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comparison kma_map.xml @ 3:d9bc3ec3a710 draft default tip

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author dfornika
date Wed, 05 Feb 2020 00:58:24 +0000
parents 1c1dba36c061
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2:1c1dba36c061 3:d9bc3ec3a710
1 <tool id="kma_map" name="Map with KMA" version="@TOOL_VERSION@+galaxy0"> 1 <tool id="kma_map" name="Map with KMA" version="@TOOL_VERSION@_galaxy0">
2 <description></description> 2 <description></description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
17 #elif $single_paired.single_paired_selector == "collection": 17 #elif $single_paired.single_paired_selector == "collection":
18 -ipe '${single_paired.input_pair.forward}' '${single_paired.input_pair.reverse}' 18 -ipe '${single_paired.input_pair.forward}' '${single_paired.input_pair.reverse}'
19 #else: 19 #else:
20 -i '${single_paired.input_sequences}' 20 -i '${single_paired.input_sequences}'
21 #end if 21 #end if
22 -o output && 22 #if str($settings.advanced) == "advanced"
23 gunzip output.frag.gz 23 #if str($settings.kmer_size)
24 -k '${settings.kmer_size}'
25 #end if
26 #if str($settings.p_value)
27 -p '${settings.p_value}'
28 #end if
29 ${settings.decontaminate}
30 ${settings.dense}
31 ${settings.ref_fsa}
32 ${settings.matrix}
33 ${settings.all_best_mappings}
34 #if str($settings.minimum_phred_score)
35 -mp '${settings.minimum_phred_score}'
36 #end if
37 #if str($settings.cut_5_prime)
38 -5p '${settings.cut_5_prime}'
39 #end if
40 ${settings.only_count_kmers}
41 #if str($settings.min_id)
42 -ID '${settings.min_id}'
43 #end if
44 ${settings.force_end_to_end}
45 #end if
46 -o output
47
48 #if str($settings.advanced) == "advanced" and $settings.matrix
49 && gunzip output.mat.gz
50 #end if
51 && gunzip output.frag.gz
24 ]]> 52 ]]>
25 </command> 53 </command>
26 <inputs> 54 <inputs>
27 <conditional name="single_paired"> 55 <conditional name="single_paired">
28 <param name="single_paired_selector" type="select" label="Single or paired reads" help="--paired"> 56 <param name="single_paired_selector" type="select" label="Single or paired reads" help="--paired">
39 </when> 67 </when>
40 <when value="no"> 68 <when value="no">
41 <param format="fastq" label="Input sequences" name="input_sequences" type="data" help="FASTQ datasets"/> 69 <param format="fastq" label="Input sequences" name="input_sequences" type="data" help="FASTQ datasets"/>
42 </when> 70 </when>
43 </conditional> 71 </conditional>
72
44 <param name="kma_index" type="select"> 73 <param name="kma_index" type="select">
45 <options from_data_table="kma_index"> 74 <options from_data_table="kma_index">
46 <validator type="no_options" message="No KMA index available" /> 75 <validator type="no_options" message="No KMA index available" />
47 </options> 76 </options>
48 </param> 77 </param>
78
79 <conditional name="settings">
80 <param name="advanced" type="select" label="Specify advanced parameters">
81 <option value="simple" selected="true">No, use program defaults.</option>
82 <option value="advanced">Yes, see full parameter list.</option>
83 </param>
84 <when value="simple">
85 </when>
86 <when value="advanced">
87 <param name="kmer_size" type="integer" min="4" value="16" max="32" label="Kmer Size" />
88 <param name="p_value" type="float" min="0.0" value="0.05" max="1.0" label="p-value"/>
89 <param name="exhaustive_mode" type="boolean" truevalue="-ex_mode" falsevalue="" label="Exhaustive Mode" />
90 <param name="decontaminate" type="boolean" truevalue="-deCon" falsevalue="" label="Decontaminate" />
91 <param name="dense" type="boolean" truevalue="-dense" falsevalue="" label="Do not allow insertions in assembly" />
92 <param name="ref_fsa" type="boolean" truevalue="-ref_fsa" falsevalue="" label="Consensus sequence has 'n' instead of gaps" />
93 <param name="matrix" type="boolean" truevalue="-matrix" falsevalue="" label="Print assembly matrix" />
94 <param name="all_best_mappings" type="boolean" truevalue="-a" falsevalue="" label="Print all best mappings" />
95 <param name="minimum_phred_score" type="integer" min="0" value="20" max="60" label="Minimum phred score" />
96 <param name="cut_5_prime" type="integer" min="0" value="0" max="64" label="Cut a constant number of nucleotides from the 5 prime" />
97 <param name="only_count_kmers" type="boolean" truevalue="-Sparse" falsevalue="" label="Only count kmers" />
98 <param name="min_id" type="float" min="0.0" value="1.0" max="100.0" label="Minimum percent identity"/>
99 <param name="force_end_to_end" type="boolean" truevalue="-1t1" falsevalue="" label="Force end to end mapping" />
100 </when>
101 </conditional>
49 </inputs> 102 </inputs>
50 <outputs> 103 <outputs>
51 <data name="result_overview" label="Result overview" format="tabular" from_work_dir="output.res" /> 104 <data name="result_overview" label="Result overview" format="tabular" from_work_dir="output.res" />
52 <data name="consensus_alignment" label="Consensus alignment" format="text" from_work_dir="output.aln" /> 105 <data name="consensus_alignment" label="Consensus alignment" format="fasta" from_work_dir="output.aln" />
53 <data name="consensus_sequences" label="Consensus sequences" format="fasta" from_work_dir="output.fsa" /> 106 <data name="consensus_sequences" label="Consensus sequences" format="fasta" from_work_dir="output.fsa" />
54 <data name="read_mapping" label="Read mapping info" format="tabular" from_work_dir="output.frag" /> 107 <data name="read_mapping" label="Read mapping info" format="tabular" from_work_dir="output.frag" />
108 <data name="assembly_matrix" label="Assembly matrix" format="txt" from_work_dir="output.mat">
109 <filter>settings['matrix']</filter>
110 </data>
55 </outputs> 111 </outputs>
56 <tests> 112 <tests>
113 <test>
114 <param name="single_paired_selector" value="no"/>
115 <param name="input_sequences" value="ERR884056_ecoli_b0842.mapped_R1.fastq" ftype="fastq"/>
116 <param name="advanced" value="advanced"/>
117 <param name="kmer_size" value="8"/>
118 <param name="kma_index" value="test_index"/>
119 <output name="result_overview" file="ERR884056.res" ftype="tabular"/>
120 <output name="consensus_alignment" file="ERR884056.aln" ftype="fasta"/>
121 <output name="consensus_sequences" file="ERR884056.fsa" ftype="fasta"/>
122 <output name="read_mapping" file="ERR884056.frag" ftype="tabular"/>
123 </test>
124 <test>
125 <param name="single_paired_selector" value="no"/>
126 <param name="input_sequences" value="ERR884056_ecoli_b0842.mapped_R1.fastq" ftype="fastq"/>
127 <param name="advanced" value="advanced"/>
128 <param name="kmer_size" value="8"/>
129 <param name="matrix" value="true"/>
130 <param name="kma_index" value="test_index"/>
131 <output name="assembly_matrix" file="ERR884056.mat" ftype="txt"/>
132 </test>
57 </tests> 133 </tests>
58 <help> 134 <help>
59 <![CDATA[ 135 <![CDATA[
60 ]]> 136 ]]>
61 </help> 137 </help>