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annotate blast_report.xml @ 4:d6423655d2b5 draft

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planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit e8b469f0fed66159f07bfc3904b0c4bce9a16d09-dirty
author dfornika
date Thu, 12 Sep 2019 00:26:04 -0400
parents a56a5519d60a
children 0f048e2548cb
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1 <tool id="blast_report" name="BLAST report" force_history_refresh="true" version="1.1.0">
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2 <description>Report on BLAST results</description>
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3 <command >
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4 <![CDATA[
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5 '$__tool_directory__/blast_report.py'
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6 '${in_tab}'
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7 '${tmpl}'
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8 '${out_html}'
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9 '${out_tab}'
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10 -f '{$filter_pident}:$filter_kws'
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11 #if str($bins) == "None"
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12 #pass
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13 #else
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14 -b "${bins}"
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15 #end if
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16 #if $hsp_bool
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17 -r
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18 #end if
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19 ]]>
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20 </command>
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21 <inputs>
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22 <param name="in_tab" type="data" format="tabular" label="Tabular BLAST results (extended 26 columns)"/>
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23 <param name="tmpl" type="select" optional="false" label="Report template">
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24 <options from_data_table="blast_report_templates">
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25 <column name="value" index="0"/>
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26 <column name="name" index="1"/>
0
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27 </options>
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28 </param>
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29 <param name="filter_pident" type="integer" min="90" max="100" value="97" label="Minimum percentage identity"/>
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30 <param name="filter_kws" type="text" size="50" label="Comma-separated list of description keyword filters" value="bovine,clone,environmental,swine,uncultivated,uncultured,unidentified"/>
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31 <param name="bins" type="select" label="Database bins" multiple="true" display="checkboxes">
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32 <options from_data_table="blast_report_bins">
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33 <column name="value" index="0"/>
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34 <column name="name" index="1"/>
0
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35 </options>
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36 </param>
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37 <!--<repeat name="hist_bins" title="History database bins">
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38 <param name="filter" type="data" format="csv" label="History database bin"/>
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39 </repeat>-->
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40 <param name="hsp_bool" type="boolean" label="Throw out redundant hits?"/>
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41 <param name="tab_bool" type="boolean" label="Output tabular file?"/>
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42 </inputs>
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43 <outputs>
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44 <data name="out_html" format="html" label="$tool.name on data $in_tab.hid: report"/>
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45 <data name="out_tab" format="tabular" label="$tool.name on data $in_tab.hid: tabular results">
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46 <filter> tab_bool </filter>
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47 </data>
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48 </outputs>
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49 <help>
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50 .. class:: infomark
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51
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52 **What it does**
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53
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54 This tool produces a HTML report for each query in a tabular BLAST file.
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56 ----
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58 **Tabular BLAST results**
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60 One or more query's BLAST results in extended 26 column tabular format.
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61
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62 ----
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64 **Report template**
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65
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66 The report template dictates the format of the HTML report.
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67 Note that changing the template from the standard "Top 20 hits shown, toggle remainder" to "Euzby results shown first" causes
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68 the order of the results in the HTML report and the tabular BLAST results (if outputted) to be inconsistent with each other.
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69
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70 ----
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72 **Minimum percentage identity**
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74 Filter by percentage identity. This filter is applied before the description keyword filters.
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76 ----
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78 **Comma-separated list of description keyword filters**
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80 Filter by description keywords. Do not include spaces (unless your keyword is two words). These are applied
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81 after the percentage identity filter.
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83 ----
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85 **Database bins**
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87 Bin the results by accession number into "database bins."
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88
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89 ----
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90
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91 **Throw out redundant hits?**
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92
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93 Only the first hit for any accession number will be reported.
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94
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95 ----
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96
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97 **Output tabular BLAST results?**
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98
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99 This option produces a tabular BLAST file with the same results as those shown in the report.
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100
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101 </help>
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102 </tool>