Mercurial > repos > iuc > hamronize_summarize

annotate hamronize_summarize.xml @ 0:ef76d74a7171 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
author iuc
date Tue, 16 Mar 2021 12:39:05 +0000
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children a84e3131ae6a
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ef76d74a7171 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
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1 <tool id="hamronize_summarize" name="summarize" version="@VERSION@+galaxy0">
ef76d74a7171 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
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2 <description> harmorization reports</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6
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7 <expand macro="requirements" />
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8 <expand macro="version_command" />
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9
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10 <command detect_errors="exit_code"><![CDATA[
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11 #for $counter, $report in enumerate($reports):
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12 #if $report.is_of_type('tsv', 'tabular'):
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13 #set $ext = 'tsv'
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14 #elif $report.is_of_type('json'):
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15 #set $ext = 'json'
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16 #end if
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17 ln -s '$report' ./report_${counter}.${ext} &&
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18 #end for
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19
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20 hamronize summarize
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21 --summary_type $summary_type
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22 #if $summary_type == "tsv"
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23 --output output.tsv
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24 #elif $summary_type == "json"
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25 --output output.json
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26 #else
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27 --output output.html
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28 #end if
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29 *.tsv
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30 *.json
ef76d74a7171 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
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31 ]]> </command>
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32
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33 <inputs>
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34 <param name="reports" type="data" multiple="true" format="tsv,json" label="Report files"/>
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35 <param name="summary_type" type="select" label="Output format" multiple="false">
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36 <option value="tsv">tsv</option>
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37 <option value="json">json</option>
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38 <option value="interactive">interactive</option>
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39 </param>
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40 </inputs>
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41
ef76d74a7171 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
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42 <outputs>
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43 <data format="tsv" name="output_tsv" label="${tool.name} on ${on_string}: Output" from_work_dir="output.tsv">
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44 <filter>summary_type == "tsv"</filter>
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45 </data>
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46 <data format="json" name="output_json" label="${tool.name} on ${on_string}: Output" from_work_dir="output.json">
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47 <filter>summary_type == "json"</filter>
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48 </data>
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49 <data format="html" name="output_html" label="${tool.name} on ${on_string}: Output" from_work_dir="output.html">
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50 <filter>summary_type == "interactive"</filter>
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51 </data>
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52 </outputs>
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53 <tests>
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54 <!-- tsv output -->
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55 <test expect_num_outputs="1">
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56 <param name="reports" value="hamronized_abricate.tsv,hamronized_abricate.json,hamronized_ariba.tsv,hamronized_ariba.json,hamronized_rgi.tsv,hamronized_rgi.json" />
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57 <param name="summary_type" value="tsv" />
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58 <output name="output_tsv" ftype="tsv" file="summary.tsv" />
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59 </test>
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60 <!-- json output -->
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61 <test expect_num_outputs="1">
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62 <param name="reports" value="hamronized_abricate.tsv,hamronized_abricate.json,hamronized_ariba.tsv,hamronized_ariba.json,hamronized_rgi.tsv,hamronized_rgi.json" />
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63 <param name="summary_type" value="json" />
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64 <output name="output_json" ftype="json">
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65 <assert_contents>
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66 <has_text text="GCF_010120755.1_ASM1012075v1_genomic" />
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67 <has_text text="H_NS.3000676.BA000007.3.1737690_1738104.5476" />
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68 <has_text text="NODE_9_length_203843_cov_42.4911_20" />
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69 </assert_contents>
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70 </output>
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71 </test>
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72 </tests>
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73 <help>
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74 <![CDATA[
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75 **What it does**
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76 This tool will take a list of report and create single sorted report in the specified format just containing the unique entries across input reports. It can handle mixed json and tsv hamronized report formats
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77
ef76d74a7171 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
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78 **Inputs**
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79 A list of hamronize reports
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80 ]]>
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81 </help>
ef76d74a7171 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
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82 </tool>