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comparison varreport.xml @ 0:aa82b2e54055 draft

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planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
author wolma
date Sat, 11 Nov 2017 18:19:22 -0500
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children 1425ea794026
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-1:000000000000 0:aa82b2e54055
1 <tool id="mimodd_varreport" name="MiModD Report Variants"
2 version="@MIMODD_WRAPPER_VERSION@">
3 <description>
4 in a human-friendly format that simplifies data exploration
5 </description>
6 <macros>
7 <import>macros.xml</import>
8 </macros>
9 <expand macro="requirements" />
10 <expand macro="stdio" />
11 <expand macro="version_command" />
12 <command><![CDATA[
13 #if $str($formatting.oformat) == 'html':
14 mkdir '$ofile.files_path' &&
15 #end if
16 mimodd varreport
17 '$inputfile' --oformat ${formatting.oformat}
18 #if $str($formatting.oformat) == 'html':
19 #if $str($formatting.species):
20 --species '${formatting.species}'
21 #end if
22 #if $formatting.link_formatter:
23 --link '${formatting.link_formatter}'
24 #end if
25 --ofile '${ofile.files_path}/variant_report.html'
26 && echo
27 '<html><body><p>MiModD has generated the variant report you requested, but for technical reasons, we have to take you through this little detour to display the report in Galaxy.</p><p>Proceed to <a href="variant_report.html">the variant report</a>.</p></body></html>'
28 > '$ofile'
29 #else
30 --ofile '$ofile'
31 #end if
32 ]]></command>
33
34 <inputs>
35 <param name="inputfile" type="data" format="vcf"
36 label="The VCF input with the variants to be reported" />
37 <conditional name="formatting">
38 <param name="oformat" type="select"
39 label="Format to use for the report">
40 <option value="html">HTML</option>
41 <option value="text">Tab-separated plain text</option>
42 </param>
43 <when value="html">
44 <param name="species" type="text" label="Species"
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." />
46 <param name="link_formatter" type="data" format="txt" optional="true"
47 label="Optional file with species-specific hyperlink formatting instructions"
48 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." />
49 </when>
50 <when value="text">
51 <param name="species" type="hidden" value="" />
52 </when>
53 </conditional>
54 </inputs>
55
56 <outputs>
57 <data name="ofile" format="html">
58 <change_format>
59 <when input="formatting.oformat" value="text" format="tabular"/>
60 </change_format>
61 </data>
62 </outputs>
63
64 <tests>
65 <test>
66 <param name="inputfile" value="a.vcf" />
67 <conditional name="formatting">
68 <param name="oformat" value="html" />
69 <param name="species" value="C. elegans" />
70 </conditional>
71 <output name="ofile" ftype="html">
72 <extra_files type="file" name="variant_report.html" ftype="html">
73 <assert_contents>
74 <has_line_matching expression=".+tools/genome/gbrowse/c_elegans_PRJNA13758.+" />
75 </assert_contents>
76 </extra_files>
77 </output>
78 </test>
79 <test>
80 <param name="inputfile" value="a.vcf" />
81 <conditional name="formatting">
82 <param name="oformat" value="text" />
83 </conditional>
84 <output name="ofile" ftype="tabular">
85 <assert_contents>
86 <has_n_columns n="11" />
87 <has_line_matching expression="Chromosome&#009;Position&#009;Affected Gene&#009;Transcript&#009;Effects&#009;genotype N2&#009;.+genotype ot266&#009;.+" />
88 <has_line_matching expression="chrI&#009;.+" />
89 </assert_contents>
90 </output>
91 </test>
92 </tests>
93
94 <help><![CDATA[
95 .. class:: infomark
96
97 **What it does**
98
99 The tool turns a variant list in VCF format into a more readable summary table
100 listing variant sites and effects.
101
102
103 **Html output enriched with species-specific hyperlinks**
104
105 If you select html as the output format, the tool can insert species- and
106 variant-specific hyperlinks to public genome browsers and databases into the
107 report. This is a useful feature to explore medium-size lists of variants, but
108 requires that the tool knows:
109
110 1) the species that you are analyzing data for
111
112 The tool can autodetect the species if the input dataset has been generated
113 with the *MiModD Variant Annotation* tool. Alternatively, you can declare
114 the species you are working with explicitly.
115
116 2) how to generate hyperlinks for this species
117
118 The tool has built-in support for a number of standard model organisms.
119 If your organism is not in that list or if you find that the default
120 hyperlinks for a supported species are outdated, you can provide your own
121 recipe to generate correct hyperlinks through a `custom hyperlink template
122 file`_.
123
124 **TIP:**
125 MiModD's built-in hyperlink formatting tables are actively maintained and
126 extended with every new version! If you find the tool produces outdated
127 hyperlinks for any supported species or if you would like to see additional
128 species supported, do not hesitate to `tell us about it`_.
129 If you have a custom hyperlink template file that is working for you, that
130 is even better. We may use it as a starting point for a built-in recipe and,
131 while we are working on that and with your permission, we can post it on the
132 package home page for other users who may need it.
133
134 .. _custom hyperlink template file: http://mimodd.readthedocs.io/en/@MIMODD_REAL_VERSION@/recipes.html#hyperlink-template-file
135 .. _tell us about it: mailto:mimodd@googlegroups.com
136
137 @HELP_FOOTER@
138 ]]></help>
139 <expand macro="citations" />
140 </tool>