Mercurial > repos > iuc > gemini_stats

annotate gemini_stats.xml @ 11:478a2edd1901 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit f7bdf08922aaf4119aefe7041e754a69cf64aebd
author iuc
date Wed, 13 Jul 2022 15:10:08 +0000
parents 100f73f4878d
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
6
c60ef99f03d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 85a2af25c79df4758afe9f846e11ef0af16b1c1f
iuc
parents: 5
diff changeset
1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@">
0
544f687c4534 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
2 <description>Compute useful variant statistics</description>
10
100f73f4878d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 7
diff changeset
3 <expand macro="bio_tools"/>
0
544f687c4534 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
4 <macros>
544f687c4534 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
5 <import>gemini_macros.xml</import>
544f687c4534 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
6 <token name="@BINARY@">stats</token>
544f687c4534 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
7 </macros>
544f687c4534 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
8 <expand macro="requirements" />
544f687c4534 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
9 <expand macro="stdio" />
544f687c4534 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
10 <expand macro="version_command" />
544f687c4534 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
11 <command>
544f687c4534 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
12 <![CDATA[
544f687c4534 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
13 gemini @BINARY@
7
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
14 #if str($stats.type) == "gts-stats":
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
15 #set $multiline_sql_expr = $stats.variants.gt_filter
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
16 #set $cmdln_param = "--gt-filter"
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
17 @MULTILN_SQL_EXPR_TO_CMDLN@
0
544f687c4534 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
18
7
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
19 #if str($stats.variants.constraint).strip():
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
20 #set $multiline_sql_expr = "select * from variants WHERE " + str($stats.variants.constraint)
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
21 #else:
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
22 #set $multiline_sql_expr = "select * from variants"
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
23 #end if
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
24 #set $cmdln_param = "--summarize"
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
25 @MULTILN_SQL_EXPR_TO_CMDLN@
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
26 #else:
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
27 ${stats.stats_option}
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
28 #end if
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
29 '$infile'
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
30 > '$outfile'
0
544f687c4534 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
31 ]]>
544f687c4534 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
32 </command>
544f687c4534 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
33 <inputs>
544f687c4534 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
34 <expand macro="infile" />
544f687c4534 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
35
7
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
36 <conditional name="stats">
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
37 <param name="type" type="select"
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
38 label="Select the type of statistics you are interested in" help="">
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
39 <option value="gts-stats">Genotype counts tabulated by sample (--summarize)</option>
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
40 <option value="snp-counts">Counts of SNPs by nucleotide change (--snp-counts)</option>
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
41 <option value="tstv-stats">Transition / transversion statistics for the SNPs in the dataset</option>
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
42 <option value="aaf">Alternate allele frequency spectrum of all variants (--sfs)</option>
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
43 <option value="sample-distance">Pair-wise genetic distances between for all samples (--mds)</option>
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
44 </param>
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
45 <when value="snp-counts">
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
46 <param name="stats_option" type="hidden" value="--snp-counts" />
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
47 </when>
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
48 <when value="aaf">
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
49 <param name="stats_option" type="hidden" value="--sfs" />
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
50 </when>
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
51 <when value="sample-distance">
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
52 <param name="stats_option" type="hidden" value="--mds" />
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
53 </when>
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
54 <when value="tstv-stats">
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
55 <param name="stats_option" type="select"
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
56 label="Calculate Ts/Tv statistics based on"
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
57 help="Restricting the calculation to coding/noncoding regions will only produce meaningful results with preannotated variants. If you haven't annotated your variants with SnpEff or VEP before loading them into GEMINI, select All SNPs.">
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
58 <option value="--tstv">All SNPs (--tstv)</option>
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
59 <option value="--tstv-coding">SNPs in coding regions (--tstv-coding)</option>
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
60 <option value="--tstv-noncoding">SNPs in non-coding regions (--tstv-noncoding)</option>
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
61 </param>
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
62 </when>
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
63 <when value="gts-stats">
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
64 <param name="stats_option" type="hidden" value="" />
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
65 <conditional name="variants">
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
66 <param name="keep" type="select"
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
67 label="Compute the genotype counts table based on"
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
68 help="If you select All variants the genotype counts will be produced using --summarize with the wildcard query &quot;select * from variants&quot;.">
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
69 <option value="all">All variants</option>
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
70 <option value="custom">Custom filtered variants</option>
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
71 </param>
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
72 <when value="all">
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
73 <param name="gt_filter" type="hidden" value="" />
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
74 <param name="constraint" type="hidden" value="" />
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
75 </when>
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
76 <when value="custom">
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
77 <param argument="--gt-filter" name="gt_filter" type="text" area="True" size="5x50"
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
78 label="Restrictions to apply to genotype values"
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
79 help="">
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
80 <expand macro="sanitize_query" />
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
81 </param>
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
82 <param name="constraint" type="text" area="True" size="5x50"
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
83 label="Additional constraints on the variants"
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
84 help="Enter valid constraints for the WHERE clause of a GEMINI query here. You could use, for example: chrom = 'chr1' or impact_severity = 'HIGH', to include only high-impact variants on chromosome 1 in the counts table.">
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
85 <expand macro="sanitize_query" />
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
86 </param>
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
87 </when>
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
88 </conditional>
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
89 </when>
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
90 </conditional>
0
544f687c4534 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
91 </inputs>
544f687c4534 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
92 <outputs>
544f687c4534 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
93 <data name="outfile" format="tabular" />
544f687c4534 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
94 </outputs>
544f687c4534 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
95 <tests>
544f687c4534 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
96 <test>
5
78e971dd87ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents: 4
diff changeset
97 <!-- test vars-by-sample report -->
7
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
98 <param name="infile" value="gemini_load_result1.db" ftype="gemini.sqlite" />
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
99 <conditional name="stats">
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
100 <param name="type" value="tstv-stats" />
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
101 <param name="stats_option" value="--tstv-coding" />
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
102 </conditional>
5
78e971dd87ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents: 4
diff changeset
103 <output name="outfile">
78e971dd87ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents: 4
diff changeset
104 <assert_contents>
7
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
105 <!-- since the input file is not annotated
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
106 no variants will be considered to be in coding regions -->
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
107 <has_line line="ts&#009;tv&#009;ts/tv" />
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
108 <has_line line="0&#009;0&#009;0" />
5
78e971dd87ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents: 4
diff changeset
109 </assert_contents>
78e971dd87ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents: 4
diff changeset
110 </output>
78e971dd87ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents: 4
diff changeset
111 </test>
78e971dd87ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents: 4
diff changeset
112 <test>
78e971dd87ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents: 4
diff changeset
113 <!-- test gts-by-sample report -->
78e971dd87ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents: 4
diff changeset
114 <param name="infile" value="gemini_de_novo_input.db" ftype="gemini.sqlite" />
7
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
115 <conditional name="stats">
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
116 <param name="type" value="gts-stats" />
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
117 <conditional name="variants">
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
118 <param name="keep" value="all" />
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
119 </conditional>
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
120 </conditional>
5
78e971dd87ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents: 4
diff changeset
121 <output name="outfile">
78e971dd87ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents: 4
diff changeset
122 <assert_contents>
7
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
123 <has_line_matching expression="sample&#009;total&#009;num_het&#009;num_hom_alt&#009;num_hom_ref" />
5
78e971dd87ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents: 4
diff changeset
124 </assert_contents>
78e971dd87ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents: 4
diff changeset
125 </output>
0
544f687c4534 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
126 </test>
544f687c4534 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
127 </tests>
544f687c4534 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
128 <help><![CDATA[
544f687c4534 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
129 **What it does**
544f687c4534 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
130
7
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
131 The stats tool computes one of the following useful variant statistics for a GEMINI database:
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
132
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
133 **Genotype counts tabulated by sample**:
0
544f687c4534 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
134
7
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
135 This mode uses the ``gemini stats --summarize`` option to produce a table with
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
136 one row per sample, which tabulates the numbers of sites, for which a given
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
137 sample shows a:
0
544f687c4534 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
138
7
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
139 - non-reference genotype (*total* column; the sum of the *num_het* and *num_hom_alt* columns next to it)
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
140 - heterozygous genotype (*num_het* column)
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
141 - homozygous variant genotype (*num_hom_alt* column)
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
142 - homozygous reference genotype (*num_hom_ref* column)
0
544f687c4534 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
143
7
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
144 You can choose to calculate the table based on all variants in your database,
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
145 or to filter the variants before the calculation using GEMINI genotype filter
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
146 expressions and/or WHERE clauses of GEMINI queries.
0
544f687c4534 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
147
7
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
148 **Counts of SNPs by nucleotide change**:
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
149
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
150 This runs ``gemini stats`` with the ``--snp-count`` option. The result is a
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
151 simple table listing the number of occurences of each observed REF->ALT change
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
152 in your database, e.g.::
0
544f687c4534 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
153
544f687c4534 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
154 type count
544f687c4534 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
155 A->G 2
544f687c4534 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
156 C->T 1
544f687c4534 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
157 G->A 1
544f687c4534 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
158
7
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
159 **Transition / transversion statistics**
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
160
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
161 This mode uses ``gemini stats`` with the ``--tstv``, ``--tstv-coding``, or
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
162 ``--tstv-noncoding`` option to compute the transition/transversion ratios for
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
163 all SNPs, for SNPs in coding, or SNPs in non-coding regions, respectively.
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
164
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
165 The result is presented in a 1x3 table listing the number of
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
166 transitions (*ts* column), transversions (*tv* column) and the ratio of the two
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
167 (*ts/tv* column), e.g.::
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
168
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
169 ts tv ts/tv
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
170 126 39 3.2307
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
171
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
172 **Alternate allele frequency spectrum**
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
173
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
174 Runs ``gemini stats --sfs`` to produce binned alternate allele frequency counts
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
175 in a table like::
0
544f687c4534 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
176
544f687c4534 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
177 aaf count
544f687c4534 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
178 0.125 2
544f687c4534 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
179 0.375 1
544f687c4534 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
180
7
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
181 **Pairwise genetic distances**
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
182
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
183 Runs ``gemini stats --mds`` and tabulates all pairwise genetic distance for the
c54b9472915a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
184 samples in your database. An example could look like this::
0
544f687c4534 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
185
544f687c4534 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
186 sample1 sample2 distance
544f687c4534 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
187 M10500 M10500 0.0
544f687c4534 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
188 M10475 M10478 1.25
544f687c4534 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
189 M10500 M10475 2.0
544f687c4534 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
190 M10500 M10478 0.5714
544f687c4534 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
191
544f687c4534 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
192 ]]></help>
544f687c4534 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
193 <expand macro="citations"/>
544f687c4534 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
194 </tool>