Mercurial > repos > ulfschaefer > phephenix

comparison vcfs2fasta.xml @ 8:f05fa489089b draft

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Uploaded
author ulfschaefer
date Thu, 16 Jun 2016 06:40:13 -0400
parents 2cb7b6e42f72
children 1ec00e184217
comparison
equal deleted inserted replaced
7:29a682a7dd16 8:f05fa489089b
15 <exit_code range="1:" /> 15 <exit_code range="1:" />
16 <exit_code range=":-1" /> 16 <exit_code range=":-1" />
17 </stdio> 17 </stdio>
18 <command interpreter="bash"> 18 <command interpreter="bash">
19 vcfs2fasta.sh 19 vcfs2fasta.sh
20 $output 20 $output
21 #if str($mix_cond.mix) == "yes": 21 #if str($mix_cond.mix) == "yes":
22 $mix_cond.mix_value 22 $mix_cond.mix_value
23 #else 23 #else
24 NOTTHERE 24 NOTTHERE
25 #end if 25 #end if
26 #if str($cols_cond.cols) == "yes": 26 #if str($coln_cond.coln) == "yes":
27 $cols_cond.column_ns 27 $coln_cond.column_ns
28 #else 28 #else
29 NOTTHERE 29 NOTTHERE
30 #end if 30 #end if
31 #if str($sample_cond.sample) == "yes": 31 #if str($colgap_cond.colgap) == "yes":
32 $sample_cond.sample_ns 32 $colgap_cond.column_ns
33 #else 33 #else
34 NOTTHERE 34 NOTTHERE
35 #end if 35 #end if
36 #if str($reference_cond.reference) == "yes": 36 #if str($samplen_cond.samplen) == "yes":
37 $reference_cond.ref_fa 37 $samplen_cond.sample_ns
38 #else 38 #else
39 NOTTHERE 39 NOTTHERE
40 #end if 40 #end if
41 #if str($include_cond.include) == "yes": 41 #if str($samplegap_cond.samplegap) == "yes":
42 $include_cond.in_bed 42 $samplegap_cond.sample_gaps
43 #else 43 #else
44 NOTTHERE 44 NOTTHERE
45 #end if 45 #end if
46 #if str($exclude_cond.exclude) == "yes": 46 #if str($reference_cond.reference) == "yes":
47 $exclude_cond.ex_bed 47 $reference_cond.ref_fa
48 #else 48 #else
49 NOTTHERE 49 NOTTHERE
50 #end if 50 #end if
51 #for $i, $input_vcf in enumerate( $input_vcfs ): 51 #if str($include_cond.include) == "yes":
52 $include_cond.in_bed
53 #else
54 NOTTHERE
55 #end if
56 #if str($exclude_cond.exclude) == "yes":
57 $exclude_cond.ex_bed
58 #else
59 NOTTHERE
60 #end if
61 #if $withstats:
62 $statsfile
63 #else
64 NOTTHERE
65 #end if
66 #for $i, $input_vcf in enumerate( $input_vcfs ):
52 "${input_vcf}" 67 "${input_vcf}"
53 #end for 68 #end for
54 </command> 69 </command>
55 70
56 <inputs> 71 <inputs>
57 <param name="input_vcfs" type="data" multiple="true" format="vcf" label="Input VCF file(s)" /> 72 <param name="input_vcfs" type="data" multiple="true" format="vcf" label="Input VCF file(s)" />
58 <conditional name="mix_cond"> 73
74 <conditional name="mix_cond">
59 <param name="mix" type="select" label="With Mixtures" help="Specify this option with a threshold to output mixtures above this threshold."> 75 <param name="mix" type="select" label="With Mixtures" help="Specify this option with a threshold to output mixtures above this threshold.">
60 <option value="yes">Specify</option> 76 <option value="yes">Specify</option>
61 <option value="no" selected="true">Do not specify</option> 77 <option value="no" selected="true">Do not specify</option>
62 </param> 78 </param>
63 <when value="yes"> 79 <when value="yes">
64 <param name="mix_value" type="float" value="0.5" label="Mixture value" /> 80 <param name="mix_value" type="float" value="0.5" label="Mixture value" />
65 </when> 81 </when>
66 </conditional> 82 </conditional>
67 <conditional name="cols_cond"> 83
68 <param name="cols" type="select" label="Column Ns" help="Keeps columns with fraction of Ns below specified threshold."> 84 <conditional name="coln_cond">
85 <param name="coln" type="select" label="Column Ns" help="Keeps columns with fraction of Ns below specified threshold.">
69 <option value="yes">Specify</option> 86 <option value="yes">Specify</option>
70 <option value="no" selected="true">Do not specify</option> 87 <option value="no" selected="true">Do not specify</option>
71 </param> 88 </param>
72 <when value="yes"> 89 <when value="yes">
73 <param name="column_ns" type="float" value="0.5" label="Column Ns value" /> 90 <param name="column_ns" type="float" value="0.5" label="Column Ns value" />
74 </when> 91 </when>
75 </conditional> 92 </conditional>
76 <conditional name="sample_cond"> 93
77 <param name="sample" type="select" label="Sample Ns" help="Keeps samples with fraction of Ns below specified threshold."> 94 <conditional name="colgap_cond">
95 <param name="colgap" type="select" label="Column Gaps" help="Keeps columns with fraction of gaps below specified threshold.">
78 <option value="yes">Specify</option> 96 <option value="yes">Specify</option>
79 <option value="no" selected="true">Do not specify</option> 97 <option value="no" selected="true">Do not specify</option>
80 </param> 98 </param>
81 <when value="yes"> 99 <when value="yes">
82 <param name="sample_ns" type="float" value="0.5" label="Sample Ns value" /> 100 <param name="column_gaps" type="float" value="0.5" label="Column gaps value" />
83 </when> 101 </when>
84 </conditional> 102 </conditional>
85 <conditional name="reference_cond"> 103
104 <conditional name="samplen_cond">
105 <param name="samplen" type="select" label="Sample Ns" help="Keeps samples with fraction of Ns below specified threshold.">
106 <option value="yes">Specify</option>
107 <option value="no" selected="true">Do not specify</option>
108 </param>
109 <when value="yes">
110 <param name="sample_ns" type="float" value="0.5" label="Sample Ns value" />
111 </when>
112 </conditional>
113
114 <conditional name="samplegap_cond">
115 <param name="samplegap" type="select" label="Sample gaps" help="Keeps samples with fraction of gaps below specified threshold.">
116 <option value="yes">Specify</option>
117 <option value="no" selected="true">Do not specify</option>
118 </param>
119 <when value="yes">
120 <param name="sample_gaps" type="float" value="0.5" label="Sample gaps value" />
121 </when>
122 </conditional>
123
124 <conditional name="reference_cond">
86 <param name="reference" type="select" label="Reference genome file" help="If path to reference specified, then whole genome will be outputted."> 125 <param name="reference" type="select" label="Reference genome file" help="If path to reference specified, then whole genome will be outputted.">
87 <option value="yes">Specify</option> 126 <option value="yes">Specify</option>
88 <option value="no" selected="true">Do not specify</option> 127 <option value="no" selected="true">Do not specify</option>
89 </param> 128 </param>
90 <when value="yes"> 129 <when value="yes">
91 <param name="ref_fa" type="data" format="fasta" label="Reference fasta file" help="Fasta format"/> 130 <param name="ref_fa" type="data" format="fasta" label="Reference fasta file" help="Fasta format"/>
92 </when> 131 </when>
93 </conditional> 132 </conditional>
94 <conditional name="include_cond"> 133
134 <conditional name="include_cond">
95 <param name="include" type="select" label="Include region" help="Specify regions to include in a bed file."> 135 <param name="include" type="select" label="Include region" help="Specify regions to include in a bed file.">
96 <option value="yes">Specify</option> 136 <option value="yes">Specify</option>
97 <option value="no" selected="true">Do not specify</option> 137 <option value="no" selected="true">Do not specify</option>
98 </param> 138 </param>
99 <when value="yes"> 139 <when value="yes">
100 <param name="in_bed" type="data" format="bed" label="Include regions bed file" help="bed format"/> 140 <param name="in_bed" type="data" format="bed" label="Include regions bed file" help="bed format"/>
101 </when> 141 </when>
102 </conditional> 142 </conditional>
103 <conditional name="exclude_cond"> 143
144 <conditional name="exclude_cond">
104 <param name="exclude" type="select" label="Exclude region" help="Specify regions to exclude in a bed file."> 145 <param name="exclude" type="select" label="Exclude region" help="Specify regions to exclude in a bed file.">
105 <option value="yes">Specify</option> 146 <option value="yes">Specify</option>
106 <option value="no" selected="true">Do not specify</option> 147 <option value="no" selected="true">Do not specify</option>
107 </param> 148 </param>
108 <when value="yes"> 149 <when value="yes">
109 <param name="ex_bed" type="data" format="bed" label="Exclude regions bed file" help="bed format"/> 150 <param name="ex_bed" type="data" format="bed" label="Exclude regions bed file" help="bed format"/>
110 </when> 151 </when>
111 </conditional> 152 </conditional>
153
112 </inputs> 154 </inputs>
113 155
114 <outputs> 156 <outputs>
115 <data format="fasta" name="output" label="${tool.name} on ${on_string}: FASTA file" /> 157 <data format="fasta" name="output" label="${tool.name} on ${on_string}: FASTA file" />
116 </outputs> 158 </outputs>