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comparison metagene_annotator.xml @ 1:17c7ab82bfbc draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit f66aa9a65aaf45ac4888ca26f5af661f73b46fdc
author galaxyp
date Mon, 18 Mar 2024 12:34:58 +0000
parents b04960a7abf5
children
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0:b04960a7abf5 1:17c7ab82bfbc
1 <tool id="metagene_annotator" name="MetaGeneAnnotator" version="1.0.0"> 1 <tool id="metagene_annotator" name="MetaGeneAnnotator" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 <description>gene-finding program for prokaryote and phage (used by sixgill)</description> 2 <description>gene-finding program for prokaryote and phage (used by sixgill)</description>
3 <macros>
4 <token name="@TOOL_VERSION@">1.0</token>
5 <token name="@VERSION_SUFFIX@">1</token>
6 </macros>
7 <xrefs>
8 <xref type="bio.tools">metageneannotator</xref>
9 </xrefs>
3 <requirements> 10 <requirements>
4 <requirement type="package">metagene_annotator</requirement> 11 <requirement type="package" version="@TOOL_VERSION@">metagene_annotator</requirement>
5 <requirement type="package">python</requirement> 12 <requirement type="package" version="3.10">python</requirement>
6 </requirements> 13 </requirements>
7 <command detect_errors="exit_code"><![CDATA[ 14 <command detect_errors="exit_code"><![CDATA[
8 #set $output_list = str($output_formats).split(',') 15 #set $output_list = str($output_formats).split(',')
9 touch mga_output 16 touch mga_output
10 #for $input in $inputs: 17 #for $input in $inputs:
48 default="chrom,chromStart,chromEnd,name,score,strand,thickStart,thickEnd,itemRgb,blockCount,blockSizes,blockStarts"/> 55 default="chrom,chromStart,chromEnd,name,score,strand,thickStart,thickEnd,itemRgb,blockCount,blockSizes,blockStarts"/>
49 </actions> 56 </actions>
50 </data> 57 </data>
51 </outputs> 58 </outputs>
52 <tests> 59 <tests>
53 <test> 60 <test expect_num_outputs="1">
54 <param name="inputs" value="metasequences.fasta" ftype="fasta"/> 61 <param name="inputs" value="metasequences.fasta" ftype="fasta"/>
55 <param name="multiple_species" value="True"/> 62 <param name="multiple_species" value="True"/>
56 <param name="output_formats" value="txt"/> 63 <param name="output_formats" value="txt"/>
57 <output name="mga_txt"> 64 <output name="mga_txt">
58 <assert_contents> 65 <assert_contents>
59 <has_text_matching expression="# 1/1\s# gc = 0.275862, rbs = -1\s# self: -" /> 66 <has_text_matching expression="# 1/1\s# gc = 0.275862, rbs = -1\s# self: -" />
60 <has_text_matching expression="gene_1\t1812\t1994\t-\t0\t11\t14.10\d+\tb\t2002\t2007\t2.11\d+" /> 67 <has_text_matching expression="gene_1\t1812\t1994\t-\t0\t11\t14.10\d+\tb\t2002\t2007\t2.11\d+" />
61 </assert_contents> 68 </assert_contents>
62 </output> 69 </output>
63 </test> 70 </test>
64 <test> 71 <test expect_num_outputs="1">
65 <param name="inputs" value="metasequences.fasta" ftype="fasta"/> 72 <param name="inputs" value="metasequences.fasta" ftype="fasta"/>
66 <param name="multiple_species" value="False"/> 73 <param name="multiple_species" value="False"/>
67 <param name="output_formats" value="txt"/> 74 <param name="output_formats" value="txt"/>
68 <output name="mga_txt"> 75 <output name="mga_txt">
69 <assert_contents> 76 <assert_contents>