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comparison tools/cgatools17/listvariants_v17.xml @ 5:64017ce705b6 draft

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planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit c475b4222a15cdadc6085865f4d13426249fec25-dirty
author yhoogstrate
date Wed, 11 Nov 2015 03:51:05 -0500
parents 3a2e0f376f26
children ff641b41735f
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4:418343b53afd 5:64017ce705b6
1 <tool id="cg_listvariant" name="ListVariants" version="1.7.1"> 1 <tool id="cg_listvariant" name="ListVariants" version="1.7.1">
2 2
3 <description>Lists all variants present in CG var or masterVar file</description> 3 <description>Lists all variants present in CG var or masterVar file</description>
4 4
5 <requirements> 5 <requirements>
6 <requirement type="package" version="1">cgatools17</requirement> 6 <requirement type="package" version="1">cgatools17</requirement>
7 </requirements> 7 </requirements>
8 8
9 <command> <!--run executable--> 9 <version_command>cgatools | head -1</version_command>
10 echo \$PATH;
11 cgatools | head -1;
12 cgatools listvariants
13 --beta
14 --reference ${crr.fields.crr_path}
15 --output $output
16 #if $include_list.listing == "yes" <!--only added when yes-->
17 --variant-listing $include_list.list
18 #end if
19 $longvar
20 --variants
21 #for $v in $file_types.varfiles <!--get each var/mastervar file-->
22 ${v.input}
23 #end for
24 10
25 11 <command> <!--run executable-->
26 </command> 12 cgatools
13 listvariants
14 --beta
27 15
28 <inputs> 16 #if $reference_gene_sets_source.source_select == "indexed_filtered"
29 <!--form field to select crr file--> 17 ${reference_gene_sets_source.crr.fields.crr_path}
30 <param name="crr" type="select" label="Reference genome (.crr file)"> 18 #else if $reference_gene_sets_source.source_select == "history"
31 <options from_data_table="cg_anno_files" /> 19 ${reference_gene_sets_source.crr}
32 </param> 20 #end if
21
22 --output $output
23 #if $include_list.listing == "yes" <!--only added when yes-->
24 --variant-listing $include_list.list
25 #end if
26 $longvar
27 --variants
28 #for $v in $file_types.varfiles <!--get each var/mastervar file-->
29 ${v.input}
30 #end for
33 31
34 <conditional name="file_types"> 32 </command>
35 <param name="file_type" type="select" label="Select the input file type">
36 <option value="var" selected="true">var files</option>
37 <option value="mastervar">mastervar files</option>
38 </param>
39 <when value="var">
40 <repeat name="varfiles" title="Variant files" min="1">
41 <param name="input" type="data" format="cg_var" label="Dataset"/>
42 </repeat>
43 </when>
44 <when value="mastervar">
45 <repeat name="varfiles" title="Variant files" min="1">
46 <param name="input" type="data" format="cg_mastervar" label="Dataset"/>
47 </repeat>
48 </when>
49 </conditional>
50 33
51 <param name="longvar" type="select" label="List long variants?"> 34 <inputs>
52 <option value="" selected="true">no</option> 35 <!--form field to select crr file-->
53 <option value="--list-long-variants">yes</option> 36 <conditional name="reference_gene_sets_source">
54 </param> 37 <param name="source_select" type="select" label="GFF/GTF Source">
38 <option value="indexed_filtered">Use a built-in index (which fits your reference)</option>
39 <option value="history">Use reference from the history</option>
40 </param>
41 <when value="indexed_filtered">
42 <param name="crr" type="select" label="Reference Build">
43 <options from_data_table="cg_anno_files" />
44 </param>
45 </when>
46 <when value="history">
47 <param name="crr" format="crr" type="data" label="Reference build" help="In crr format (you can use fasta2crr for conversion)" />
48 </when>
49 </conditional>
55 50
56 <conditional name="include_list"> 51 <conditional name="file_types">
57 <param name="listing" type="select" label="Include variant listing?"> 52 <param name="file_type" type="select" label="Select the input file type">
58 <option value="no" selected="true">no</option> 53 <option value="var" selected="true">var files</option>
59 <option value="yes">yes</option> 54 <option value="mastervar">mastervar files</option>
60 </param> 55 </param>
61 <when value="yes"> 56 <when value="var">
62 <param name="list" type="data" format="tabular" label="Variant listing"/> 57 <repeat name="varfiles" title="Variant files" min="1">
63 </when> 58 <param name="input" type="data" format="cg_var" label="Dataset"/>
64 </conditional> 59 </repeat>
65 <param name="fname" type="text" value="" label="Prefix for your output file" help="Optional"/> 60 </when>
66 </inputs> 61 <when value="mastervar">
62 <repeat name="varfiles" title="Variant files" min="1">
63 <param name="input" type="data" format="cg_mastervar" label="Dataset"/>
64 </repeat>
65 </when>
66 </conditional>
67
68 <param name="longvar" type="select" label="List long variants?">
69 <option value="" selected="true">no</option>
70 <option value="--list-long-variants">yes</option>
71 </param>
72
73 <conditional name="include_list">
74 <param name="listing" type="select" label="Include variant listing?">
75 <option value="no" selected="true">no</option>
76 <option value="yes">yes</option>
77 </param>
78 <when value="yes">
79 <param name="list" type="data" format="tabular" label="Variant listing"/>
80 </when>
81 </conditional>
82 <param name="fname" type="text" value="" label="Prefix for your output file" help="Optional"/>
83 </inputs>
67 84
68 <outputs> 85 <outputs>
69 <data format="tabular" name="output" label="$fname ${tool.name} on ${on_string}"/> 86 <data format="tabular" name="output" label="$fname ${tool.name} on ${on_string}"/>
70 </outputs> 87 </outputs>
71 88
72 <help> 89 <help>
73 **What it does** 90 **What it does**
74 91
75 This tool uses the cgatools listvariants to list all called variants present in the var or mastervar files. 92 This tool uses the cgatools listvariants to list all called variants present in the var or mastervar files.
76 93
77 **cgatools 1.7.1 Documentation** 94 **cgatools 1.7.1 Documentation**
80 97
81 Release notes: http://cgatools.sourceforge.net/docs/1.7.1/cgatools-release-notes.pdf 98 Release notes: http://cgatools.sourceforge.net/docs/1.7.1/cgatools-release-notes.pdf
82 99
83 **Command line reference**:: 100 **Command line reference**::
84 101
85 COMMAND NAME 102 COMMAND NAME
86 listvariants - Lists the variants present in a variant file. 103 listvariants - Lists the variants present in a variant file.
87 104
88 DESCRIPTION 105 DESCRIPTION
89 Lists all called variants present in the specified variant files, in a 106 Lists all called variants present in the specified variant files, in a
90 format suitable for processing by the testvariants command. The output is a 107 format suitable for processing by the testvariants command. The output is a
91 tab-delimited file consisting of the following columns: 108 tab-delimited file consisting of the following columns:
92 109
93 variantId Sequential id assigned to each variant. 110 variantId Sequential id assigned to each variant.
94 chromosome The chromosome of the variant. 111 chromosome The chromosome of the variant.
95 begin 0-based reference offset of the beginning of the variant. 112 begin 0-based reference offset of the beginning of the variant.
96 end 0-based reference offset of the end of the variant. 113 end 0-based reference offset of the end of the variant.
97 varType The varType as extracted from the variant file. 114 varType The varType as extracted from the variant file.
98 reference The reference sequence. 115 reference The reference sequence.
99 alleleSeq The variant allele sequence as extracted from the variant 116 alleleSeq The variant allele sequence as extracted from the variant
100 file. 117 file.
101 xRef The xRef as extrated from the variant file. 118 xRef The xRef as extrated from the variant file.
102 119
103 OPTIONS 120 OPTIONS
104 -h [ --help ] 121 -h [ --help ]
105 Print this help message. 122 Print this help message.
106 123
107 --beta 124 --beta
108 This is a beta command. To run this command, you must pass the --beta 125 This is a beta command. To run this command, you must pass the --beta
109 flag. 126 flag.
110 127
111 --reference arg 128 --reference arg
112 The reference crr file. 129 The reference crr file.
113 130
114 --output arg (=STDOUT) 131 --output arg (=STDOUT)
115 The output file (may be omitted for stdout). 132 The output file (may be omitted for stdout).
116 133
117 --variants arg 134 --variants arg
118 The input variant files (may be positional args). 135 The input variant files (may be positional args).
119 136
120 --variant-listing arg 137 --variant-listing arg
121 The output of another listvariants run, to be merged in to produce the 138 The output of another listvariants run, to be merged in to produce the
122 output of this run. 139 output of this run.
123 140
124 --list-long-variants 141 --list-long-variants
125 In addition to listing short variants, list longer variants as well 142 In addition to listing short variants, list longer variants as well
126 (10's of bases) by concatenating nearby calls. 143 (10's of bases) by concatenating nearby calls.
127 144
128 SUPPORTED FORMAT_VERSION 145 SUPPORTED FORMAT_VERSION
129 0.3 or later 146 0.3 or later
130 </help> 147 </help>
131 </tool> 148 </tool>