Mercurial > repos > iuc > hamronize_summarize

annotate hamronize_summarize.xml @ 4:f8bcc852f6b3 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b4943555d76f7e352de3f396c51d3dfb90ed633d
author iuc
date Fri, 09 Feb 2024 21:27:25 +0000
parents 243c87f34f39
children 88045b4d5597
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243c87f34f39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit f09c6b7e45ccd61956942b5aab76c0c8ccc0fe03
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1 <tool id="hamronize_summarize" name="hamronize: summarize" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@">
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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>
4
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6 <expand macro="bio_tools"/>
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7 <expand macro="requirements" />
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8 <expand macro="version_command" />
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9 <command detect_errors="exit_code"><![CDATA[
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10 #for $counter, $report in enumerate($reports):
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11 #if $report.is_of_type('tsv', 'tabular'):
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12 #set $ext = 'tsv'
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13 #elif $report.is_of_type('json'):
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14 #set $ext = 'json'
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15 #end if
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16 ln -s '$report' ./report_${counter}.${ext} &&
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17 #end for
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18
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19 hamronize summarize
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20 --summary_type $summary_type
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21 #if $summary_type == "tsv"
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22 --output output.tsv
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23 #elif $summary_type == "json"
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24 --output output.json
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25 #else
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26 --output output.html
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27 #end if
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28 ./report_*
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29 ]]> </command>
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30
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31 <inputs>
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32 <param name="reports" type="data" multiple="true" format="tabular,json" label="Report files"/>
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33 <param name="summary_type" type="select" label="Output format" multiple="false">
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34 <option value="tsv">tsv</option>
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35 <option value="json">json</option>
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36 <option value="interactive">interactive</option>
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37 </param>
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38 </inputs>
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39
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40 <outputs>
4
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41 <data format="tabular" name="output_tsv" label="${tool.name} on ${on_string}: Table" from_work_dir="output.tsv">
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42 <filter>summary_type == "tsv"</filter>
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43 </data>
4
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44 <data format="json" name="output_json" label="${tool.name} on ${on_string}: JSON" from_work_dir="output.json">
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45 <filter>summary_type == "json"</filter>
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46 </data>
4
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47 <data format="html" name="output_html" label="${tool.name} on ${on_string}: Interactive" from_work_dir="output.html">
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48 <filter>summary_type == "interactive"</filter>
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49 </data>
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50 </outputs>
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51 <tests>
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52 <!-- tsv output -->
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53 <test expect_num_outputs="1">
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54 <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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55 <param name="summary_type" value="tsv" />
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56 <output name="output_tsv" ftype="tabular" file="summary.tsv" />
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57 </test>
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58 <!-- json output -->
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59 <test expect_num_outputs="1">
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60 <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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61 <param name="summary_type" value="json" />
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62 <output name="output_json" ftype="json">
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63 <assert_contents>
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64 <has_text text="GCF_010120755.1_ASM1012075v1_genomic" />
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65 <has_text text="H_NS.3000676.BA000007.3.1737690_1738104.5476" />
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66 <has_text text="NODE_9_length_203843_cov_42.4911_20" />
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67 </assert_contents>
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68 </output>
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69 </test>
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70 </tests>
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71 <help>
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72 <![CDATA[
3
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73 **What it does**
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74 This tool will take a list of report and create single sorted report in the specified format
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75 just containing the unique entries across input reports. It can handle mixed json and tsv hamronized report formats
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76 **Inputs**
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77 A list of hamronize reports
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78
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79 ]]>
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80 </help>
4
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81 <expand macro="citations"/>
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82 </tool>