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comparison trinotate.xml @ 4:2b093007fab9 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate commit a01a55b03c6160fa665e678131f9ac1318577ba0"
author iuc
date Sun, 21 Nov 2021 17:18:27 +0000
parents 4383070d29ed
children
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3:4383070d29ed 4:2b093007fab9
1 <tool id="trinotate" name="Trinotate" version="3.2.1"> 1 <tool id="trinotate" name="Trinotate" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
2 <description>functional transcript annotation</description>
3 <macros>
4 <token name="@TOOL_VERSION@">3.2.2</token>
5 <token name="@VERSION_SUFFIX@">0</token>
6 </macros>
2 <requirements> 7 <requirements>
3 <requirement type="package" version="3.2.1">trinotate</requirement> 8 <requirement type="package" version="@TOOL_VERSION@">trinotate</requirement>
4 <requirement type="package" version="1.18">gnu-wget</requirement> 9 <requirement type="package" version="1.18">gnu-wget</requirement>
5 </requirements> 10 </requirements>
6 <stdio> 11 <xrefs>
7 <exit_code range="1:" /> 12 <xref type="bio.tools">trinotate</xref>
8 </stdio> 13 </xrefs>
9 <version_command><![CDATA[ 14 <version_command><![CDATA[
10 Trinotate version 3.2.1 15 Trinotate version @TOOL_VERSION@
11 ]]></version_command> 16 ]]></version_command>
12 <command><![CDATA[ 17 <command detect_errors="exit_code"><![CDATA[
13 18
14 #if str($cond_download.select_download) == "yes": 19 #if str($cond_download.select_download) == "yes":
15 Build_Trinotate_Boilerplate_SQLite_db.pl Trinotate && 20 Build_Trinotate_Boilerplate_SQLite_db.pl Trinotate &&
16 #else: 21 #else:
17 ln -s '$cond_download.trinotate_sqlite_in' Trinotate.sqlite && 22 ln -s '$cond_download.trinotate_sqlite_in' Trinotate.sqlite &&
105 <section name="report_option"> 110 <section name="report_option">
106 <param name="incl_pep" value="true" /> 111 <param name="incl_pep" value="true" />
107 <param name="incl_trans" value="true" /> 112 <param name="incl_trans" value="true" />
108 </section> 113 </section>
109 <param name="keep_sqlite" value="true" /> 114 <param name="keep_sqlite" value="true" />
110 <output name="trinotate_out" file="trinotate_annotation_report_minus_tmhmm_signalp.xls" /> 115 <output name="trinotate_out" ftype="tabular" >
116 <assert_contents>
117 <has_size value="573911" delta="100"/>
118 <has_text text="Meiotically up-regulated gene 56 protein"/>
119 <has_text text="Serine/threonine-protein kinase tor1"/>
120 </assert_contents>
121 </output>
111 </test> 122 </test>
112 </tests> 123 </tests>
113 <help><![CDATA[ 124 <help><![CDATA[
114 .. class:: infomark 125 .. class:: infomark
115 126