Mercurial > repos > wolma > mimodd_main

annotate varreport.xml @ 0:f0f2795de2c7 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
author wolma
date Tue, 19 Dec 2017 04:54:04 -0500
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
1 <tool id="mimodd_varreport" name="MiModD Report Variants"
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
2 version="@MIMODD_WRAPPER_VERSION@">
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
3 <description>
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
4 in a human-friendly format that simplifies data exploration
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
5 </description>
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
6 <macros>
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
7 <import>macros.xml</import>
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
8 </macros>
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
9 <expand macro="requirements" />
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
10 <expand macro="stdio" />
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
11 <expand macro="version_command" />
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
12 <command><![CDATA[
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
13 #if $str($formatting.oformat) == 'html':
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
14 mkdir '$ofile.files_path' &&
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
15 #end if
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
16 mimodd varreport
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
17 '$inputfile' --oformat ${formatting.oformat}
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
18 #if $str($formatting.oformat) == 'html':
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
19 #if $str($formatting.species):
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
20 --species '${formatting.species}'
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
21 #end if
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
22 #if $formatting.link_formatter:
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
23 --link '${formatting.link_formatter}'
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
24 #end if
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
25 --ofile '${ofile.files_path}/variant_report.html'
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
26 && echo
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
27 '<html><body><p>MiModD has generated the variant report you requested, but for technical reasons, we have to take you through this little detour to display the report in Galaxy.</p><p>Proceed to <a href="variant_report.html">the variant report</a>.</p></body></html>'
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
28 > '$ofile'
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
29 #else
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
30 --ofile '$ofile'
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
31 #end if
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
32 ]]></command>
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
33
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
34 <inputs>
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
35 <param name="inputfile" type="data" format="vcf"
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
36 label="The VCF input with the variants to be reported" />
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
37 <conditional name="formatting">
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
38 <param name="oformat" type="select"
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
39 label="Format to use for the report">
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
40 <option value="html">HTML</option>
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
41 <option value="text">Tab-separated plain text</option>
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
42 </param>
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
43 <when value="html">
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
44 <param name="species" type="text" label="Species"
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
45 help="If you declare the species your input data comes from, variant reports in html format can have hyperlinks to species-specific databases and genome browsers added. If you have used the MiModD Variant Annotation tool to generate the input dataset, the species information will already be recorded in the dataset, but you can overwrite it if you wish.">
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
46 <expand macro="lex_sam_header" message="Non-ASCII characters are not allowed in species names." />
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
47 </param>
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
48 <param name="link_formatter" type="data" format="txt" optional="true"
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
49 label="Optional file with species-specific hyperlink formatting instructions"
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
50 help="If the tool has no built-in support for your species, i.e., it does not know how to generate hyperlinks for it, you can provide a custom recipe here." />
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
51 </when>
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
52 <when value="text">
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
53 <param name="species" type="hidden" value="" />
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
54 </when>
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
55 </conditional>
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
56 </inputs>
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
57
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
58 <outputs>
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
59 <data name="ofile" format="html">
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
60 <change_format>
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
61 <when input="formatting.oformat" value="text" format="tabular"/>
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
62 </change_format>
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
63 </data>
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
64 </outputs>
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
65
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
66 <tests>
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
67 <test>
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
68 <param name="inputfile" value="a.vcf" />
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
69 <conditional name="formatting">
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
70 <param name="oformat" value="html" />
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
71 <param name="species" value="C. elegans" />
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
72 </conditional>
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
73 <output name="ofile" ftype="html">
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
74 <extra_files type="file" name="variant_report.html" ftype="html">
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
75 <assert_contents>
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
76 <has_line_matching expression=".+tools/genome/gbrowse/c_elegans_PRJNA13758.+" />
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
77 </assert_contents>
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
78 </extra_files>
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
79 </output>
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
80 </test>
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
81 <test>
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
82 <param name="inputfile" value="a.vcf" />
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
83 <conditional name="formatting">
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
84 <param name="oformat" value="text" />
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
85 </conditional>
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
86 <output name="ofile" ftype="tabular">
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
87 <assert_contents>
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
88 <has_n_columns n="11" />
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
89 <has_line_matching expression="Chromosome&#009;Position&#009;Affected Gene&#009;Transcript&#009;Effects&#009;genotype N2&#009;.+genotype ot266&#009;.+" />
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
90 <has_line_matching expression="chrI&#009;.+" />
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
91 </assert_contents>
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
92 </output>
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
93 </test>
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
94 </tests>
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
95
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
96 <help><![CDATA[
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
97 .. class:: infomark
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
98
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
99 **What it does**
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
100
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
101 The tool turns a variant list in VCF format into a more readable summary table
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
102 listing variant sites and effects.
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
103
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
104
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
105 **Html output enriched with species-specific hyperlinks**
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
106
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
107 If you select html as the output format, the tool can insert species- and
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
108 variant-specific hyperlinks to public genome browsers and databases into the
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
109 report. This is a useful feature to explore medium-size lists of variants, but
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
110 requires that the tool knows:
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
111
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
112 1) the species that you are analyzing data for
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
113
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
114 The tool can autodetect the species if the input dataset has been generated
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
115 with the *MiModD Variant Annotation* tool. Alternatively, you can declare
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
116 the species you are working with explicitly.
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
117
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
118 2) how to generate hyperlinks for this species
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
119
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
120 The tool has built-in support for a number of standard model organisms.
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
121 If your organism is not in that list or if you find that the default
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
122 hyperlinks for a supported species are outdated, you can provide your own
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
123 recipe to generate correct hyperlinks through a `custom hyperlink template
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
124 file`_.
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
125
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
126 **TIP:**
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
127 MiModD's built-in hyperlink formatting tables are actively maintained and
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
128 extended with every new version! If you find the tool produces outdated
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
129 hyperlinks for any supported species or if you would like to see additional
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
130 species supported, do not hesitate to `tell us about it`_.
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
131 If you have a custom hyperlink template file that is working for you, that
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
132 is even better. We may use it as a starting point for a built-in recipe and,
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
133 while we are working on that and with your permission, we can post it on the
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
134 package home page for other users who may need it.
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
135
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
136 .. _custom hyperlink template file: http://mimodd.readthedocs.io/en/@MIMODD_REAL_VERSION@/recipes.html#hyperlink-template-file
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
137 .. _tell us about it: mailto:mimodd@googlegroups.com
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
138
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
139 @HELP_FOOTER@
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
140 ]]></help>
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
141 <expand macro="citations" />
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
diff changeset
142 </tool>