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comparison bigscape.xml @ 3:3447eb0ce896 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4
author iuc
date Sun, 11 Aug 2024 21:09:00 +0000
parents ad2f19722a0e
children
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2:ad2f19722a0e 3:3447eb0ce896
1 <tool id="bigscape" name="BiG-SCAPE" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> 1 <tool id="bigscape" name="BiG-SCAPE" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
2 <description>Construct sequence similarity networks of BGCs and group them into GCF</description> 2 <description>Construct sequence similarity networks of BGCs and group them into GCF</description>
3 <macros> 3 <macros>
4 <token name="@TOOL_VERSION@">1.1.9</token> 4 <token name="@TOOL_VERSION@">1.1.9</token>
5 <token name="@VERSION_SUFFIX@">1</token> 5 <token name="@VERSION_SUFFIX@">2</token>
6 </macros> 6 </macros>
7 <xrefs> 7 <xrefs>
8 <xref type="bio.tools">BiG-SCAPE</xref> 8 <xref type="bio.tools">BiG-SCAPE</xref>
9 </xrefs> 9 </xrefs>
10 <requirements> 10 <requirements>
15 15
16 #set $path_to_html = $html.files_path 16 #set $path_to_html = $html.files_path
17 mkdir -p '$path_to_html' result input && 17 mkdir -p '$path_to_html' result input &&
18 #for $files in $inputdir: 18 #for $files in $inputdir:
19 #set $filename = "region." + $files.element_identifier 19 #set $filename = "region." + $files.element_identifier
20 ln -s '$files' './input/$filename' && 20 ln -s '$files' './input/${filename}.gbk' &&
21 #end for 21 #end for
22 22
23 mkdir pfam && 23 mkdir pfam &&
24 ln -s '$pfam_dir' './pfam/$pfam_dir.element_identifier' && 24 ln -s '$pfam_dir' './pfam/$pfam_dir.element_identifier' &&
25 hmmpress './pfam/Pfam-A.hmm' && 25 hmmpress './pfam/Pfam-A.hmm' &&
294 </element> 294 </element>
295 </output_collection> 295 </output_collection>
296 </test> 296 </test>
297 <test expect_num_outputs="5"> 297 <test expect_num_outputs="5">
298 <param name="pfam_dir" value="Pfam-A.hmm" ftype="hmm3"/> 298 <param name="pfam_dir" value="Pfam-A.hmm" ftype="hmm3"/>
299 <param name="inputdir" value="NC_010530.1.region005.gbk,NC_012963.1.region001.gbk,NW_009799099.1.region003.gbk,NW_021940918.1.region003.gbk,NW_009799102.1.region001.gbk,NW_022985561.1.region002.gbk,NW_022985549.1.region005.gbk,NW_022985575.1.region001.gbk" ftype="genbank" /> 299 <param name="inputdir" value="NC_012963.1.region001.no-genbank-suffix,NC_010530.1.region005.gbk,NC_012963.1.region001.gbk,NW_009799099.1.region003.gbk,NW_021940918.1.region003.gbk,NW_009799102.1.region001.gbk,NW_022985561.1.region002.gbk,NW_022985549.1.region005.gbk,NW_022985575.1.region001.gbk" ftype="genbank" />
300 <param name="log" value="true" />
301 <param name="clans_off" value="true" />
302 </test>
303 <test expect_num_outputs="5">
304 <param name="pfam_dir" value="Pfam-A.hmm" ftype="hmm3"/>
305 <param name="inputdir" value="NC_012963.1.region001.no-genbank-suffix,NC_010530.1.region005.gbk" ftype="genbank" />
300 <param name="log" value="true" /> 306 <param name="log" value="true" />
301 <param name="clans_off" value="true" /> 307 <param name="clans_off" value="true" />
302 </test> 308 </test>
303 </tests> 309 </tests>
304 <help> 310 <help>