to convert the output phylip in fasta format ? " /> 54 <param name="fasta_out" type="boolean" checked="true" label="Do you want to convert the output phylip in fasta format ? " />
55 </inputs> 55 </inputs>
56 56
57 <outputs> 57 <outputs>
58 <data format="phylip" name="phy" from_work_dir="out.phy" label="Alignment of ${input.name} in phylip" hidden="True"/> 58 <!-- visible="true" ? -->
59 <data format="nexus" name="nxs" from_work_dir="out.nxs" label="Alignment of ${input.name} in nexus" hidden="True"/> 59 <data format="phylip" name="phy" from_work_dir="out.phy" label="Alignment of ${input.name} in phylip" />
60 <data format="fasta" name="fasta" from_work_dir="out.fasta" label="Alignment of ${input.name} in fasta" hidden="True"> 60 <data format="nexus" name="nxs" from_work_dir="out.nxs" label="Alignment of ${input.name} in nexus" />
61 <data format="fasta" name="fasta" from_work_dir="out.fasta" label="Alignment of ${input.name} in fasta" />
61 <filter>fasta_out == True</filter> 62 <filter>fasta_out == True</filter>
62 </data> 63 </data>
63 </outputs> 64 </outputs>
64 65
65 <tests> 66 <tests>
102 </section> 103 </section>
103 <param name="fasta_out" value="False" /> 104 <param name="fasta_out" value="False" />
104 <output name="phy" value="outputs/locus3_sp2.phy" /> 105 <output name="phy" value="outputs/locus3_sp2.phy" />
105 <output name="nxs" value="outputs/locus3_sp2.nxs" /> 106 <output name="nxs" value="outputs/locus3_sp2.nxs" />
106 </test> 107 </test>
107 <test>
108 <param name="input" ftype="fasta" value="inputs/locus8_sp2.fasta" />
109 <section name="advanced_option">
110 <param name="m" value="95" />
111 <param name="r" value="" />
112 <param name="x" value="" />
113 <param name="n" value="False" />
114 <param name="s" value="0" />
115 </section>
116 <param name="fasta_out" value="True" />
117 <output name="phy" value="outputs/locus8_sp2.phy" />
118 <output name="nxs" value="outputs/locus8_sp2.nxs" />
119 <output name="fasta" value="outputs/locus8_sp2.fasta" />
120 </test>
121
122 <!--locus10_sp2.fasta locus1_sp3.fasta locus2_sp2.fasta locus3_sp2.fasta locus4_sp2.fasta locus5_sp2.fasta locus6_sp2.fasta locus7_sp2.fasta locus8_sp2.fasta locus9_sp2.fasta-->
123 </tests> 108 </tests>
124 109
125 <help> 110 <help>
126 <![CDATA[ 111 <![CDATA[
127 112