Mercurial > repos > iuc > gemini_set_somatic

comparison gemini_set_somatic.xml @ 0:230c975e7759 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
author iuc
date Thu, 18 Feb 2016 08:57:23 -0500
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children 7b031989ea12
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-1:000000000000 0:230c975e7759
1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0">
2 <description>Tag somatic mutations in a GEMINI database</description>
3 <macros>
4 <import>gemini_macros.xml</import>
5 <token name="@BINARY@">set_somatic</token>
6 </macros>
7 <expand macro="requirements" />
8 <expand macro="stdio" />
9 <expand macro="version_command" />
10 <command>
11 <![CDATA[
12 cp "${ infile }" "${ outfile }" &&
13
14 gemini @BINARY@
15
16 #if float($min_depth) >= 0:
17 --min-depth $min_depth
18 #end if
19
20 #if float($min_quality) >= 0:
21 --min-qual $min_quality
22 #end if
23
24 #if float($min_somatic_score) >= 0:
25 --min-somatic-score $min_somatic_score
26 #end if
27
28 #if float($max_norm_alt_freq) >= 0:
29 --max-norm-alt-freq $max_norm_alt_freq
30 #end if
31
32 #if int($max_norm_alt_count) >= 0:
33 --max-norm-alt-count $max_norm_alt_count
34 #end if
35
36 #if int($min_norm_depth) >= 0:
37 --min-norm-depth $min_norm_depth
38 #end if
39
40 #if float($min_tumor_alt_freq) >= 0:
41 --min-tumor-alt-freq $min_tumor_alt_freq
42 #end if
43
44 #if int($min_tumor_alt_count) >= 0:
45 --min-tumor-alt-count $min_tumor_alt_count
46 #end if
47
48 #if int($min_tumor_depth) >= 0:
49 --min-tumor-depth $min_tumor_depth
50 #end if
51
52 #if str($chrom).strip():
53 --chrom "$chrom"
54 #end if
55 "${ outfile }"
56 ]]>
57 </command>
58 <inputs>
59
60 <expand macro="infile" />
61 <param name="min_depth" type="float" value="-1" label="The min combined depth for tumor + normal" help="default: -1 (not set) (--min-depth)"/>
62 <param name="min_quality" type="float" value="-1" label="The min variant quality (VCF QUAL)" help="default: -1 (not set) (--min-qual)"/>
63 <param name="min_somatic_score" type="float" value="-1" label="The min somatic score (SSC)" help="default: -1 (not set) (--min-somatic-score)"/>
64 <param name="max_norm_alt_freq" type="float" value="-1" label="The max frequency of the alternative allele in the normal sample" help="default: -1 (not set) (--max-norm-alt-freq)"/>
65 <param name="max_norm_alt_count" type="integer" value="-1" min="-1" label="The max count of the alternative allele in the normal sample" help="default: -1 (not set) (--max-norm-alt-count)"/>
66 <param name="min_norm_depth" type="integer" value="-1" min="-1" label="The minimum depth allowed in the normal sample to believe somatic" help="default: -1 (not set) (--min-norm-depth)"/>
67 <param name="min_tumor_alt_freq" type="float" value="-1" label="The minimum frequency of the alternative allele in the tumor sample" help="default: -1 (not set) (--min-tumor-alt-freq)"/>
68 <param name="min_tumor_alt_count" type="integer" value="-1" min="-1" label="The minimum count of the alternative allele in the tumor sample" help="default: -1 (not set) (--min-tumor-alt-count)"/>
69 <param name="min_tumor_depth" type="integer" value="-1" min="-1" label="The minimum depth allowed in the tumor sample to believe somatic" help="default: -1 (not set) (--min-tumor-depth)"/>
70 <param name="chrom" type="text" label="A specific chromosome on which to tag somatic mutations" help="e.g. chrom12 (--chrom)" />
71
72 </inputs>
73 <outputs>
74 <data name="outfile" format="gemini.sqlite" />
75 </outputs>
76 <tests>
77 <test>
78 <!-- A very basic test with a nonsensical input db. The example
79 databases that would produce something meaningful are >100 Mbyte -->
80 <param name="infile" value="gemini_amend_input.db" ftype="gemini.sqlite" />
81 <param name="min_somatic_score" value="5.65" />
82 <output name="outfile" file="gemini_is_somatic_result.db" />
83 </test>
84 </tests>
85 <help>
86 <![CDATA[
87 **What it does**
88
89 Gemini set_somatic sets the flag "is_somatic" by comparing tumor/normal pairs in an already loaded Gemini database.
90
91 ]]>
92 </help>
93 <expand macro="citations"/>
94 </tool>