Mercurial > repos > iuc > hamronize_summarize

comparison hamronize_summarize.xml @ 3:243c87f34f39 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit f09c6b7e45ccd61956942b5aab76c0c8ccc0fe03
author iuc
date Fri, 05 Aug 2022 12:58:46 +0000
parents 6e2731b13533
children f8bcc852f6b3
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2:6e2731b13533 3:243c87f34f39
1 <tool id="hamronize_summarize" name="hamronize: summarize" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@"> 1 <tool id="hamronize_summarize" name="hamronize: summarize" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@">
2 <description> harmorization reports</description> 2 <description> harmorization reports</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
10 #if $report.is_of_type('tsv', 'tabular'): 10 #if $report.is_of_type('tsv', 'tabular'):
11 #set $ext = 'tsv' 11 #set $ext = 'tsv'
12 #elif $report.is_of_type('json'): 12 #elif $report.is_of_type('json'):
13 #set $ext = 'json' 13 #set $ext = 'json'
14 #end if 14 #end if
15 ln -s '$report' ./report_${counter}.${ext} && 15 ln -s '$report' ./report_${counter}.${ext} &&
16 #end for 16 #end for
17 17
18 hamronize summarize 18 hamronize summarize
19 --summary_type $summary_type 19 --summary_type $summary_type
20 #if $summary_type == "tsv" 20 #if $summary_type == "tsv"
21 --output output.tsv 21 --output output.tsv
22 #elif $summary_type == "json" 22 #elif $summary_type == "json"
23 --output output.json 23 --output output.json
24 #else 24 #else
25 --output output.html 25 --output output.html
26 #end if 26 #end if
27 *.tsv 27 ./report_*
28 *.json
29 ]]> </command> 28 ]]> </command>
30 29
31 <inputs> 30 <inputs>
32 <param name="reports" type="data" multiple="true" format="tabular,json" label="Report files"/> 31 <param name="reports" type="data" multiple="true" format="tabular,json" label="Report files"/>
33 <param name="summary_type" type="select" label="Output format" multiple="false"> 32 <param name="summary_type" type="select" label="Output format" multiple="false">
68 </output> 67 </output>
69 </test> 68 </test>
70 </tests> 69 </tests>
71 <help> 70 <help>
72 <![CDATA[ 71 <![CDATA[
73 **What it does** 72 **What it does**
74 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 73 This tool will take a list of report and create single sorted report in the specified format
75 74 just containing the unique entries across input reports. It can handle mixed json and tsv hamronized report formats
76 **Inputs** 75 **Inputs**
77 A list of hamronize reports 76 A list of hamronize reports
78 ]]> 77
78 ]]>
79 </help> 79 </help>
80 </tool> 80 </tool>