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comparison tools/cgatools17/testvariants_v17.xml @ 3:91e163b708d3 draft

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planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 18aaf80ea6ec743f134895c4a9a098a9e6146710-dirty
author yhoogstrate
date Tue, 10 Nov 2015 11:05:48 -0500
parents 3a2e0f376f26
children 418343b53afd
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2:977861cbcf10 3:91e163b708d3
1 <tool id="cg_testvariants" name="TestVariants" version="1.7.1"> 1 <tool id="cg_testvariants" name="TestVariants" version="1.7.1.b">
2 <description>Test for the presence of variants</description>
2 3
3 <description>Test for the presence of variants</description> 4 <requirements>
5 <requirement type="package" version="1">cgatools17</requirement>
6 </requirements>
4 7
5 <requirements> 8 <version_command>cgatools | head -1</version_command>
6 <requirement type="package" version="1">cgatools17</requirement>
7 </requirements>
8 9
9 <command> <!--run executable--> 10 <command>
10 cgatools | head -1; 11 cgatools testvariants
11 cgatools testvariants 12 --beta
12 --beta 13 --reference
13 --reference ${crr.fields.crr_path} 14
14 --output $output 15 #if $reference_gene_sets_source.source_select == "indexed_filtered"
15 --input $listing 16 ${reference_gene_sets_source.crr.fields.crr_path}
16 --variants 17 #else if $reference_gene_sets_source.source_select == "history"
17 #for $v in $file_types.varfiles <!--get each var/mastervar file--> 18 ${reference_gene_sets_source.crr}
18 ${v.input} 19 #end if
19 #end for 20
20 </command> 21 --output $output
22 --input $listing
23 --variants
24 #for $v in $file_types.varfiles <!--get each var/mastervar file-->
25 ${v.input}
26 #end for
27 </command>
21 28
22 <inputs> 29 <inputs>
23 <!--form field to select crr file--> 30 <!--form field to select crr file-->
24 <param name="crr" type="select" label="Reference Build"> 31
25 <options from_data_table="cg_anno_files" /> 32 <conditional name="reference_gene_sets_source">
26 </param> 33 <param name="source_select" type="select" label="GFF/GTF Source">
34 <option value="indexed_filtered">Use a built-in index (which fits your reference)</option>
35 <option value="history">Use reference from the history</option>
36 </param>
37 <when value="indexed_filtered">
38 <param name="crr" type="select" label="Reference Build">
39 <options from_data_table="cg_anno_files" />
40 </param>
41 </when>
42 <when value="history">
43 <param name="crr" format="crr" type="data" label="Reference build" help="In crr format (you can use fasta2crr for conversion)" />
44 </when>
45 </conditional>
27 46
28 <!--form fields to select variant list--> 47 <!--form fields to select variant list-->
29 <param name="listing" type="data" format="tabular" label="Select variant list"/> 48 <param name="listing" type="data" format="tabular" label="Select variant list"/>
30 49
31 <!--conditional to select input file type--> 50 <!--conditional to select input file type-->
32 <conditional name="file_types"> 51 <conditional name="file_types">
33 <param name="file_type" type="select" label="Select the input file type"> 52 <param name="file_type" type="select" label="Select the input file type">
34 <option value="var" selected="true">var files</option> 53 <option value="var" selected="true">var files</option>
35 <option value="mastervar">mastervar files</option> 54 <option value="mastervar">mastervar files</option>
36 </param> 55 </param>
37 <when value="var"> 56 <when value="var">
38 <repeat name="varfiles" title="Variant files"> 57 <repeat name="varfiles" title="Variant files">
39 <param name="input" type="data" format="cg_var" label="Dataset"/> 58 <param name="input" type="data" format="cg_var" label="Dataset"/>
40 </repeat> 59 </repeat>
41 </when> 60 </when>
42 <when value="mastervar"> 61 <when value="mastervar">
43 <repeat name="varfiles" title="Variant files"> 62 <repeat name="varfiles" title="Variant files">
44 <param name="input" type="data" format="cg_mastervar" label="Dataset"/> 63 <param name="input" type="data" format="cg_mastervar" label="Dataset"/>
45 </repeat> 64 </repeat>
46 </when> 65 </when>
47 </conditional> 66 </conditional>
48 67
49 <!-- prefix for output file so you dont have to manually rename history items --> 68 <!-- prefix for output file so you dont have to manually rename history items -->
50 <param name="fname" type="text" value="" label="Prefix for your output file" help="Optional"/> 69 <param name="fname" type="text" value="" label="Prefix for your output file" help="Optional"/>
51 </inputs> 70 </inputs>
52 71
53 72
54 <outputs> 73 <outputs>
55 <data format="tabular" name="output" label="$fname ${tool.name} on ${on_string}"/> 74 <data format="tabular" name="output" label="$fname ${tool.name} on ${on_string}"/>
56 </outputs> 75 </outputs>
57 76
58 <help> 77 <help>
59 **What it does** 78 **What it does**
60 79
61 This tool uses the cgatools testvariants to test variant or mastervar files for the presence of variants. 80 This tool uses the cgatools testvariants to test variant or mastervar files for the presence of variants.
62 81
63 **cgatools 1.7.1 Documentation** 82 **cgatools 1.7.1 Documentation**
66 85
67 Release notes: http://cgatools.sourceforge.net/docs/1.7.1/cgatools-release-notes.pdf 86 Release notes: http://cgatools.sourceforge.net/docs/1.7.1/cgatools-release-notes.pdf
68 87
69 **Command line reference**:: 88 **Command line reference**::
70 89
71 COMMAND NAME 90 COMMAND NAME
72 testvariants - Tests variant files for presence of variants. 91 testvariants - Tests variant files for presence of variants.
73 92
74 DESCRIPTION 93 DESCRIPTION
75 Tests variant files for presence of variants. The output is a tab-delimited 94 Tests variant files for presence of variants. The output is a tab-delimited
76 file consisting of the columns of the input variants file, plus a column 95 file consisting of the columns of the input variants file, plus a column
77 for each assembly results file that contains a character code for each 96 for each assembly results file that contains a character code for each
78 allele. The character codes have meaning as follows: 97 allele. The character codes have meaning as follows:
79 98
80 0 This allele of this genome is consistent with the reference at this 99 0 This allele of this genome is consistent with the reference at this
81 locus but inconsistent with the variant. 100 locus but inconsistent with the variant.
82 1 This allele of this genome has the input variant at this locus. 101 1 This allele of this genome has the input variant at this locus.
83 N This allele of this genome has no-calls but is consistent with the 102 N This allele of this genome has no-calls but is consistent with the
84 input variant. 103 input variant.
85 104
86 OPTIONS 105 OPTIONS
87 -h [ --help ] 106 -h [ --help ]
88 Print this help message. 107 Print this help message.
89 108
90 --beta 109 --beta
91 This is a beta command. To run this command, you must pass the --beta 110 This is a beta command. To run this command, you must pass the --beta
92 flag. 111 flag.
93 112
94 --reference arg 113 --reference arg
95 The reference crr file. 114 The reference crr file.
96 115
97 --input arg (=STDIN) 116 --input arg (=STDIN)
98 The input variants to test for. 117 The input variants to test for.
99 118
100 --output arg (=STDOUT) 119 --output arg (=STDOUT)
101 The output file (may be omitted for stdout). 120 The output file (may be omitted for stdout).
102 121
103 --variants arg 122 --variants arg
104 The input variant files (may be passed in as arguments at the end of 123 The input variant files (may be passed in as arguments at the end of
105 the command). 124 the command).
106 125
107 SUPPORTED FORMAT_VERSION 126 SUPPORTED FORMAT_VERSION
108 0.3 or later 127 0.3 or later
109 </help> 128 </help>
110 </tool> 129 </tool>