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comparison spotyping.xml @ 2:0061b5818bb5 draft default tip

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planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 059ddaa55a5e4bdac5aaba74fe489e9268731390
author iuc
date Sun, 21 Oct 2018 13:02:43 -0400
parents ee9f908ce860
children
comparison
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1:ee9f908ce860 2:0061b5818bb5
1 <tool id="spotyping" name="SpoTyping" version="@TOOL_VERSION@+galaxy1" profile="17.01"> 1 <tool id="spotyping" name="SpoTyping" version="@TOOL_VERSION@+galaxy2" profile="17.01">
2 <description>fast and accurate in silico Mycobacterium spoligotyping from sequence reads</description> 2 <description>fast and accurate in silico Mycobacterium spoligotyping from sequence reads</description>
3 3
4 <macros> 4 <macros>
5 <import>spotyping_macros.xml</import> 5 <import>spotyping_macros.xml</import>
6 </macros> 6 </macros>
7 7
8 <requirements> 8 <requirements>
9 <requirement type="package" version="@TOOL_VERSION@">spotyping</requirement> 9 <requirement type="package" version="@TOOL_VERSION@">spotyping</requirement>
10 </requirements> 10 </requirements>
11 11
12 <command detect_errors="exit_code"><![CDATA[ 12 <command detect_errors="aggressive"><![CDATA[
13 #set $input_file='input.' + $input.extension 13 #set $input_file='input.' + $input.extension
14 ln -s '${input}' $input_file && 14 ln -s '${input}' $input_file &&
15 SpoTyping.py 15 SpoTyping.py
16 $advanced.noQuery 16 $advanced.noQuery
17 $advanced.seq 17 $advanced.seq
57 <output name="output_txt"> 57 <output name="output_txt">
58 <assert_contents> 58 <assert_contents>
59 <has_text text="1111111111111111101111111111111100001111111" /> 59 <has_text text="1111111111111111101111111111111100001111111" />
60 </assert_contents> 60 </assert_contents>
61 </output> 61 </output>
62 </test>
63 <test expect_failure="true">
64 <param name="input" value="input.fastq.gz" ftype="fastq.gz" />
65 <param name="seq" value="--seq" />
66 <assert_stderr>
67 <has_text text="BLAST options error" />
68 </assert_stderr>
62 </test> 69 </test>
63 <test expect_num_outputs="2"> 70 <test expect_num_outputs="2">
64 <param name="input" value="input.fastq.gz" ftype="fastq.gz" /> 71 <param name="input" value="input.fastq.gz" ftype="fastq.gz" />
65 <param name="noQuery" value="" /> 72 <param name="noQuery" value="" />
66 <output name="output_txt"> 73 <output name="output_txt">