Mercurial > repos > iuc > kofamscan

comparison kofamscan.xml @ 1:23494763e39e draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit 06d0ecf1815937976a81b356372b1b808782cd0a"
author iuc
date Wed, 16 Feb 2022 09:25:13 +0000
parents 24adf43898ec
children 95c71179a054
comparison
equal deleted inserted replaced
0:24adf43898ec 1:23494763e39e
1 <tool id="kofamscan" name="KofamScan" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> 1 <tool id="kofamscan" name="KofamScan" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 <description>gene function annotation based on KEGG orthology and HMM</description> 2 <description>gene function annotation based on KEGG orthology and HMM</description>
3 <macros> 3 <macros>
4 <token name="@TOOL_VERSION@">1.3.0</token> 4 <token name="@TOOL_VERSION@">1.3.0</token>
5 <token name="@VERSION_SUFFIX@">0</token> 5 <token name="@VERSION_SUFFIX@">1</token>
6 <xml name="reportannotation" token_selected=""> 6 <xml name="reportannotation" token_selected="">
7 <param name="reportannotation" type="boolean" truevalue="--report-unannotated" falsevalue="--no-report-unannotated" checked="@SELECTED@" label="Include sequence name to outputs even if no KOs are assigned?"/> 7 <param name="reportannotation" type="boolean" truevalue="--report-unannotated" falsevalue="--no-report-unannotated" checked="@SELECTED@" label="Include sequence name to outputs even if no KOs are assigned?"/>
8 </xml> 8 </xml>
9 </macros> 9 </macros>
10 <requirements> 10 <requirements>
12 <requirement type="package" version="3.0">zip</requirement> 12 <requirement type="package" version="3.0">zip</requirement>
13 </requirements> 13 </requirements>
14 <version_command><![CDATA[sansa -v | grep "Sansa " | cut -d "v" -f 3]]></version_command> 14 <version_command><![CDATA[sansa -v | grep "Sansa " | cut -d "v" -f 3]]></version_command>
15 <command detect_errors="exit_code"><![CDATA[ 15 <command detect_errors="exit_code"><![CDATA[
16 ## preprocessing 16 ## preprocessing
17 mkdir 'profile' && 17 mkdir ./profile &&
18 mkdir ./temp_extract &&
18 #if $p_cond.p_sel == 'compressed' 19 #if $p_cond.p_sel == 'compressed'
19 tar -xf '${p_cond.p}' -C 'profile' && 20 tar -xf '${p_cond.p}' -C temp_extract &&
21 find ./temp_extract/ -name '*.hmm' -exec mv {} ./profile \; &&
22 find ./temp_extract/ -name '*.hal' -exec mv {} ./profile \; &&
20 #elif $p_cond.p_sel == 'hmm' 23 #elif $p_cond.p_sel == 'hmm'
21 ## input files require prefix 'K' and file extension '.hmm' 24 ## input files require prefix 'K' and file extension '.hmm'
22 #for $i, $current in enumerate($p_cond.p) 25 #for $i, $current in enumerate($p_cond.p)
23 ln -s '$current' 'profile/K${i}.hmm' && 26 ln -s '$current' 'profile/K${i}.hmm' &&
24 #end for 27 #end for
199 <has_n_lines n="7"/> 202 <has_n_lines n="7"/>
200 <has_line line="sp|P19858|LDHA_BOVIN"/> 203 <has_line line="sp|P19858|LDHA_BOVIN"/>
201 </assert_contents> 204 </assert_contents>
202 </output> 205 </output>
203 </test> 206 </test>
207 <!-- #5 -->
208 <test expect_num_outputs="1">
209 <param name="query" value="query.fasta"/>
210 <conditional name="p_cond">
211 <param name="p_sel" value="compressed"/>
212 <param name="p" value="profilesTyp2.tar.gz"/>
213 </conditional>
214 <param name="k" value="ko"/>
215 <output name="out_result">
216 <assert_contents>
217 <has_n_lines n="5"/>
218 <has_text_matching expression=".+sp\|P00329\|ADH1_MOUSE.+"/>
219 </assert_contents>
220 </output>
221 </test>
204 </tests> 222 </tests>
205 <help><![CDATA[ 223 <help><![CDATA[
206 .. class:: infomark 224 .. class:: infomark
207 225
208 **What it does** 226 **What it does**