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annotate varreport.xml @ 1:bfcd121b99bf draft default tip

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planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 44e872b808f88eacd05963fc2478da2c07b50228
author wolma
date Thu, 22 Mar 2018 10:32:39 -0400
parents f0f2795de2c7
children
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f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
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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[
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
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13 #if $str($formatting.oformat) == 'html':
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
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14 mkdir '$ofile.files_path' &&
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
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15 #end if
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16 mimodd varreport
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17 '$inputfile' --oformat ${formatting.oformat}
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18 #if $str($formatting.oformat) == 'html':
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19 #if $str($formatting.species):
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
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20 --species '${formatting.species}'
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
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21 #end if
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22 #if $formatting.link_formatter:
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
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23 --link '${formatting.link_formatter}'
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
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24 #end if
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
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25 --ofile '${ofile.files_path}/variant_report.html'
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
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26 && echo
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
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27 '<html><body><p>MiModD has generated the variant report you requested, but for technical reasons, we have to take you through this little detour to display the report in Galaxy.</p><p>Proceed to <a href="variant_report.html">the variant report</a>.</p></body></html>'
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
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28 > '$ofile'
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29 #else
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
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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
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
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34 <inputs>
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
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35 <param name="inputfile" type="data" format="vcf"
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
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36 label="The VCF input with the variants to be reported" />
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37 <conditional name="formatting">
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
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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>
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
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41 <option value="text">Tab-separated plain text</option>
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
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42 </param>
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
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43 <when value="html">
f0f2795de2c7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
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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 <expand macro="lex_sam_header" message="Non-ASCII characters are not allowed in species names." />
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47 </param>
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48 <param name="link_formatter" type="data" format="txt" optional="true"
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49 label="Optional file with species-specific hyperlink formatting instructions"
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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." />
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51 </when>
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52 <when value="text">
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53 <param name="species" type="hidden" value="" />
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54 </when>
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55 </conditional>
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56 </inputs>
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57
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58 <outputs>
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59 <data name="ofile" format="html">
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60 <change_format>
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61 <when input="formatting.oformat" value="text" format="tabular"/>
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62 </change_format>
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63 </data>
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64 </outputs>
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65
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66 <tests>
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67 <test>
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68 <param name="inputfile" value="a.vcf" />
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69 <conditional name="formatting">
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70 <param name="oformat" value="html" />
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71 <param name="species" value="C. elegans" />
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72 </conditional>
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73 <output name="ofile" ftype="html">
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74 <extra_files type="file" name="variant_report.html" ftype="html">
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75 <assert_contents>
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76 <has_line_matching expression=".+tools/genome/gbrowse/c_elegans_PRJNA13758.+" />
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77 </assert_contents>
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78 </extra_files>
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79 </output>
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80 </test>
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81 <test>
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82 <param name="inputfile" value="a.vcf" />
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83 <conditional name="formatting">
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84 <param name="oformat" value="text" />
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85 </conditional>
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86 <output name="ofile" ftype="tabular">
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87 <assert_contents>
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88 <has_n_columns n="11" />
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89 <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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90 <has_line_matching expression="chrI&#009;.+" />
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91 </assert_contents>
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92 </output>
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93 </test>
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94 </tests>
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95
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96 <help><![CDATA[
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97 .. class:: infomark
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98
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99 **What it does**
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100
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101 The tool turns a variant list in VCF format into a more readable summary table
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102 listing variant sites and effects.
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103
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104
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105 **Html output enriched with species-specific hyperlinks**
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106
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107 If you select html as the output format, the tool can insert species- and
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108 variant-specific hyperlinks to public genome browsers and databases into the
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109 report. This is a useful feature to explore medium-size lists of variants, but
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110 requires that the tool knows:
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111
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112 1) the species that you are analyzing data for
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113
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114 The tool can autodetect the species if the input dataset has been generated
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115 with the *MiModD Variant Annotation* tool. Alternatively, you can declare
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116 the species you are working with explicitly.
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117
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118 2) how to generate hyperlinks for this species
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119
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120 The tool has built-in support for a number of standard model organisms.
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121 If your organism is not in that list or if you find that the default
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122 hyperlinks for a supported species are outdated, you can provide your own
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123 recipe to generate correct hyperlinks through a `custom hyperlink template
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124 file`_.
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125
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126 **TIP:**
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127 MiModD's built-in hyperlink formatting tables are actively maintained and
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128 extended with every new version! If you find the tool produces outdated
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129 hyperlinks for any supported species or if you would like to see additional
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130 species supported, do not hesitate to `tell us about it`_.
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131 If you have a custom hyperlink template file that is working for you, that
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132 is even better. We may use it as a starting point for a built-in recipe and,
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133 while we are working on that and with your permission, we can post it on the
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134 package home page for other users who may need it.
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135
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136 .. _custom hyperlink template file: http://mimodd.readthedocs.io/en/@MIMODD_REAL_VERSION@/recipes.html#hyperlink-template-file
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137 .. _tell us about it: mailto:mimodd@googlegroups.com
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138
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139 @HELP_FOOTER@
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140 ]]></help>
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141 <expand macro="citations" />
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142 </tool>