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comparison amrfinderplus.xml @ 2:a9e5d593228e draft default tip

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planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/ncbi-armfinderplus commit 2c3091cc8850849ac99884f92f195e4de9774f99
author thanhlv
date Wed, 11 Sep 2019 09:51:28 -0400
parents f92ab7729a35
children
comparison
equal deleted inserted replaced
1:f92ab7729a35 2:a9e5d593228e
27 -p '$input_selection.pro_file' 27 -p '$input_selection.pro_file'
28 #if $input_selection.gff.use == 'gff_yes' 28 #if $input_selection.gff.use == 'gff_yes'
29 -g '$input_selection.gff.gff_file' 29 -g '$input_selection.gff.gff_file'
30 #end if 30 #end if
31 #end if 31 #end if
32 #if str($organism) != 'none' 32 #if str($organism) != 'None'
33 -O $organism 33 -O $organism
34 #end if 34 #end if
35 -o results.tsv 35 -o results.tsv
36 $report_common 36 $report_common
37 #if $point_mut_all 37 #if $point_mut_all
85 <options from_data_table="amrfinder_databases"> 85 <options from_data_table="amrfinder_databases">
86 <validator message="No database is available" type="no_options" /> 86 <validator message="No database is available" type="no_options" />
87 </options> 87 </options>
88 </param> 88 </param>
89 <param name="organism" type="select" optional="true" label="Get organism-specific results"> 89 <param name="organism" type="select" optional="true" label="Get organism-specific results">
90 <option value="none" selected="true">None</option>
91 <option value="Campylobacter">Campylobacter</option> 90 <option value="Campylobacter">Campylobacter</option>
92 <option value="Escherichia">Escherichia</option> 91 <option value="Escherichia">Escherichia</option>
93 <option value="Klebsiella">Klebsiella</option> 92 <option value="Klebsiella">Klebsiella</option>
94 <option value="Salmonella">Salmonella</option> 93 <option value="Salmonella">Salmonella</option>
95 <option value="Staphylococcus">Staphylococcus</option> 94 <option value="Staphylococcus">Staphylococcus</option>
110 </data> 109 </data>
111 </outputs> 110 </outputs>
112 111
113 <tests> 112 <tests>
114 <test> <!-- dna input--> 113 <test> <!-- dna input-->
115 <param name="input_selection|input_source_selector" value="nuc"/> 114 <param name="input_source_selector" value="nuc"/>
116 <param name="fasta_file" value="test_dna.fa" ftype="fasta"/> 115 <param name="fasta_file" value="test_dna.fa" ftype="fasta"/>
117 <param name="amrfinder_databases" value="2019-08-27.1" /> 116 <param name="amrfinder_databases" value="2019-08-27.1" />
118 <output name="result" file="test_dna.expected" lines_diff="1"/> 117 <output name="result" file="test_dna.expected" lines_diff="1"/>
119 </test> 118 </test>
120 <test> <!-- dna input and organism, plus gene--> 119 <test> <!-- dna input and organism, plus gene-->
121 <param name="input_selection|input_source_selector" value="nuc"/> 120 <param name="input_source_selector" value="nuc"/>
122 <param name="fasta_file" value="test_dna.fa" ftype="fasta"/> 121 <param name="fasta_file" value="test_dna.fa" ftype="fasta"/>
123 <param name="organism" value="Escherichia" /> 122 <param name="organism" value="Escherichia" />
124 <param name="plus" value="true" /> 123 <param name="plus" value="true" />
125 <param name="amrfinder_databases" value="2019-08-27.1" /> 124 <param name="amrfinder_databases" value="2019-08-27.1" />
126 <output name="result" file="test_dna_Escherichia.expected" lines_diff="1"/> 125 <output name="result" file="test_dna_Escherichia.expected" lines_diff="1"/>
127 </test> 126 </test>
128 <test> <!-- AA input--> 127 <test> <!-- AA input-->
129 <param name="input_selection|input_source_selector" value="pro"/> 128 <param name="input_source_selector" value="pro"/>
130 <param name="fasta_file" value="test_prot.fa" ftype="fasta"/> 129 <param name="fasta_file" value="test_prot.fa" ftype="fasta"/>
131 <param name="amrfinder_databases" value="2019-08-27.1" /> 130 <param name="amrfinder_databases" value="2019-08-27.1" />
132 <output name="result" file="test_prot.expected" lines_diff="1"/> 131 <output name="result" file="test_prot.expected" lines_diff="1"/>
133 </test> 132 </test>
134 <test> <!-- DNA and AA input--> 133 <test> <!-- DNA and AA input-->
135 <param name="input_selection|input_source_selector" value="both"/> 134 <param name="input_source_selector" value="both"/>
136 <param name="input_selection|input_source_selector|gff|use" value="gff_yes"/> 135 <param name="use" value="gff_yes"/>
137 <param name="nuc_file" value="test_dna.fa" ftype="fasta"/> 136 <param name="nuc_file" value="test_dna.fa" ftype="fasta"/>
138 <param name="pro_file" value="test_prot.fa" ftype="fasta"/> 137 <param name="pro_file" value="test_prot.fa" ftype="fasta"/>
139 <param name="input_selection|gff|use" value="gff_yes"/> 138 <param name="use" value="gff_yes"/>
140 <param name="gff_file" value="test_prot.gff" ftype="gff3"/> 139 <param name="gff_file" value="test_prot.gff" ftype="gff3"/>
141 <param name="amrfinder_databases" value="2019-08-27.1" /> 140 <param name="amrfinder_databases" value="2019-08-27.1" />
142 <output name="result" file="test_both.expected" lines_diff="1"/> 141 <output name="result" file="test_both.expected" lines_diff="1"/>
143 </test> 142 </test>
144 </tests> 143 </tests>