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annotate varreport.xml @ 2:36b4be01cce4 draft default tip

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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 16:39:44 -0500
parents 85576338fbcf
children
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85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797
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1 <tool id="mimodd_varreport" name="MiModD Report Variants"
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2 version="@MIMODD_WRAPPER_VERSION@">
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3 <description>
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4 in a human-friendly format that simplifies data exploration
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5 </description>
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6 <macros>
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7 <import>macros.xml</import>
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8 </macros>
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9 <expand macro="requirements" />
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10 <expand macro="stdio" />
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11 <expand macro="version_command" />
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12 <command><![CDATA[
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13 #if $str($formatting.oformat) == 'html':
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14 mkdir '$ofile.files_path' &&
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15 #end if
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16 mimodd varreport
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17 '$inputfile' --oformat ${formatting.oformat}
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18 #if $str($formatting.oformat) == 'html':
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19 #if $str($formatting.species):
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20 --species '${formatting.species}'
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21 #end if
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22 #if $formatting.link_formatter:
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23 --link '${formatting.link_formatter}'
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24 #end if
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25 --ofile '${ofile.files_path}/variant_report.html'
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26 && echo
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27 '<html><body><p>MiModD has generated the variant report you requested, but for technical reasons, we have to take you through this little detour to display the report in Galaxy.</p><p>Proceed to <a href="variant_report.html">the variant report</a>.</p></body></html>'
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28 > '$ofile'
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29 #else
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30 --ofile '$ofile'
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31 #end if
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32 ]]></command>
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33
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34 <inputs>
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35 <param name="inputfile" type="data" format="vcf"
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36 label="The VCF input with the variants to be reported" />
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37 <conditional name="formatting">
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38 <param name="oformat" type="select"
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39 label="Format to use for the report">
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40 <option value="html">HTML</option>
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41 <option value="text">Tab-separated plain text</option>
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42 </param>
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43 <when value="html">
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44 <param name="species" type="text" label="Species"
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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." />
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46 <param name="link_formatter" type="data" format="txt" optional="true"
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47 label="Optional file with species-specific hyperlink formatting instructions"
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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." />
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49 </when>
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50 <when value="text">
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51 <param name="species" type="hidden" value="" />
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52 </when>
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53 </conditional>
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54 </inputs>
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55
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56 <outputs>
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57 <data name="ofile" format="html">
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58 <change_format>
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59 <when input="formatting.oformat" value="text" format="tabular"/>
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60 </change_format>
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61 </data>
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62 </outputs>
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63
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64 <tests>
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65 <test>
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66 <param name="inputfile" value="a.vcf" />
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67 <conditional name="formatting">
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68 <param name="oformat" value="html" />
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69 <param name="species" value="C. elegans" />
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70 </conditional>
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71 <output name="ofile" ftype="html">
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72 <extra_files type="file" name="variant_report.html" ftype="html">
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73 <assert_contents>
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74 <has_line_matching expression=".+tools/genome/gbrowse/c_elegans_PRJNA13758.+" />
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75 </assert_contents>
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76 </extra_files>
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77 </output>
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78 </test>
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79 <test>
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80 <param name="inputfile" value="a.vcf" />
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81 <conditional name="formatting">
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82 <param name="oformat" value="text" />
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83 </conditional>
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84 <output name="ofile" ftype="tabular">
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85 <assert_contents>
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86 <has_n_columns n="11" />
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87 <has_line_matching expression="Chromosome&#009;Position&#009;Affected Gene&#009;Transcript&#009;Effects&#009;genotype N2&#009;.+genotype ot266&#009;.+" />
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88 <has_line_matching expression="chrI&#009;.+" />
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89 </assert_contents>
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90 </output>
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91 </test>
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92 </tests>
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93
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94 <help><![CDATA[
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95 .. class:: infomark
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96
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97 **What it does**
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98
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99 The tool turns a variant list in VCF format into a more readable summary table
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100 listing variant sites and effects.
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101
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102
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103 **Html output enriched with species-specific hyperlinks**
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104
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105 If you select html as the output format, the tool can insert species- and
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106 variant-specific hyperlinks to public genome browsers and databases into the
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107 report. This is a useful feature to explore medium-size lists of variants, but
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108 requires that the tool knows:
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109
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110 1) the species that you are analyzing data for
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111
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112 The tool can autodetect the species if the input dataset has been generated
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113 with the *MiModD Variant Annotation* tool. Alternatively, you can declare
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114 the species you are working with explicitly.
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115
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116 2) how to generate hyperlinks for this species
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117
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118 The tool has built-in support for a number of standard model organisms.
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119 If your organism is not in that list or if you find that the default
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120 hyperlinks for a supported species are outdated, you can provide your own
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121 recipe to generate correct hyperlinks through a `custom hyperlink template
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122 file`_.
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123
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124 **TIP:**
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125 MiModD's built-in hyperlink formatting tables are actively maintained and
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126 extended with every new version! If you find the tool produces outdated
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127 hyperlinks for any supported species or if you would like to see additional
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128 species supported, do not hesitate to `tell us about it`_.
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129 If you have a custom hyperlink template file that is working for you, that
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130 is even better. We may use it as a starting point for a built-in recipe and,
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131 while we are working on that and with your permission, we can post it on the
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132 package home page for other users who may need it.
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133
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134 .. _custom hyperlink template file: http://mimodd.readthedocs.io/en/@MIMODD_REAL_VERSION@/recipes.html#hyperlink-template-file
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135 .. _tell us about it: mailto:mimodd@googlegroups.com
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136
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137 @HELP_FOOTER@
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138 ]]></help>
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139 <expand macro="citations" />
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140 </tool>